From 2b3941c80f0cdfdd0231e307fd2cda0ca9b4c941 Mon Sep 17 00:00:00 2001 From: Robert Oostenveld Date: Thu, 28 Nov 2024 11:44:01 +0100 Subject: [PATCH] updated tags --- _data/tag/anatomical.yml | 4 +- _data/tag/anonymize.yml | 14 +++--- _data/tag/artifact.yml | 32 +++++++------- _data/tag/atlas.yml | 3 -- _data/tag/brainvision.yml | 2 +- _data/tag/cluster.yml | 14 +++--- _data/tag/coherence.yml | 10 ++--- _data/tag/connectivity.yml | 2 +- _data/tag/continuous.yml | 8 ++-- _data/tag/coordinate.yml | 30 ++++++------- _data/tag/corrupt.yml | 12 +++--- _data/tag/crash.yml | 8 ++-- _data/tag/ct.yml | 32 +++++++------- _data/tag/ctf.yml | 28 ++++++------ _data/tag/cvs.yml | 8 ++-- _data/tag/data.yml | 8 ++-- _data/tag/databrowser.yml | 4 +- _data/tag/dataformat.yml | 28 ++++++------ _data/tag/datatype.yml | 12 +++--- _data/tag/debug.yml | 2 +- _data/tag/development.yml | 10 ++--- _data/tag/distcomp.yml | 10 ++--- _data/tag/documentation.yml | 2 +- _data/tag/download.yml | 18 ++++---- _data/tag/edf.yml | 2 +- _data/tag/eeg.yml | 38 ++++++++-------- _data/tag/eeglab.yml | 2 +- _data/tag/egi.yml | 2 +- _data/tag/electrode.yml | 10 ++--- _data/tag/email.yml | 22 +++++----- _data/tag/event.yml | 2 +- _data/tag/eventtype.yml | 2 +- _data/tag/eventvalue.yml | 2 +- _data/tag/fiducial.yml | 14 +++--- _data/tag/filter.yml | 16 +++---- _data/tag/freq.yml | 68 ++++++++++++++--------------- _data/tag/function.yml | 10 ++--- _data/tag/git.yml | 10 ++--- _data/tag/head.yml | 2 +- _data/tag/headmodel.yml | 52 +++++++++++----------- _data/tag/ica.yml | 16 +++---- _data/tag/interpolate.yml | 3 -- _data/tag/inverse.yml | 2 +- _data/tag/label.yml | 3 -- _data/tag/layout.yml | 14 +++--- _data/tag/localization.yml | 2 +- _data/tag/localspheres.yml | 2 +- _data/tag/logo.yml | 2 +- _data/tag/matlab.yml | 58 ++++++++++++------------- _data/tag/meg.yml | 30 ++++++------- _data/tag/memory.yml | 10 ++--- _data/tag/mex.yml | 20 ++++----- _data/tag/mri.yml | 46 ++++++++++---------- _data/tag/mtmconvol.yml | 16 +++---- _data/tag/mtmfft.yml | 6 +-- _data/tag/neuromag.yml | 8 ++-- _data/tag/neuroscan.yml | 2 +- _data/tag/noise.yml | 2 +- _data/tag/normalization.yml | 2 +- _data/tag/octave.yml | 2 +- _data/tag/openmeeg.yml | 2 +- _data/tag/parfor.yml | 8 ++-- _data/tag/path.yml | 14 +++--- _data/tag/phase.yml | 2 +- _data/tag/plotting.yml | 30 ++++++------- _data/tag/polhemus.yml | 2 +- _data/tag/preprocessing.yml | 86 ++++++++++++++++++------------------- _data/tag/qsub.yml | 10 ++--- _data/tag/raw.yml | 38 ++++++++-------- _data/tag/realtime.yml | 18 ++++---- _data/tag/reference.yml | 4 +- _data/tag/release.yml | 10 ++--- _data/tag/seg.yml | 2 +- _data/tag/segmentation.yml | 2 +- _data/tag/sharing.yml | 30 ++++++------- _data/tag/source.yml | 65 +++++++++++++--------------- _data/tag/sourcemodel.yml | 6 +-- _data/tag/spm.yml | 2 +- _data/tag/statistics.yml | 44 +++++++++---------- _data/tag/support.yml | 2 +- _data/tag/surf.yml | 2 +- _data/tag/svn.yml | 8 ++-- _data/tag/template.yml | 2 +- _data/tag/timelock.yml | 2 +- _data/tag/toolbox.yml | 12 +++--- _data/tag/topo.yml | 2 +- _data/tag/topoplot.yml | 2 +- _data/tag/trialdef.yml | 8 ++-- _data/tag/trialfun.yml | 16 +++---- _data/tag/trialinfo.yml | 8 ++-- _data/tag/trigger.yml | 2 +- _data/tag/type.yml | 16 +++---- _data/tag/values.yml | 2 +- _data/tag/volume.yml | 10 ++--- _data/tag/warning.yml | 4 +- _data/tag/wavelet.yml | 10 ++--- _data/tag/workshop.yml | 4 +- tag/interpolate.md | 4 -- tag/label.md | 4 -- 99 files changed, 638 insertions(+), 658 deletions(-) delete mode 100644 _data/tag/interpolate.yml delete mode 100644 _data/tag/label.yml delete mode 100644 tag/interpolate.md delete mode 100644 tag/label.md diff --git a/_data/tag/anatomical.yml b/_data/tag/anatomical.yml index 601617b74..c40b08a97 100644 --- a/_data/tag/anatomical.yml +++ b/_data/tag/anatomical.yml @@ -1,6 +1,6 @@ - name: What is the plotting convention for anatomical MRIs? - link: /faq/what_is_the_plotting_convention_for_anatomical_mris + link: /faq/anat_plottingconvention - name: Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot? - link: /faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot + link: /faq/anat_upsidedownplotting diff --git a/_data/tag/anonymize.yml b/_data/tag/anonymize.yml index d96dc8562..00f4441e1 100644 --- a/_data/tag/anonymize.yml +++ b/_data/tag/anonymize.yml @@ -1,18 +1,18 @@ - name: Converting the combined MEG/fMRI MOUS dataset for sharing in BIDS link: /example/bids_mous +- name: How can I anonymize or deidentify an anatomical MRI? + link: /faq/anonymization_anatomical + - name: How can I anonymize or deidentify a BrainVision dataset? - link: /faq/how_can_i_anonymize_a_brainvision_dataset + link: /faq/anonymization_brainvision - name: How can I anonymize or deidentify a CTF dataset? - link: /faq/how_can_i_anonymize_a_ctf_dataset - -- name: How can I anonymize or deidentify an anatomical MRI? - link: /faq/how_can_i_anonymize_an_anatomical_mri + link: /faq/anonymization_ctf - name: How can I anonymize or deidentify DICOM files? - link: /faq/how_can_i_anonymize_dicom_files + link: /faq/anonymization_dicom - name: How can I anonymize data processed in FieldTrip? - link: /faq/how_can_i_anonymize_fieldtrip_data + link: /faq/anonymization_fieldtripdata diff --git a/_data/tag/artifact.yml b/_data/tag/artifact.yml index b246e9107..9d1206b05 100644 --- a/_data/tag/artifact.yml +++ b/_data/tag/artifact.yml @@ -13,35 +13,35 @@ - name: Use denoising source separation (DSS) to remove ECG artifacts link: /example/use_denoising_source_separation_dss_to_remove_ecg_artifacts -- name: Which datasets are used in the documentation and where are they used? - link: /faq/datasets +- name: How can I interpret the different types of padding in FieldTrip? + link: /faq/artifact_padding - name: How can I consistently represent artifacts in my data? - link: /faq/how_can_i_consistently_represent_artifacts_in_my_data - -- name: How can I interpret the different types of padding in FieldTrip? - link: /faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts + link: /faq/artifact_representation - name: How can I use the databrowser? - link: /faq/how_can_i_use_the_databrowser + link: /faq/databrowser -- name: How does the filter padding in preprocessing work? - link: /faq/how_does_the_filter_padding_in_preprocessing_work +- name: Which datasets are used in the documentation and where are they used? + link: /faq/datasets + +- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? + link: /faq/dftfilter_residual - name: I am getting strange artifacts in figures that use opacity - link: /faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity + link: /faq/opacityrendering - name: What kind of filters can I apply to my data? - link: /faq/what_kind_of_filters_can_i_apply_to_my_data + link: /faq/preproc_filtertypes + +- name: How does the filter padding in preprocessing work? + link: /faq/preproc_padding - name: Why does my TFR look strange (part I, demeaning)? - link: /faq/why_does_my_tfr_look_strange + link: /faq/tfr_strangedemean - name: Why does my TFR look strange (part II, detrending)? - link: /faq/why_does_my_tfr_look_strange_part_ii - -- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? - link: /faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter + link: /faq/tfr_strangedetrend - name: Introduction on dealing with artifacts link: /tutorial/artifacts diff --git a/_data/tag/atlas.yml b/_data/tag/atlas.yml index 987a8eb52..0d78e94fb 100644 --- a/_data/tag/atlas.yml +++ b/_data/tag/atlas.yml @@ -1,6 +1,3 @@ -- name: How can I map source locations onto an anatomical label in an atlas? - link: /faq/how_can_i_map_source_locations_between_two_different_representations - - name: Template anatomical atlases and parcellation schemes link: /template/atlas diff --git a/_data/tag/brainvision.yml b/_data/tag/brainvision.yml index 5907169f4..6f31bd04b 100644 --- a/_data/tag/brainvision.yml +++ b/_data/tag/brainvision.yml @@ -2,7 +2,7 @@ link: /development/realtime/rda - name: How can I anonymize or deidentify a BrainVision dataset? - link: /faq/how_can_i_anonymize_a_brainvision_dataset + link: /faq/anonymization_brainvision - name: Getting started with BrainVision Analyzer and Easycap link: /getting_started/brainvision diff --git a/_data/tag/cluster.yml b/_data/tag/cluster.yml index b404515dd..d7f15e4d1 100644 --- a/_data/tag/cluster.yml +++ b/_data/tag/cluster.yml @@ -13,15 +13,15 @@ - name: Use simulated ERPs to explore cluster statistics link: /example/use_simulated_erps_to_explore_cluster_statistics -- name: How can I define neighbouring sensors? - link: /faq/how_can_i_define_neighbouring_sensors +- name: Why should I use the cfg.correcttail option when using statistics_montecarlo? + link: /faq/clusterstats_correcttail - name: How does ft_prepare_neighbours work? - link: /faq/how_does_ft_prepare_neighbours_work + link: /faq/neighbours_prepare -- name: What is the idea behind statistical inference at the second-level? - link: /faq/what_is_the_idea_behind_statistical_inference_at_the_second-level +- name: How can I define neighbouring sensors? + link: /faq/sensors_neighbours -- name: Why should I use the cfg.correcttail option when using statistics_montecarlo? - link: /faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo +- name: What is the idea behind statistical inference at the second-level? + link: /faq/statistics_secondlevel diff --git a/_data/tag/coherence.yml b/_data/tag/coherence.yml index 2f650e0fb..3b3bb8e12 100644 --- a/_data/tag/coherence.yml +++ b/_data/tag/coherence.yml @@ -4,17 +4,17 @@ - name: Correlation analysis of fMRI data link: /example/correlation_analysis_in_fmri_data -- name: How to interpret the sign of the phase slope index? - link: /faq/how_to_interpret_the_sign_of_the_phase_slope_index +- name: What is the difference between coherence and coherency? + link: /faq/coherence_coherency - name: In what way can frequency domain data be represented in FieldTrip? - link: /faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip + link: /faq/datatype_freq - name: How can I compute inter-trial coherence? link: /faq/itc -- name: What is the difference between coherence and coherency? - link: /faq/what_is_the_difference_between_coherence_and_coherency +- name: How to interpret the sign of the phase slope index? + link: /faq/phaseslopeindex - name: References to implemented methods link: /references_to_implemented_methods diff --git a/_data/tag/connectivity.yml b/_data/tag/connectivity.yml index 1f0a04212..a4270a2ad 100644 --- a/_data/tag/connectivity.yml +++ b/_data/tag/connectivity.yml @@ -5,7 +5,7 @@ link: /example/connectivity_conditional_granger - name: In what way can frequency domain data be represented in FieldTrip? - link: /faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip + link: /faq/datatype_freq - name: Analysis of corticomuscular coherence link: /tutorial/coherence diff --git a/_data/tag/continuous.yml b/_data/tag/continuous.yml index f33ef5d41..0af068a53 100644 --- a/_data/tag/continuous.yml +++ b/_data/tag/continuous.yml @@ -1,11 +1,11 @@ - name: Why should I set continuous to yes for CTF data? link: /faq/continuous -- name: How can I do time-frequency analysis on continuous data? - link: /faq/how_can_i_do_time-frequency_analysis_on_continuous_data - - name: How can I process continuous data without triggers? - link: /faq/how_can_i_process_continuous_data_without_triggers + link: /faq/preproc_continuous + +- name: How can I do time-frequency analysis on continuous data? + link: /faq/tfr_continuous - name: Preprocessing - Reading continuous EEG and MEG data link: /tutorial/continuous diff --git a/_data/tag/coordinate.yml b/_data/tag/coordinate.yml index 3c67a5b0a..614859984 100644 --- a/_data/tag/coordinate.yml +++ b/_data/tag/coordinate.yml @@ -1,29 +1,29 @@ - name: What is the difference between the ACPC, MNI, SPM and TAL coordinate systems? link: /faq/acpc -- name: How are the different head and MRI coordinate systems defined? - link: /faq/coordsys +- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? + link: /faq/anat_coreg -- name: How do homogenous coordinate transformation matrices work? - link: /faq/homogenous +- name: How can I convert an anatomical MRI from DICOM into CTF format? + link: /faq/anat_dicom2ctf - name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - link: /faq/how_are_the_lpa_and_rpa_points_defined - -- name: How can I convert an anatomical MRI from DICOM into CTF format? - link: /faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format + link: /faq/anat_landmarks - name: How to change the MRI orientation, the voxel size or the field-of-view? - link: /faq/how_change_mri_orientation_size_fov + link: /faq/anat_reslice -- name: How should I report the positions of the fiducial points on the head? - link: /faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head +- name: My MRI is upside down, is this a problem? + link: /faq/anat_upsidedown -- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? - link: /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions +- name: How are the different head and MRI coordinate systems defined? + link: /faq/coordsys -- name: My MRI is upside down, is this a problem? - link: /faq/my_mri_is_upside_down_is_this_a_problem +- name: How should I report the positions of the fiducial points on the head? + link: /faq/fiducials_definition + +- name: How do homogenous coordinate transformation matrices work? + link: /faq/homogenous - name: Getting started with Yokogawa data link: /getting_started/yokogawa diff --git a/_data/tag/corrupt.yml b/_data/tag/corrupt.yml index d5a37644a..d627e75b7 100644 --- a/_data/tag/corrupt.yml +++ b/_data/tag/corrupt.yml @@ -1,12 +1,12 @@ -- name: How can I deal with a discontinuous Neuralynx LFP recording? - link: /faq/discontinuous_neuralynx - - name: How can I fix a corrupt CTF meg4 file? - link: /faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file + link: /faq/ctf_fixmeg4 - name: How can I fix a corrupt CTF res4 header file? - link: /faq/how_can_i_fix_a_corrupt_ctf_res4_header_file + link: /faq/ctf_fixres4 - name: How can I read corrupted (unsaved) CTF data? - link: /faq/how_can_i_read_corrupted_unsaved_ctf_data + link: /faq/ctf_readcorrupted + +- name: How can I deal with a discontinuous Neuralynx LFP recording? + link: /faq/discontinuous_neuralynx diff --git a/_data/tag/crash.yml b/_data/tag/crash.yml index b3e3990e2..e2233764d 100644 --- a/_data/tag/crash.yml +++ b/_data/tag/crash.yml @@ -1,6 +1,6 @@ -- name: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? - link: /faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that - - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash + +- name: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? + link: /faq/ica_crash diff --git a/_data/tag/ct.yml b/_data/tag/ct.yml index cab385680..7bc84a4e5 100644 --- a/_data/tag/ct.yml +++ b/_data/tag/ct.yml @@ -13,35 +13,35 @@ - name: Use denoising source separation (DSS) to remove ECG artifacts link: /example/use_denoising_source_separation_dss_to_remove_ecg_artifacts -- name: Which datasets are used in the documentation and where are they used? - link: /faq/datasets +- name: How can I interpret the different types of padding in FieldTrip? + link: /faq/artifact_padding - name: How can I consistently represent artifacts in my data? - link: /faq/how_can_i_consistently_represent_artifacts_in_my_data - -- name: How can I interpret the different types of padding in FieldTrip? - link: /faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts + link: /faq/artifact_representation - name: How can I use the databrowser? - link: /faq/how_can_i_use_the_databrowser + link: /faq/databrowser -- name: How does the filter padding in preprocessing work? - link: /faq/how_does_the_filter_padding_in_preprocessing_work +- name: Which datasets are used in the documentation and where are they used? + link: /faq/datasets + +- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? + link: /faq/dftfilter_residual - name: I am getting strange artifacts in figures that use opacity - link: /faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity + link: /faq/opacityrendering - name: What kind of filters can I apply to my data? - link: /faq/what_kind_of_filters_can_i_apply_to_my_data + link: /faq/preproc_filtertypes + +- name: How does the filter padding in preprocessing work? + link: /faq/preproc_padding - name: Why does my TFR look strange (part I, demeaning)? - link: /faq/why_does_my_tfr_look_strange + link: /faq/tfr_strangedemean - name: Why does my TFR look strange (part II, detrending)? - link: /faq/why_does_my_tfr_look_strange_part_ii - -- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? - link: /faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter + link: /faq/tfr_strangedetrend - name: Introduction on dealing with artifacts link: /tutorial/artifacts diff --git a/_data/tag/ctf.yml b/_data/tag/ctf.yml index 3796acdb0..b9340a948 100644 --- a/_data/tag/ctf.yml +++ b/_data/tag/ctf.yml @@ -16,35 +16,35 @@ - name: Can I create an artificial CTF dataset using MATLAB? link: /example/writing_simulated_data_to_a_ctf_dataset -- name: Why should I set continuous to yes for CTF data? - link: /faq/continuous +- name: How can I convert an anatomical MRI from DICOM into CTF format? + link: /faq/anat_dicom2ctf - name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - link: /faq/how_are_the_lpa_and_rpa_points_defined + link: /faq/anat_landmarks - name: How can I anonymize or deidentify a CTF dataset? - link: /faq/how_can_i_anonymize_a_ctf_dataset + link: /faq/anonymization_ctf + +- name: Why should I set continuous to yes for CTF data? + link: /faq/continuous - name: How can I change the head localization in a CTF dataset? - link: /faq/how_can_i_change_the_head_localization_in_a_ctf_dataset + link: /faq/ctf_changeheadloc -- name: How can I convert an anatomical MRI from DICOM into CTF format? - link: /faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format +- name: I am having problems reading the CTF .hc headcoordinates file + link: /faq/ctf_fixhc - name: How can I fix a corrupt CTF meg4 file? - link: /faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file + link: /faq/ctf_fixmeg4 - name: How can I fix a corrupt CTF res4 header file? - link: /faq/how_can_i_fix_a_corrupt_ctf_res4_header_file + link: /faq/ctf_fixres4 - name: How can I read corrupted (unsaved) CTF data? - link: /faq/how_can_i_read_corrupted_unsaved_ctf_data + link: /faq/ctf_readcorrupted - name: How does the CTF higher-order gradiometer work? - link: /faq/how_does_the_ctf_higher-order_gradiometer_work - -- name: I am having problems reading the CTF .hc headcoordinates file - link: /faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file + link: /faq/ctf_syntheticgradient - name: Getting started with CTF data link: /getting_started/ctf diff --git a/_data/tag/cvs.yml b/_data/tag/cvs.yml index 26b741e22..f03629d91 100644 --- a/_data/tag/cvs.yml +++ b/_data/tag/cvs.yml @@ -4,9 +4,9 @@ - name: Accessing the FieldTrip source code through SVN link: /development/svn -- name: How can I keep track of changes to the code? - link: /faq/how_can_i_keep_track_of_the_changes_to_the_code - - name: Why was FieldTrip maintained in SVN and not in Git? - link: /faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git + link: /faq/svnversusgit + +- name: How can I keep track of changes to the code? + link: /faq/trackchanges diff --git a/_data/tag/data.yml b/_data/tag/data.yml index b3e3990e2..e2233764d 100644 --- a/_data/tag/data.yml +++ b/_data/tag/data.yml @@ -1,6 +1,6 @@ -- name: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? - link: /faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that - - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash + +- name: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? + link: /faq/ica_crash diff --git a/_data/tag/databrowser.yml b/_data/tag/databrowser.yml index b1fb541e3..ac204418b 100644 --- a/_data/tag/databrowser.yml +++ b/_data/tag/databrowser.yml @@ -1,6 +1,6 @@ - name: How can I use the databrowser? - link: /faq/how_can_i_use_the_databrowser + link: /faq/databrowser - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash diff --git a/_data/tag/dataformat.yml b/_data/tag/dataformat.yml index 6178e8cfc..790929aa7 100644 --- a/_data/tag/dataformat.yml +++ b/_data/tag/dataformat.yml @@ -10,35 +10,35 @@ - name: Can I create an artificial CTF dataset using MATLAB? link: /example/writing_simulated_data_to_a_ctf_dataset +- name: How can I convert an anatomical MRI from DICOM into CTF format? + link: /faq/anat_dicom2ctf + - name: How can I append the files of two separate recordings? link: /faq/append_files +- name: How can I convert one dataformat into an other? + link: /faq/convert_dataformat + - name: What dataformats are supported? link: /faq/dataformat -- name: How are the various MATLAB data structures defined? - link: /faq/how_are_the_various_data_structures_defined - -- name: How can I convert an anatomical MRI from DICOM into CTF format? - link: /faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format +- name: How can I import my own data format? + link: /faq/dataformat_own -- name: How can I convert one dataformat into an other? - link: /faq/how_can_i_convert_one_dataformat_into_an_other +- name: How are the various MATLAB data structures defined? + link: /faq/datatype - name: How can I extend the reading functions with a new dataformat? - link: /faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat - -- name: How can I import my own data format? - link: /faq/how_can_i_import_my_own_dataformat + link: /faq/fileio_dataformat - name: How can I merge two datasets that were acquired simultaneously with different amplifiers? - link: /faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers + link: /faq/mergedata - name: I have problems reading in neuroscan .cnt files. How can I fix this? - link: /faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this + link: /faq/neuroscan - name: Reading is slow, can I write my raw data to a more efficient file format? - link: /faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format + link: /faq/writedata_matbin - name: Getting started with ANT-Neuro, ASA and EEProbe data link: /getting_started/antneuro diff --git a/_data/tag/datatype.yml b/_data/tag/datatype.yml index 1d3e47dc3..7bb335766 100644 --- a/_data/tag/datatype.yml +++ b/_data/tag/datatype.yml @@ -1,12 +1,12 @@ - name: How are the various MATLAB data structures defined? - link: /faq/how_are_the_various_data_structures_defined - -- name: How is anatomical, functional or statistical "volume data" described? - link: /faq/how_is_anatomical_functional_or_statistical_volume_data_described + link: /faq/datatype - name: How is the segmentation defined? - link: /faq/how_is_the_segmentation_defined + link: /faq/datatype_segmentation + +- name: How is anatomical, functional or statistical "volume data" described? + link: /faq/datatype_volume - name: What does a typical call to a FieldTrip function look like? - link: /faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like + link: /faq/fieldtrip_functioncall diff --git a/_data/tag/debug.yml b/_data/tag/debug.yml index 3bf87dcec..2892ed352 100644 --- a/_data/tag/debug.yml +++ b/_data/tag/debug.yml @@ -1,3 +1,3 @@ - name: How can I debug my analysis script if a FieldTrip function gives an error? - link: /faq/how_can_i_debug_my_analysis_script_if_a_fieldtrip_function_gives_an_error + link: /faq/matlab_debugging diff --git a/_data/tag/development.yml b/_data/tag/development.yml index c830ca0a2..80684f8d3 100644 --- a/_data/tag/development.yml +++ b/_data/tag/development.yml @@ -109,12 +109,12 @@ - name: Testing link: /development/testing -- name: How can I keep track of changes to the code? - link: /faq/how_can_i_keep_track_of_the_changes_to_the_code - - name: How should I share example data with the email list or developers? - link: /faq/how_should_i_send_example_data_to_the_developers + link: /faq/datasharing - name: Why was FieldTrip maintained in SVN and not in Git? - link: /faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git + link: /faq/svnversusgit + +- name: How can I keep track of changes to the code? + link: /faq/trackchanges diff --git a/_data/tag/distcomp.yml b/_data/tag/distcomp.yml index 5a8407399..6b20d898c 100644 --- a/_data/tag/distcomp.yml +++ b/_data/tag/distcomp.yml @@ -1,11 +1,11 @@ - name: How can I distribute a batch of jobs? - link: /faq/how_can_i_distribute_a_batch_of_jobs - -- name: How to get started with the MATLAB distributed computing toolbox? - link: /faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox + link: /faq/distributed_batch - name: What are the different approaches I can take for distributed computing? - link: /faq/what_are_the_different_approaches_i_can_take_for_distributed_computing + link: /faq/distributed_computing + +- name: How to get started with the MATLAB distributed computing toolbox? + link: /faq/distributed_matlab - name: Speeding up your analysis using distributed computing with parfor link: /tutorial/distributedcomputing_parfor diff --git a/_data/tag/documentation.yml b/_data/tag/documentation.yml index cf2937f81..4d10e6852 100644 --- a/_data/tag/documentation.yml +++ b/_data/tag/documentation.yml @@ -1,3 +1,3 @@ - name: Can I get an offline version of the documentation on the website? - link: /faq/can_i_get_an_offline_version_of_the_wiki_documentation + link: /faq/documentation_offline diff --git a/_data/tag/download.yml b/_data/tag/download.yml index daa261bd3..bbbb60229 100644 --- a/_data/tag/download.yml +++ b/_data/tag/download.yml @@ -1,18 +1,18 @@ - name: Download the FieldTrip toolbox link: /download -- name: Which version of FieldTrip should I download? - link: /faq/how_can_i_download_a_specific_version - -- name: How can I keep track of changes to the code? - link: /faq/how_can_i_keep_track_of_the_changes_to_the_code +- name: I am working at the Donders, should I also download FieldTrip? + link: /faq/download_donders - name: I am having problems downloading - link: /faq/i_am_having_problems_downloading + link: /faq/download_ftpproblem -- name: I am working at the Donders, should I also download FieldTrip? - link: /faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip +- name: Which version of FieldTrip should I download? + link: /faq/download_version - name: Which version of FieldTrip should I download? - link: /faq/which_version_of_fieldtrip_should_i_download + link: /faq/fieldtrip_downloadversion + +- name: How can I keep track of changes to the code? + link: /faq/trackchanges diff --git a/_data/tag/edf.yml b/_data/tag/edf.yml index 8a46d42a1..11e90d0f0 100644 --- a/_data/tag/edf.yml +++ b/_data/tag/edf.yml @@ -1,5 +1,5 @@ - name: How can I read all channels from an EDF file that contains multiple sampling rates? - link: /faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates + link: /faq/edf2fieldtrip - name: Getting started with EDF (European Data Format) data link: /getting_started/edf diff --git a/_data/tag/eeg.yml b/_data/tag/eeg.yml index 04f8b6e07..ead58a5ad 100644 --- a/_data/tag/eeg.yml +++ b/_data/tag/eeg.yml @@ -46,8 +46,8 @@ - name: Making a synchronous movie of EEG or NIRS combined with video recordings link: /example/video_eeg -- name: Can I do combined EEG and MEG source reconstruction? - link: /faq/can_i_do_combined_eeg_and_meg_source_reconstruction +- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? + link: /faq/anat_coreg - name: Can I compare EEG channels between different electrode caps? link: /faq/capmapping @@ -55,35 +55,35 @@ - name: Which datasets are used in the documentation and where are they used? link: /faq/datasets +- name: How is the segmentation defined? + link: /faq/datatype_segmentation + - name: How should I specify the fiducials for electrode realignment? link: /faq/fiducial -- name: How are electrodes, magnetometers or gradiometers described? - link: /faq/how_are_electrodes_magnetometers_or_gradiometers_described - - name: How can I inspect the electrode impedances of my data? - link: /faq/how_can_i_inspect_the_electrode_impedances_of_my_data + link: /faq/impedancecheck - name: How can I merge two datasets that were acquired simultaneously with different amplifiers? - link: /faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers - -- name: How do I install the OpenMEEG binaries - link: /faq/how_do_i_install_the_openmeeg_binaries - -- name: How is the segmentation defined? - link: /faq/how_is_the_segmentation_defined - -- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? - link: /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions + link: /faq/mergedata - name: I have problems reading in neuroscan .cnt files. How can I fix this? - link: /faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this + link: /faq/neuroscan + +- name: How do I install the OpenMEEG binaries + link: /faq/openmeeg - name: Is it important to have accurate measurements of electrode locations for EEG source reconstruction? - link: /faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction + link: /faq/sensors_accuracy + +- name: How are electrodes, magnetometers or gradiometers described? + link: /faq/sensors_definition - name: Why should I use an average reference for EEG source reconstruction? - link: /faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction + link: /faq/sourcerecon_avgref + +- name: Can I do combined EEG and MEG source reconstruction? + link: /faq/sourcerecon_meeg - name: Getting started with 20%, 10% and 5% electrode arrangements link: /getting_started/1020 diff --git a/_data/tag/eeglab.yml b/_data/tag/eeglab.yml index d3affce44..37beb7247 100644 --- a/_data/tag/eeglab.yml +++ b/_data/tag/eeglab.yml @@ -1,5 +1,5 @@ - name: Why is FieldTrip developed separately from EEGLAB? - link: /faq/why_is_fieldtrip_developed_separately_from_eeglab + link: /faq/fieldtrip_eeglab - name: Getting started with EEGLAB link: /getting_started/eeglab diff --git a/_data/tag/egi.yml b/_data/tag/egi.yml index 6d4a8a973..3f09cae94 100644 --- a/_data/tag/egi.yml +++ b/_data/tag/egi.yml @@ -1,5 +1,5 @@ - name: How can I read EGI mff data without the JVM? - link: /faq/how_can_i_read_egi_mff_data_without_the_jvm + link: /faq/egi_nojvm - name: Getting started with EGI/Philips/Magstim data link: /getting_started/egi diff --git a/_data/tag/electrode.yml b/_data/tag/electrode.yml index f84cc9aae..41f5883ec 100644 --- a/_data/tag/electrode.yml +++ b/_data/tag/electrode.yml @@ -4,14 +4,14 @@ - name: How should I specify the fiducials for electrode realignment? link: /faq/fiducial -- name: How are electrodes, magnetometers or gradiometers described? - link: /faq/how_are_electrodes_magnetometers_or_gradiometers_described +- name: How should I report the positions of the fiducial points on the head? + link: /faq/fiducials_definition - name: How can I inspect the electrode impedances of my data? - link: /faq/how_can_i_inspect_the_electrode_impedances_of_my_data + link: /faq/impedancecheck -- name: How should I report the positions of the fiducial points on the head? - link: /faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head +- name: How are electrodes, magnetometers or gradiometers described? + link: /faq/sensors_definition - name: Should I use a Polhemus or a Structure Sensor to record electrode positions? link: /faq/structuresensor diff --git a/_data/tag/email.yml b/_data/tag/email.yml index 94c7bc0ce..e24200716 100644 --- a/_data/tag/email.yml +++ b/_data/tag/email.yml @@ -1,21 +1,21 @@ -- name: How many people are subscribed to the email discussion list? - link: /faq/how_many_people_are_subscribed_to_the_email_discussion_list - - name: How should I share example data with the email list or developers? - link: /faq/how_should_i_send_example_data_to_the_developers + link: /faq/datasharing + +- name: Why am I receiving warnings about too many bouncing emails? + link: /faq/emaillist_bounces - name: How to ask good questions to the community? - link: /faq/how_to_ask_good_questions_to_the_community + link: /faq/emaillist_howtoask - name: Why am I not allowed to post to the discussion list? - link: /faq/why_am_i_not_allowed_to_post_to_the_discussion_list + link: /faq/emaillist_nopost - name: Why am I not receiving emails from the discussion list? - link: /faq/why_am_i_not_receiving_emails_from_the_discussion_list - -- name: Why am I receiving warnings about too many bouncing emails? - link: /faq/why_am_i_receiving_warnings_about_too_many_bouncing_emails + link: /faq/emaillist_noreceive - name: Why is my message rejected from the email discussion list? - link: /faq/why_is_my_message_rejected_from_the_email_discussion_list + link: /faq/emaillist_rejected + +- name: How many people are subscribed to the email discussion list? + link: /faq/emaillist_subscribers diff --git a/_data/tag/event.yml b/_data/tag/event.yml index 3e5d21a4d..a7abbd05c 100644 --- a/_data/tag/event.yml +++ b/_data/tag/event.yml @@ -1,3 +1,3 @@ - name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data + link: /faq/inspect_events diff --git a/_data/tag/eventtype.yml b/_data/tag/eventtype.yml index 3e5d21a4d..a7abbd05c 100644 --- a/_data/tag/eventtype.yml +++ b/_data/tag/eventtype.yml @@ -1,3 +1,3 @@ - name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data + link: /faq/inspect_events diff --git a/_data/tag/eventvalue.yml b/_data/tag/eventvalue.yml index 3e5d21a4d..a7abbd05c 100644 --- a/_data/tag/eventvalue.yml +++ b/_data/tag/eventvalue.yml @@ -1,3 +1,3 @@ - name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data + link: /faq/inspect_events diff --git a/_data/tag/fiducial.yml b/_data/tag/fiducial.yml index 8ec46012a..844202b66 100644 --- a/_data/tag/fiducial.yml +++ b/_data/tag/fiducial.yml @@ -1,3 +1,6 @@ +- name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? + link: /faq/anat_landmarks + - name: Where is the anterior commissure? link: /faq/anterior_commissure @@ -7,14 +10,11 @@ - name: How should I specify the fiducials for electrode realignment? link: /faq/fiducial -- name: How are electrodes, magnetometers or gradiometers described? - link: /faq/how_are_electrodes_magnetometers_or_gradiometers_described - -- name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - link: /faq/how_are_the_lpa_and_rpa_points_defined - - name: How should I report the positions of the fiducial points on the head? - link: /faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head + link: /faq/fiducials_definition + +- name: How are electrodes, magnetometers or gradiometers described? + link: /faq/sensors_definition - name: Localizing electrodes using a 3D-scanner link: /tutorial/electrode diff --git a/_data/tag/filter.yml b/_data/tag/filter.yml index 0be8429f7..eedeb674e 100644 --- a/_data/tag/filter.yml +++ b/_data/tag/filter.yml @@ -2,17 +2,17 @@ link: /example/determine_the_filter_characteristics - name: How can I interpret the different types of padding in FieldTrip? - link: /faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts + link: /faq/artifact_padding -- name: How does the filter padding in preprocessing work? - link: /faq/how_does_the_filter_padding_in_preprocessing_work +- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? + link: /faq/dftfilter_residual - name: What kind of filters can I apply to my data? - link: /faq/what_kind_of_filters_can_i_apply_to_my_data + link: /faq/preproc_filtertypes -- name: Why does my TFR look strange (part II, detrending)? - link: /faq/why_does_my_tfr_look_strange_part_ii +- name: How does the filter padding in preprocessing work? + link: /faq/preproc_padding -- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? - link: /faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter +- name: Why does my TFR look strange (part II, detrending)? + link: /faq/tfr_strangedetrend diff --git a/_data/tag/freq.yml b/_data/tag/freq.yml index 0fec32cf7..d74d50195 100644 --- a/_data/tag/freq.yml +++ b/_data/tag/freq.yml @@ -25,62 +25,62 @@ - name: Analyze Steady-State Visual Evoked Potentials (SSVEPs) link: /example/ssvep -- name: Does it make sense to subtract the ERP prior to time frequency analysis, to distinguish evoked from induced power? - link: /faq/evoked_vs_induced - -- name: How can I do time-frequency analysis on continuous data? - link: /faq/how_can_i_do_time-frequency_analysis_on_continuous_data - - name: How can I test whether a behavioral measure is phasic? - link: /faq/how_can_i_test_whether_a_behavioral_measure_is_phasic + link: /faq/behavior_cosinefit - name: In what way can frequency domain data be represented in FieldTrip? - link: /faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip + link: /faq/datatype_freq -- name: How does MTMCONVOL work? - link: /faq/mtmconvol +- name: Does it make sense to subtract the ERP prior to time frequency analysis, to distinguish evoked from induced power? + link: /faq/evoked_vs_induced -- name: What is meant by time-frequency trade off? - link: /faq/timefreqtradeoff +- name: Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalysis? + link: /faq/freqanalysis_foimismatchmtmconvol + +- name: Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalysis + link: /faq/freqanalysis_foimismatchmtmfft -- name: What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalyis? - link: /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalyis +- name: Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? + link: /faq/freqanalysis_foimismatchwavelet -- name: What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalyis? - link: /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalyis +- name: Why am I not getting integer frequencies? + link: /faq/freqanalysis_foinoninteger -- name: What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? - link: /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalyis +- name: What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalysis? + link: /faq/freqanalysis_mtmconvol_new -- name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? - link: /faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft +- name: What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalysis? + link: /faq/freqanalysis_mtmfft_new - name: What does "padding not sufficient for requested frequency resolution" mean? - link: /faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean + link: /faq/freqanalysis_paddinginsufficient -- name: What kind of filters can I apply to my data? - link: /faq/what_kind_of_filters_can_i_apply_to_my_data +- name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? + link: /faq/freqanalysis_phasedefinition -- name: Why am I not getting integer frequencies? - link: /faq/why_am_i_not_getting_exact_integer_frequencies +- name: What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? + link: /faq/freqanalysis_wavelet_new -- name: Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalyis? - link: /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis +- name: How does MTMCONVOL work? + link: /faq/mtmconvol -- name: Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalyis - link: /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmfft_in_ft_freqanalyis +- name: What kind of filters can I apply to my data? + link: /faq/preproc_filtertypes -- name: Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? - link: /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis +- name: How can I do time-frequency analysis on continuous data? + link: /faq/tfr_continuous - name: Why does my TFR contain NaNs? - link: /faq/why_does_my_tfr_contain_nans + link: /faq/tfr_nans - name: Why does my TFR look strange (part I, demeaning)? - link: /faq/why_does_my_tfr_look_strange + link: /faq/tfr_strangedemean - name: Why does my TFR look strange (part II, detrending)? - link: /faq/why_does_my_tfr_look_strange_part_ii + link: /faq/tfr_strangedetrend + +- name: What is meant by time-frequency trade off? + link: /faq/timefreqtradeoff - name: Why is the largest peak in the spectrum at the frequency which is 1/segment length? link: /faq/why_largest_peak_spectrum diff --git a/_data/tag/function.yml b/_data/tag/function.yml index 7aa3ae2d3..d8d71c155 100644 --- a/_data/tag/function.yml +++ b/_data/tag/function.yml @@ -1,9 +1,9 @@ -- name: MATLAB does not see the functions in the "private" directory - link: /faq/matlab_does_not_see_the_functions_in_the_private_directory - - name: What does a typical call to a FieldTrip function look like? - link: /faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like + link: /faq/fieldtrip_functioncall + +- name: MATLAB does not see the functions in the "private" directory + link: /faq/matlab_privatefunctions - name: Why are so many of the interesting functions in the private directories? - link: /faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories + link: /faq/privatefunctions_why diff --git a/_data/tag/git.yml b/_data/tag/git.yml index 2c877e6f2..959344adf 100644 --- a/_data/tag/git.yml +++ b/_data/tag/git.yml @@ -7,12 +7,12 @@ - name: Accessing the FieldTrip source code through SVN link: /development/svn -- name: How can I keep track of changes to the code? - link: /faq/how_can_i_keep_track_of_the_changes_to_the_code - - name: How should I share example data with the email list or developers? - link: /faq/how_should_i_send_example_data_to_the_developers + link: /faq/datasharing - name: Why was FieldTrip maintained in SVN and not in Git? - link: /faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git + link: /faq/svnversusgit + +- name: How can I keep track of changes to the code? + link: /faq/trackchanges diff --git a/_data/tag/head.yml b/_data/tag/head.yml index 8ea6feed6..584479ae3 100644 --- a/_data/tag/head.yml +++ b/_data/tag/head.yml @@ -1,3 +1,3 @@ - name: How can I visualize the neuromag head position indicator coils? - link: /faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils + link: /faq/neuromag_hpi diff --git a/_data/tag/headmodel.yml b/_data/tag/headmodel.yml index b59c2c7e0..1744082dd 100644 --- a/_data/tag/headmodel.yml +++ b/_data/tag/headmodel.yml @@ -25,47 +25,47 @@ - name: Testing BEM created EEG lead fields link: /example/testing_bem_created_leadfields -- name: Can I do combined EEG and MEG source reconstruction? - link: /faq/can_i_do_combined_eeg_and_meg_source_reconstruction +- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? + link: /faq/anat_coreg -- name: Can I restrict the source reconstruction to the grey matter? - link: /faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter +- name: How can I fine-tune my BEM volume conduction model? + link: /faq/bem_finetune + +- name: What is the conductivity of the brain, CSF, skull and skin tissue? + link: /faq/conductivity_defaults - name: How are the different head and MRI coordinate systems defined? link: /faq/coordsys -- name: How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? - link: /faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer +- name: What kind of volume conduction models of the head (head models) are implemented? + link: /faq/datatype_headmodel -- name: How can I fine-tune my BEM volume conduction model? - link: /faq/how_can_i_fine-tune_my_bem_volume_conduction_model +- name: How is the segmentation defined? + link: /faq/datatype_segmentation + +- name: Where can I find the dipoli command-line executable? + link: /faq/dipoli_filelocation - name: How can I visualize a localspheres volume conductor model? - link: /faq/how_can_i_visualize_a_localspheres_volume_conductor_model + link: /faq/headmodel_localspheres + +- name: Why does my EEG headmodel look funny? + link: /faq/headmodel_meshingproblem - name: How can I visualize the different geometrical objects that are needed for forward and inverse computations? - link: /faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations + link: /faq/inspect_geometries - name: How do I install the OpenMEEG binaries - link: /faq/how_do_i_install_the_openmeeg_binaries - -- name: How is the segmentation defined? - link: /faq/how_is_the_segmentation_defined - -- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? - link: /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions - -- name: What is the conductivity of the brain, CSF, skull and skin tissue? - link: /faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue + link: /faq/openmeeg -- name: What kind of volume conduction models of the head (head models) are implemented? - link: /faq/what_kind_of_volume_conduction_models_are_implemented +- name: How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? + link: /faq/sourcerecon_checkalignment -- name: Where can I find the dipoli command-line executable? - link: /faq/where_can_i_find_the_dipoli_command-line_executable +- name: Can I restrict the source reconstruction to the grey matter? + link: /faq/sourcerecon_greymatter -- name: Why does my EEG headmodel look funny? - link: /faq/why_does_my_eegheadmodel_look_funny +- name: Can I do combined EEG and MEG source reconstruction? + link: /faq/sourcerecon_meeg - name: Getting started with MeshLab link: /getting_started/meshlab diff --git a/_data/tag/ica.yml b/_data/tag/ica.yml index 5b2178830..b2712137d 100644 --- a/_data/tag/ica.yml +++ b/_data/tag/ica.yml @@ -7,17 +7,17 @@ - name: Use denoising source separation (DSS) to remove ECG artifacts link: /example/use_denoising_source_separation_dss_to_remove_ecg_artifacts -- name: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? - link: /faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that - -- name: Should I rereference prior to or after ICA for artifact removal? - link: /faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal - - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash - name: Why does my ICA output contain complex numbers? - link: /faq/why_does_my_ica_output_contain_complex_numbers + link: /faq/ica_complexvalues + +- name: I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that? + link: /faq/ica_crash + +- name: Should I rereference prior to or after ICA for artifact removal? + link: /faq/ica_rereference - name: Dealing with artifacts link: /workshop/practicalmeeg2022/handson_artifacts diff --git a/_data/tag/interpolate.yml b/_data/tag/interpolate.yml deleted file mode 100644 index 63479a5d6..000000000 --- a/_data/tag/interpolate.yml +++ /dev/null @@ -1,3 +0,0 @@ -- name: How can I map source locations onto an anatomical label in an atlas? - link: /faq/how_can_i_map_source_locations_between_two_different_representations - diff --git a/_data/tag/inverse.yml b/_data/tag/inverse.yml index 2b8e080df..8f660e1c0 100644 --- a/_data/tag/inverse.yml +++ b/_data/tag/inverse.yml @@ -2,5 +2,5 @@ link: /development/module/inverse - name: How can I visualize the different geometrical objects that are needed for forward and inverse computations? - link: /faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations + link: /faq/inspect_geometries diff --git a/_data/tag/label.yml b/_data/tag/label.yml deleted file mode 100644 index 63479a5d6..000000000 --- a/_data/tag/label.yml +++ /dev/null @@ -1,3 +0,0 @@ -- name: How can I map source locations onto an anatomical label in an atlas? - link: /faq/how_can_i_map_source_locations_between_two_different_representations - diff --git a/_data/tag/layout.yml b/_data/tag/layout.yml index c42dbf780..0d9f68dd5 100644 --- a/_data/tag/layout.yml +++ b/_data/tag/layout.yml @@ -1,17 +1,17 @@ - name: Creating a layout for plotting NIRS optodes and channels link: /example/nirs_layout -- name: How are electrodes, magnetometers or gradiometers described? - link: /faq/how_are_electrodes_magnetometers_or_gradiometers_described - - name: How do I construct a layout file for the plotting functions? - link: /faq/how_do_i_construct_a_layout_file_for_the_plotting_functions + link: /faq/layout_creation + +- name: What is the format of the layout file which is used for plotting? + link: /faq/layout_fileformat - name: What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for? - link: /faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for + link: /faq/layout_magandgrad -- name: What is the format of the layout file which is used for plotting? - link: /faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting +- name: How are electrodes, magnetometers or gradiometers described? + link: /faq/sensors_definition - name: Getting started with 20%, 10% and 5% electrode arrangements link: /getting_started/1020 diff --git a/_data/tag/localization.yml b/_data/tag/localization.yml index cc8beac45..cf17f9d17 100644 --- a/_data/tag/localization.yml +++ b/_data/tag/localization.yml @@ -1,5 +1,5 @@ - name: How can I visualize the neuromag head position indicator coils? - link: /faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils + link: /faq/neuromag_hpi - name: Getting started with BioImage Suite link: /getting_started/bioimage diff --git a/_data/tag/localspheres.yml b/_data/tag/localspheres.yml index 8028ddd09..086d14c1b 100644 --- a/_data/tag/localspheres.yml +++ b/_data/tag/localspheres.yml @@ -1,3 +1,3 @@ - name: How can I visualize a localspheres volume conductor model? - link: /faq/how_can_i_visualize_a_localspheres_volume_conductor_model + link: /faq/headmodel_localspheres diff --git a/_data/tag/logo.yml b/_data/tag/logo.yml index c021aea45..14f132844 100644 --- a/_data/tag/logo.yml +++ b/_data/tag/logo.yml @@ -1,3 +1,3 @@ - name: Can I use the FieldTrip logo on my poster? - link: /faq/can_i_use_the_fieldtrip_logo_on_my_poster + link: /faq/fieldtriplogo diff --git a/_data/tag/matlab.yml b/_data/tag/matlab.yml index 9ea4e2ebd..476eb1b6d 100644 --- a/_data/tag/matlab.yml +++ b/_data/tag/matlab.yml @@ -1,35 +1,38 @@ -- name: Can I prevent "external" toolboxes from being added to my MATLAB path? - link: /faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path +- name: How can I compile the mex files on 64-bit Windows? + link: /faq/compile_windows - name: Can I use FieldTrip without MATLAB license? link: /faq/compiled -- name: Which external toolboxes are used by FieldTrip? - link: /faq/external +- name: Where can I find the dipoli command-line executable? + link: /faq/dipoli_filelocation -- name: How can I compile the mex files on 64-bit Windows? - link: /faq/how_can_i_compile_the_mex_files_on_64_bit_windows +- name: What are the different approaches I can take for distributed computing? + link: /faq/distributed_computing -- name: How can I use my MacBook Pro for stimulus presentation in the MEG lab? - link: /faq/how_can_i_use_my_macbook_pro_for_stimulus_presentation_in_the_meg_lab +- name: Which external toolboxes are used by FieldTrip? + link: /faq/external -- name: How do I prevent FieldTrip from printing the time and memory after each function call? - link: /faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call +- name: How many lines of code does FieldTrip consist of? + link: /faq/fieldtrip_codelines - name: How fast is the FieldTrip buffer for realtime data streaming? - link: /faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming + link: /faq/fieldtripbuffer_speed -- name: How many lines of code does FieldTrip consist of? - link: /faq/how_many_lines_of_code_does_fieldtrip_consist_of +- name: Why are the fileio functions stateless, does the fseek not make them very slow? + link: /faq/fileio_stateless - name: Installation and setting up the path link: /faq/installation +- name: MATLAB version 7.3 (2006b) crashes when I try to do ... + link: /faq/matlab_crash73 + - name: MATLAB complains about a missing or invalid mex file, what should I do? - link: /faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do + link: /faq/matlab_mexinvalid - name: MATLAB does not see the functions in the "private" directory - link: /faq/matlab_does_not_see_the_functions_in_the_private_directory + link: /faq/matlab_privatefunctions - name: Replacements for functions from MathWorks toolboxes link: /faq/matlab_replacements @@ -37,26 +40,23 @@ - name: What are the MATLAB requirements for using FieldTrip? link: /faq/matlab_requirements -- name: MATLAB version 7.3 (2006b) crashes when I try to do ... - link: /faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do - - name: MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified - link: /faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified + link: /faq/mex_osx -- name: What are the MATLAB and external requirements? - link: /faq/requirements +- name: Why are so many of the interesting functions in the private directories? + link: /faq/privatefunctions_why -- name: What are the different approaches I can take for distributed computing? - link: /faq/what_are_the_different_approaches_i_can_take_for_distributed_computing +- name: How can I use my MacBook Pro for stimulus presentation in the MEG lab? + link: /faq/psychtoolbox_macbook -- name: Where can I find the dipoli command-line executable? - link: /faq/where_can_i_find_the_dipoli_command-line_executable +- name: What are the MATLAB and external requirements? + link: /faq/requirements -- name: Why are so many of the interesting functions in the private directories? - link: /faq/why_are_so_many_of_the_interesting_functions_in_the_private_directories +- name: How do I prevent FieldTrip from printing the time and memory after each function call? + link: /faq/showcallinfo -- name: Why are the fileio functions stateless, does the fseek not make them very slow? - link: /faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow +- name: Can I prevent "external" toolboxes from being added to my MATLAB path? + link: /faq/toolboxes_legacyvsexternal - name: Speeding up your analysis using distributed computing with parfor link: /tutorial/distributedcomputing_parfor diff --git a/_data/tag/meg.yml b/_data/tag/meg.yml index 0db3cfdc7..3b4dd3f02 100644 --- a/_data/tag/meg.yml +++ b/_data/tag/meg.yml @@ -55,8 +55,11 @@ - name: Can I create an artificial CTF dataset using MATLAB? link: /example/writing_simulated_data_to_a_ctf_dataset -- name: Can I do combined EEG and MEG source reconstruction? - link: /faq/can_i_do_combined_eeg_and_meg_source_reconstruction +- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? + link: /faq/anat_coreg + +- name: How can I convert an anatomical MRI from DICOM into CTF format? + link: /faq/anat_dicom2ctf - name: What does the coilaccuracy parameter do? link: /faq/coilaccuracy @@ -64,26 +67,23 @@ - name: Which datasets are used in the documentation and where are they used? link: /faq/datasets +- name: How is the segmentation defined? + link: /faq/datatype_segmentation + - name: What material is used for the flexible MEG headcasts? link: /faq/headcast -- name: How are electrodes, magnetometers or gradiometers described? - link: /faq/how_are_electrodes_magnetometers_or_gradiometers_described - -- name: How can I convert an anatomical MRI from DICOM into CTF format? - link: /faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format +- name: How can I monitor a subject's head position during a MEG session? + link: /faq/headlocalizer - name: How can I merge two datasets that were acquired simultaneously with different amplifiers? - link: /faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers - -- name: How can I monitor a subject's head position during a MEG session? - link: /faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session + link: /faq/mergedata -- name: How is the segmentation defined? - link: /faq/how_is_the_segmentation_defined +- name: How are electrodes, magnetometers or gradiometers described? + link: /faq/sensors_definition -- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? - link: /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions +- name: Can I do combined EEG and MEG source reconstruction? + link: /faq/sourcerecon_meeg - name: Getting started with BabySQUID data link: /getting_started/babysquid diff --git a/_data/tag/memory.yml b/_data/tag/memory.yml index 3bda5ca52..b4e26ada4 100644 --- a/_data/tag/memory.yml +++ b/_data/tag/memory.yml @@ -1,11 +1,11 @@ -- name: How can I preprocess a dataset that is too large to fit into memory? - link: /faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory - - name: How fast is the FieldTrip buffer for realtime data streaming? - link: /faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming + link: /faq/fieldtripbuffer_speed - name: Why are the fileio functions stateless, does the fseek not make them very slow? - link: /faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow + link: /faq/fileio_stateless + +- name: How can I preprocess a dataset that is too large to fit into memory? + link: /faq/preproc_downsample - name: Preprocessing - Reading continuous EEG and MEG data link: /tutorial/continuous diff --git a/_data/tag/mex.yml b/_data/tag/mex.yml index 62d9f3c62..07221e9c8 100644 --- a/_data/tag/mex.yml +++ b/_data/tag/mex.yml @@ -1,21 +1,21 @@ - name: How can I compile the mex files and command-line executable? link: /faq/compile -- name: Can I use FieldTrip without MATLAB license? - link: /faq/compiled +- name: How can I compile the mex files on macOS? + link: /faq/compile_osx - name: How can I compile the mex files on 64-bit Windows? - link: /faq/how_can_i_compile_the_mex_files_on_64_bit_windows - -- name: How can I compile the mex files on macOS? - link: /faq/how_can_i_compile_the_mex_files_on_os_x + link: /faq/compile_windows -- name: How to select the correct SPM toolbox? - link: /faq/how_to_select_the_correct_spm_toolbox +- name: Can I use FieldTrip without MATLAB license? + link: /faq/compiled - name: MATLAB complains about a missing or invalid mex file, what should I do? - link: /faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do + link: /faq/matlab_mexinvalid - name: MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified - link: /faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified + link: /faq/mex_osx + +- name: How to select the correct SPM toolbox? + link: /faq/spmversion diff --git a/_data/tag/mri.yml b/_data/tag/mri.yml index 1b9748ac6..7f151cf8c 100644 --- a/_data/tag/mri.yml +++ b/_data/tag/mri.yml @@ -19,41 +19,41 @@ - name: What is the difference between the ACPC, MNI, SPM and TAL coordinate systems? link: /faq/acpc -- name: Can I restrict the source reconstruction to the grey matter? - link: /faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter +- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? + link: /faq/anat_coreg -- name: How are the different head and MRI coordinate systems defined? - link: /faq/coordsys +- name: How can I convert an anatomical MRI from DICOM into CTF format? + link: /faq/anat_dicom2ctf - name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - link: /faq/how_are_the_lpa_and_rpa_points_defined - -- name: How can I anonymize or deidentify an anatomical MRI? - link: /faq/how_can_i_anonymize_an_anatomical_mri - -- name: How can I anonymize or deidentify DICOM files? - link: /faq/how_can_i_anonymize_dicom_files + link: /faq/anat_landmarks -- name: How can I convert an anatomical MRI from DICOM into CTF format? - link: /faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format +- name: What is the plotting convention for anatomical MRIs? + link: /faq/anat_plottingconvention - name: How to change the MRI orientation, the voxel size or the field-of-view? - link: /faq/how_change_mri_orientation_size_fov - -- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? - link: /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions + link: /faq/anat_reslice - name: My MRI is upside down, is this a problem? - link: /faq/my_mri_is_upside_down_is_this_a_problem - -- name: What is the plotting convention for anatomical MRIs? - link: /faq/what_is_the_plotting_convention_for_anatomical_mris + link: /faq/anat_upsidedown - name: Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot? - link: /faq/why_does_my_anatomical_mri_show_upside-down_when_plotting_it_with_ft_sourceplot + link: /faq/anat_upsidedownplotting + +- name: How can I anonymize or deidentify an anatomical MRI? + link: /faq/anonymization_anatomical + +- name: How can I anonymize or deidentify DICOM files? + link: /faq/anonymization_dicom + +- name: How are the different head and MRI coordinate systems defined? + link: /faq/coordsys - name: Why is the source model deformed or incorrectly aligned after warping template? - link: /faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template + link: /faq/sourcemodel_deformation + +- name: Can I restrict the source reconstruction to the grey matter? + link: /faq/sourcerecon_greymatter - name: Getting started with fMRI timeseries data link: /getting_started/fmri diff --git a/_data/tag/mtmconvol.yml b/_data/tag/mtmconvol.yml index 716d78476..276b56b71 100644 --- a/_data/tag/mtmconvol.yml +++ b/_data/tag/mtmconvol.yml @@ -1,15 +1,15 @@ -- name: What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalyis? - link: /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmconvol_in_ft_freqanalyis +- name: Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalysis? + link: /faq/freqanalysis_foimismatchmtmconvol -- name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? - link: /faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft +- name: What are the differences between the old and the new implementation of 'mtmconvol' in ft_freqanalysis? + link: /faq/freqanalysis_mtmconvol_new -- name: Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalyis? - link: /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_mtmconvol_in_ft_freqanalyis +- name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? + link: /faq/freqanalysis_phasedefinition - name: Why does my TFR look strange (part I, demeaning)? - link: /faq/why_does_my_tfr_look_strange + link: /faq/tfr_strangedemean - name: Why does my TFR look strange (part II, detrending)? - link: /faq/why_does_my_tfr_look_strange_part_ii + link: /faq/tfr_strangedetrend diff --git a/_data/tag/mtmfft.yml b/_data/tag/mtmfft.yml index f35ea38ff..b14f63935 100644 --- a/_data/tag/mtmfft.yml +++ b/_data/tag/mtmfft.yml @@ -1,8 +1,8 @@ -- name: What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalyis? - link: /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_mtmfft_in_ft_freqanalyis +- name: What are the differences between the old and the new implementation of 'mtmftt' in ft_freqanalysis? + link: /faq/freqanalysis_mtmfft_new - name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? - link: /faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft + link: /faq/freqanalysis_phasedefinition - name: Why is the largest peak in the spectrum at the frequency which is 1/segment length? link: /faq/why_largest_peak_spectrum diff --git a/_data/tag/neuromag.yml b/_data/tag/neuromag.yml index 0aec55f15..9d96333b2 100644 --- a/_data/tag/neuromag.yml +++ b/_data/tag/neuromag.yml @@ -7,11 +7,11 @@ - name: Find the orientation of planar gradiometers link: /example/planar_orientation -- name: How can I visualize the neuromag head position indicator coils? - link: /faq/how_can_i_visualize_the_neuromag_head_position_indicator_coils - - name: Why are there multiple neighbour templates for the Neuromag306 system? - link: /faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system + link: /faq/neighbours_neuromag + +- name: How can I visualize the neuromag head position indicator coils? + link: /faq/neuromag_hpi - name: Getting started with Neuromag/Elekta/Megin data link: /getting_started/neuromag diff --git a/_data/tag/neuroscan.yml b/_data/tag/neuroscan.yml index 64d01c9fe..95bc1542a 100644 --- a/_data/tag/neuroscan.yml +++ b/_data/tag/neuroscan.yml @@ -1,3 +1,3 @@ - name: I have problems reading in neuroscan .cnt files. How can I fix this? - link: /faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this + link: /faq/neuroscan diff --git a/_data/tag/noise.yml b/_data/tag/noise.yml index 613862394..2e9752e61 100644 --- a/_data/tag/noise.yml +++ b/_data/tag/noise.yml @@ -1,3 +1,3 @@ - name: Why is there a residual 50Hz line-noise component after applying a DFT filter? - link: /faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter + link: /faq/dftfilter_residual diff --git a/_data/tag/normalization.yml b/_data/tag/normalization.yml index f541e505e..5e7a759b9 100644 --- a/_data/tag/normalization.yml +++ b/_data/tag/normalization.yml @@ -1,3 +1,3 @@ - name: Why is the source model deformed or incorrectly aligned after warping template? - link: /faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template + link: /faq/sourcemodel_deformation diff --git a/_data/tag/octave.yml b/_data/tag/octave.yml index ee7caa2f1..8a55081ae 100644 --- a/_data/tag/octave.yml +++ b/_data/tag/octave.yml @@ -1,3 +1,3 @@ - name: Can I use Octave instead of MATLAB? - link: /faq/can_i_use_octave_instead_of_matlab + link: /faq/octave diff --git a/_data/tag/openmeeg.yml b/_data/tag/openmeeg.yml index 3d1da6d43..a174a12e4 100644 --- a/_data/tag/openmeeg.yml +++ b/_data/tag/openmeeg.yml @@ -1,3 +1,3 @@ - name: How do I install the OpenMEEG binaries - link: /faq/how_do_i_install_the_openmeeg_binaries + link: /faq/openmeeg diff --git a/_data/tag/parfor.yml b/_data/tag/parfor.yml index a8fabd699..204339c5f 100644 --- a/_data/tag/parfor.yml +++ b/_data/tag/parfor.yml @@ -1,11 +1,11 @@ - name: Distributed computing link: /development/distributed -- name: How to get started with the MATLAB distributed computing toolbox? - link: /faq/how_to_get_started_with_the_matlab_distributed_computing_toolbox - - name: What are the different approaches I can take for distributed computing? - link: /faq/what_are_the_different_approaches_i_can_take_for_distributed_computing + link: /faq/distributed_computing + +- name: How to get started with the MATLAB distributed computing toolbox? + link: /faq/distributed_matlab - name: Speeding up your analysis using distributed computing with parfor link: /tutorial/distributedcomputing_parfor diff --git a/_data/tag/path.yml b/_data/tag/path.yml index 2f3da443d..ea98b7ea0 100644 --- a/_data/tag/path.yml +++ b/_data/tag/path.yml @@ -1,11 +1,5 @@ -- name: Can I prevent "external" toolboxes from being added to my MATLAB path? - link: /faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path - -- name: How to select the correct SPM toolbox? - link: /faq/how_to_select_the_correct_spm_toolbox - - name: I am working at the Donders, should I also download FieldTrip? - link: /faq/i_am_working_at_the_donders_should_i_also_download_fieldtrip + link: /faq/download_donders - name: Installation and setting up the path link: /faq/installation @@ -13,3 +7,9 @@ - name: Replacements for functions from MathWorks toolboxes link: /faq/matlab_replacements +- name: How to select the correct SPM toolbox? + link: /faq/spmversion + +- name: Can I prevent "external" toolboxes from being added to my MATLAB path? + link: /faq/toolboxes_legacyvsexternal + diff --git a/_data/tag/phase.yml b/_data/tag/phase.yml index e3b81286c..9bd38e50b 100644 --- a/_data/tag/phase.yml +++ b/_data/tag/phase.yml @@ -1,3 +1,3 @@ - name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? - link: /faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft + link: /faq/freqanalysis_phasedefinition diff --git a/_data/tag/plotting.yml b/_data/tag/plotting.yml index 90a75d228..f3eaf78ec 100644 --- a/_data/tag/plotting.yml +++ b/_data/tag/plotting.yml @@ -16,29 +16,29 @@ - name: Which colormaps are supported? link: /faq/colormap -- name: How can I define neighbouring sensors? - link: /faq/how_can_i_define_neighbouring_sensors - - name: How can I use the databrowser? - link: /faq/how_can_i_use_the_databrowser - -- name: How do I construct a layout file for the plotting functions? - link: /faq/how_do_i_construct_a_layout_file_for_the_plotting_functions + link: /faq/databrowser -- name: I am getting strange artifacts in figures that use opacity - link: /faq/i_am_getting_strange_artifacts_in_figures_that_use_opacity +- name: What is a good way to save images for later processing in other software? + link: /faq/figure_export - name: I am having problems printing figures that use opacity - link: /faq/i_am_having_problems_printing_figures_that_use_opacity + link: /faq/figure_opacity + +- name: How do I construct a layout file for the plotting functions? + link: /faq/layout_creation + +- name: What is the format of the layout file which is used for plotting? + link: /faq/layout_fileformat - name: What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for? - link: /faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for + link: /faq/layout_magandgrad -- name: What is a good way to save images for later processing in other software? - link: /faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software +- name: I am getting strange artifacts in figures that use opacity + link: /faq/opacityrendering -- name: What is the format of the layout file which is used for plotting? - link: /faq/what_is_the_format_of_the_layout_file_which_is_used_for_plotting +- name: How can I define neighbouring sensors? + link: /faq/sensors_neighbours - name: Reference documentation link: /reference diff --git a/_data/tag/polhemus.yml b/_data/tag/polhemus.yml index 6a5718ed7..5af41a1fb 100644 --- a/_data/tag/polhemus.yml +++ b/_data/tag/polhemus.yml @@ -1,5 +1,5 @@ - name: How should I report the positions of the fiducial points on the head? - link: /faq/how_should_i_report_the_positions_of_the_fiducial_points_on_the_head + link: /faq/fiducials_definition - name: Should I use a Polhemus or a Structure Sensor to record electrode positions? link: /faq/structuresensor diff --git a/_data/tag/preprocessing.yml b/_data/tag/preprocessing.yml index 1ecdd5af1..f23045dbb 100644 --- a/_data/tag/preprocessing.yml +++ b/_data/tag/preprocessing.yml @@ -31,56 +31,65 @@ - name: How can I append the files of two separate recordings? link: /faq/append_files +- name: How can I interpret the different types of padding in FieldTrip? + link: /faq/artifact_padding + +- name: How can I consistently represent artifacts in my data? + link: /faq/artifact_representation + - name: Why should I set continuous to yes for CTF data? link: /faq/continuous +- name: How can I convert one dataformat into an other? + link: /faq/convert_dataformat + +- name: How can I read corrupted (unsaved) CTF data? + link: /faq/ctf_readcorrupted + - name: What dataformats are supported? link: /faq/dataformat +- name: How can I import my own data format? + link: /faq/dataformat_own + +- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? + link: /faq/dftfilter_residual + - name: How can I deal with a discontinuous Neuralynx LFP recording? link: /faq/discontinuous_neuralynx -- name: How can I consistently represent artifacts in my data? - link: /faq/how_can_i_consistently_represent_artifacts_in_my_data +- name: How can I read all channels from an EDF file that contains multiple sampling rates? + link: /faq/edf2fieldtrip -- name: How can I convert one dataformat into an other? - link: /faq/how_can_i_convert_one_dataformat_into_an_other +- name: What is the relation between "events" (such as triggers) and "trials"? + link: /faq/eventsversustrials - name: How can I extend the reading functions with a new dataformat? - link: /faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat - -- name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data + link: /faq/fileio_dataformat -- name: How can I import my own data format? - link: /faq/how_can_i_import_my_own_dataformat +- name: Why am I not getting integer frequencies? + link: /faq/freqanalysis_foinoninteger -- name: How can I interpret the different types of padding in FieldTrip? - link: /faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts +- name: How can I find out what eventvalues and eventtypes there are in my data? + link: /faq/inspect_events - name: How can I merge two datasets that were acquired simultaneously with different amplifiers? - link: /faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers + link: /faq/mergedata -- name: How can I preprocess a dataset that is too large to fit into memory? - link: /faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory +- name: I have problems reading in neuroscan .cnt files. How can I fix this? + link: /faq/neuroscan - name: How can I process continuous data without triggers? - link: /faq/how_can_i_process_continuous_data_without_triggers + link: /faq/preproc_continuous -- name: How can I read all channels from an EDF file that contains multiple sampling rates? - link: /faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates +- name: How can I preprocess a dataset that is too large to fit into memory? + link: /faq/preproc_downsample -- name: How can I read corrupted (unsaved) CTF data? - link: /faq/how_can_i_read_corrupted_unsaved_ctf_data +- name: What kind of filters can I apply to my data? + link: /faq/preproc_filtertypes - name: How does the filter padding in preprocessing work? - link: /faq/how_does_the_filter_padding_in_preprocessing_work - -- name: I have problems reading in neuroscan .cnt files. How can I fix this? - link: /faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this - -- name: Reading is slow, can I write my raw data to a more efficient file format? - link: /faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format + link: /faq/preproc_padding - name: How can I rename channels in my data structure? link: /faq/rename_channels @@ -88,26 +97,17 @@ - name: Do I need to resample my data, and if so, how is this to be done? link: /faq/resampling_lowpassfilter -- name: How can I check or decipher the sequence of triggers in my data? - link: /faq/triggers - -- name: What is the relation between "events" (such as triggers) and "trials"? - link: /faq/what_is_the_relation_between_events_such_as_triggers_and_trials - -- name: What kind of filters can I apply to my data? - link: /faq/what_kind_of_filters_can_i_apply_to_my_data - -- name: Why am I not getting integer frequencies? - link: /faq/why_am_i_not_getting_exact_integer_frequencies - - name: Why does my TFR look strange (part I, demeaning)? - link: /faq/why_does_my_tfr_look_strange + link: /faq/tfr_strangedemean - name: Why does my TFR look strange (part II, detrending)? - link: /faq/why_does_my_tfr_look_strange_part_ii + link: /faq/tfr_strangedetrend -- name: Why is there a residual 50Hz line-noise component after applying a DFT filter? - link: /faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter +- name: How can I check or decipher the sequence of triggers in my data? + link: /faq/triggers + +- name: Reading is slow, can I write my raw data to a more efficient file format? + link: /faq/writedata_matbin - name: Introduction on dealing with artifacts link: /tutorial/artifacts diff --git a/_data/tag/qsub.yml b/_data/tag/qsub.yml index 7da12fcc0..acf7721a1 100644 --- a/_data/tag/qsub.yml +++ b/_data/tag/qsub.yml @@ -4,14 +4,14 @@ - name: Distributed computing using a Linux compute cluster link: /development/module/qsub -- name: How to compile MATLAB code into stand-alone executables? - link: /faq/how_to_compile_matlab_code_into_stand-alone_executables +- name: What are the different approaches I can take for distributed computing? + link: /faq/distributed_computing - name: How to get started with distributed computing using qsub? - link: /faq/how_to_get_started_with_distributed_computing_using_qsub + link: /faq/distributed_qsub -- name: What are the different approaches I can take for distributed computing? - link: /faq/what_are_the_different_approaches_i_can_take_for_distributed_computing +- name: How to compile MATLAB code into stand-alone executables? + link: /faq/matlab_compile - name: Speeding up your analysis using distributed computing with qsub link: /tutorial/distributedcomputing_qsub diff --git a/_data/tag/raw.yml b/_data/tag/raw.yml index f897fb3ad..ff2e4a1da 100644 --- a/_data/tag/raw.yml +++ b/_data/tag/raw.yml @@ -7,41 +7,41 @@ - name: Making your own trialfun for conditional trial definition link: /example/trialfun -- name: What dataformats are supported? - link: /faq/dataformat - - name: How can I anonymize or deidentify a BrainVision dataset? - link: /faq/how_can_i_anonymize_a_brainvision_dataset + link: /faq/anonymization_brainvision - name: How can I anonymize or deidentify a CTF dataset? - link: /faq/how_can_i_anonymize_a_ctf_dataset + link: /faq/anonymization_ctf -- name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data +- name: I am having problems reading the CTF .hc headcoordinates file + link: /faq/ctf_fixhc - name: How can I fix a corrupt CTF meg4 file? - link: /faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file + link: /faq/ctf_fixmeg4 - name: How can I fix a corrupt CTF res4 header file? - link: /faq/how_can_i_fix_a_corrupt_ctf_res4_header_file + link: /faq/ctf_fixres4 -- name: How can I merge two datasets that were acquired simultaneously with different amplifiers? - link: /faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers +- name: How can I read corrupted (unsaved) CTF data? + link: /faq/ctf_readcorrupted -- name: How can I process continuous data without triggers? - link: /faq/how_can_i_process_continuous_data_without_triggers +- name: What dataformats are supported? + link: /faq/dataformat -- name: How can I read corrupted (unsaved) CTF data? - link: /faq/how_can_i_read_corrupted_unsaved_ctf_data +- name: How can I find out what eventvalues and eventtypes there are in my data? + link: /faq/inspect_events -- name: I am having problems reading the CTF .hc headcoordinates file - link: /faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file +- name: How can I merge two datasets that were acquired simultaneously with different amplifiers? + link: /faq/mergedata - name: I have problems reading in neuroscan .cnt files. How can I fix this? - link: /faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this + link: /faq/neuroscan + +- name: How can I process continuous data without triggers? + link: /faq/preproc_continuous - name: Reading is slow, can I write my raw data to a more efficient file format? - link: /faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format + link: /faq/writedata_matbin - name: Importing your data link: /reading_data diff --git a/_data/tag/realtime.yml b/_data/tag/realtime.yml index 4ec28eaef..9334fbb5d 100644 --- a/_data/tag/realtime.yml +++ b/_data/tag/realtime.yml @@ -131,19 +131,19 @@ link: /example/measuring_the_timing_delay_and_jitter_for_a_real-time_application - name: Does the FieldTrip realtime buffer only work with MATLAB? - link: /faq/does_the_fieldtrip_realtime_buffer_only_work_with_matlab + link: /faq/fieldtripbuffer -- name: How can I monitor a subject's head position during a MEG session? - link: /faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session - -- name: What kind of cable do I need for a serial port connection between two computers? - link: /faq/how_can_i_test_the_serial_port_connection_between_two_computers +- name: How should I get started with the FieldTrip realtime buffer? + link: /faq/fieldtripbuffer_gettingstarted - name: How fast is the FieldTrip buffer for realtime data streaming? - link: /faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming + link: /faq/fieldtripbuffer_speed -- name: How should I get started with the FieldTrip realtime buffer? - link: /faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer +- name: How can I monitor a subject's head position during a MEG session? + link: /faq/headlocalizer + +- name: What kind of cable do I need for a serial port connection between two computers? + link: /faq/serialport - name: Getting started with real-time analysis for BCI/neurofeedback link: /getting_started/realtime diff --git a/_data/tag/reference.yml b/_data/tag/reference.yml index db2b769b7..919f5a057 100644 --- a/_data/tag/reference.yml +++ b/_data/tag/reference.yml @@ -1,6 +1,6 @@ - name: How should I refer to FieldTrip in my publication? - link: /faq/how_should_i_refer_to_fieldtrip_in_my_publication + link: /faq/fieldtrip_reference - name: Why should I use an average reference for EEG source reconstruction? - link: /faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction + link: /faq/sourcerecon_avgref diff --git a/_data/tag/release.yml b/_data/tag/release.yml index 029eaa026..03a73cf38 100644 --- a/_data/tag/release.yml +++ b/_data/tag/release.yml @@ -4,12 +4,12 @@ - name: Testing link: /development/testing -- name: Which version of FieldTrip should I download? - link: /faq/how_can_i_download_a_specific_version - - name: I am having problems downloading - link: /faq/i_am_having_problems_downloading + link: /faq/download_ftpproblem + +- name: Which version of FieldTrip should I download? + link: /faq/download_version - name: Which version of FieldTrip should I download? - link: /faq/which_version_of_fieldtrip_should_i_download + link: /faq/fieldtrip_downloadversion diff --git a/_data/tag/seg.yml b/_data/tag/seg.yml index dec06fb44..1a7852f9b 100644 --- a/_data/tag/seg.yml +++ b/_data/tag/seg.yml @@ -1,3 +1,3 @@ - name: How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? - link: /faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer + link: /faq/sourcerecon_checkalignment diff --git a/_data/tag/segmentation.yml b/_data/tag/segmentation.yml index cfe7ecc03..97533e0e7 100644 --- a/_data/tag/segmentation.yml +++ b/_data/tag/segmentation.yml @@ -1,5 +1,5 @@ - name: How is the segmentation defined? - link: /faq/how_is_the_segmentation_defined + link: /faq/datatype_segmentation - name: Getting started with ParaView link: /getting_started/paraview diff --git a/_data/tag/sharing.yml b/_data/tag/sharing.yml index 38306a06a..7b89f965c 100644 --- a/_data/tag/sharing.yml +++ b/_data/tag/sharing.yml @@ -34,29 +34,29 @@ - name: Converting an example video dataset for sharing in BIDS link: /example/bids_video -- name: How should I specify the coordinate systems in a BIDS dataset? - link: /faq/bids_coordsystem - -- name: Which methodological details should I report in an EEG/MEG manuscript? - link: /faq/checklist - -- name: How can I share my MEG data? - link: /faq/data_sharing +- name: How can I anonymize or deidentify an anatomical MRI? + link: /faq/anonymization_anatomical - name: How can I anonymize or deidentify a BrainVision dataset? - link: /faq/how_can_i_anonymize_a_brainvision_dataset + link: /faq/anonymization_brainvision - name: How can I anonymize or deidentify a CTF dataset? - link: /faq/how_can_i_anonymize_a_ctf_dataset - -- name: How can I anonymize or deidentify an anatomical MRI? - link: /faq/how_can_i_anonymize_an_anatomical_mri + link: /faq/anonymization_ctf - name: How can I anonymize or deidentify DICOM files? - link: /faq/how_can_i_anonymize_dicom_files + link: /faq/anonymization_dicom - name: How can I anonymize data processed in FieldTrip? - link: /faq/how_can_i_anonymize_fieldtrip_data + link: /faq/anonymization_fieldtripdata + +- name: How should I specify the coordinate systems in a BIDS dataset? + link: /faq/bids_coordsystem + +- name: Which methodological details should I report in an EEG/MEG manuscript? + link: /faq/checklist + +- name: How can I share my MEG data? + link: /faq/data_sharing - name: Where can I find open access MEG/EEG data? link: /faq/open_data diff --git a/_data/tag/source.yml b/_data/tag/source.yml index 16a920e8c..aecc3fbd7 100644 --- a/_data/tag/source.yml +++ b/_data/tag/source.yml @@ -55,59 +55,56 @@ - name: Use your own forward leadfield model in an inverse beamformer computation link: /example/use_your_own_forward_leadfield_model_in_an_inverse_beamformer_computation +- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? + link: /faq/anat_coreg + +- name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? + link: /faq/anat_landmarks + - name: Where is the anterior commissure? link: /faq/anterior_commissure -- name: Can I do combined EEG and MEG source reconstruction? - link: /faq/can_i_do_combined_eeg_and_meg_source_reconstruction +- name: How can I fine-tune my BEM volume conduction model? + link: /faq/bem_finetune -- name: Can I restrict the source reconstruction to the grey matter? - link: /faq/can_i_restrict_the_source_reconstruction_to_the_grey_matter +- name: What is the conductivity of the brain, CSF, skull and skin tissue? + link: /faq/conductivity_defaults - name: How are the different head and MRI coordinate systems defined? link: /faq/coordsys -- name: How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - link: /faq/how_are_the_lpa_and_rpa_points_defined - -- name: How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? - link: /faq/how_can_i_check_whether_the_grid_that_i_have_is_aligned_to_the_segmented_volume_and_to_the_sensor_gradiometer - -- name: How can I determine the anatomical label of a source or electrode? - link: /faq/how_can_i_determine_the_anatomical_label_of_a_source - -- name: How can I fine-tune my BEM volume conduction model? - link: /faq/how_can_i_fine-tune_my_bem_volume_conduction_model +- name: What kind of volume conduction models of the head (head models) are implemented? + link: /faq/datatype_headmodel -- name: How can I map source locations onto an anatomical label in an atlas? - link: /faq/how_can_i_map_source_locations_between_two_different_representations +- name: Where can I find the dipoli command-line executable? + link: /faq/dipoli_filelocation - name: How can I visualize the different geometrical objects that are needed for forward and inverse computations? - link: /faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations + link: /faq/inspect_geometries -- name: How to coregister an anatomical MRI with the gradiometer or electrode positions? - link: /faq/how_to_coregister_an_anatomical_mri_with_the_gradiometer_or_electrode_positions - -- name: Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed? - link: /faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed +- name: How can I determine the anatomical label of a source or electrode? + link: /faq/label_lookup - name: Is it important to have accurate measurements of electrode locations for EEG source reconstruction? - link: /faq/is_it_important_to_have_accurate_measurements_of_electrode_locations_for_eeg_source_reconstruction + link: /faq/sensors_accuracy -- name: What is the conductivity of the brain, CSF, skull and skin tissue? - link: /faq/what_is_the_conductivity_of_the_brain_csf_skull_and_skin_tissue +- name: Why should I use an average reference for EEG source reconstruction? + link: /faq/sourcerecon_avgref -- name: What kind of volume conduction models of the head (head models) are implemented? - link: /faq/what_kind_of_volume_conduction_models_are_implemented +- name: How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer? + link: /faq/sourcerecon_checkalignment -- name: Where can I find the dipoli command-line executable? - link: /faq/where_can_i_find_the_dipoli_command-line_executable +- name: Can I restrict the source reconstruction to the grey matter? + link: /faq/sourcerecon_greymatter -- name: Why is there a rim around the brain for which the source reconstruction is not computed? - link: /faq/why_is_there_a_rim_around_the_brain_for_which_the_source_reconstruction_is_not_computed +- name: Can I do combined EEG and MEG source reconstruction? + link: /faq/sourcerecon_meeg -- name: Why should I use an average reference for EEG source reconstruction? - link: /faq/why_should_i_use_an_average_reference_for_eeg_source_reconstruction +- name: Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed? + link: /faq/sourcerecon_outside + +- name: Why is there a rim around the brain for which the source reconstruction is not computed? + link: /faq/sourcerecon_rim - name: Reference documentation link: /reference diff --git a/_data/tag/sourcemodel.yml b/_data/tag/sourcemodel.yml index b9ea73bbc..9a887be79 100644 --- a/_data/tag/sourcemodel.yml +++ b/_data/tag/sourcemodel.yml @@ -1,9 +1,9 @@ +- name: Why is the source model deformed or incorrectly aligned after warping template? + link: /faq/sourcemodel_deformation + - name: Is it OK for vertices/dipoles to stick out of the volume conductor? link: /faq/sticking_out -- name: Why is the source model deformed or incorrectly aligned after warping template? - link: /faq/why_is_the_source_model_deformed_or_incorrectly_aligned_after_warping_template - - name: Template models for source reconstruction link: /template/sourcemodel diff --git a/_data/tag/spm.yml b/_data/tag/spm.yml index d46979c36..bd457c790 100644 --- a/_data/tag/spm.yml +++ b/_data/tag/spm.yml @@ -1,5 +1,5 @@ - name: How to select the correct SPM toolbox? - link: /faq/how_to_select_the_correct_spm_toolbox + link: /faq/spmversion - name: Getting started with SPM link: /getting_started/spm diff --git a/_data/tag/statistics.yml b/_data/tag/statistics.yml index 27b4ac8c7..d27bd1c96 100644 --- a/_data/tag/statistics.yml +++ b/_data/tag/statistics.yml @@ -31,41 +31,41 @@ - name: Use simulated ERPs to explore cluster statistics link: /example/use_simulated_erps_to_explore_cluster_statistics -- name: How can I define neighbouring sensors? - link: /faq/how_can_i_define_neighbouring_sensors +- name: How can I test whether a behavioral measure is phasic? + link: /faq/behavior_cosinefit -- name: How can I determine the onset of an effect? - link: /faq/how_can_i_determine_the_onset_of_an_effect +- name: How can I test for correlations between neuronal data and quantitative stimulus and behavioral variables? + link: /faq/behavior_signalcorrelation -- name: How to test an interaction effect using cluster-based permutation tests? - link: /faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests +- name: Why should I use the cfg.correcttail option when using statistics_montecarlo? + link: /faq/clusterstats_correcttail -- name: How can I test for correlations between neuronal data and quantitative stimulus and behavioral variables? - link: /faq/how_can_i_test_for_correlations_between_neuronal_data_and_quantitative_stimulus_and_behavioural_variables +- name: How to test an interaction effect using cluster-based permutation tests? + link: /faq/clusterstats_interaction -- name: How can I test whether a behavioral measure is phasic? - link: /faq/how_can_i_test_whether_a_behavioral_measure_is_phasic +- name: How NOT to interpret results from a cluster-based permutation test + link: /faq/clusterstats_interpretation - name: How can I use the ivar, uvar, wvar and cvar options to precisely control the permutations? - link: /faq/how_can_i_use_the_ivar_uvar_wvar_and_cvar_options_to_precisely_control_the_permutations + link: /faq/clusterstats_iuwcvar -- name: How does a difference in trial numbers per condition affect my statistical test - link: /faq/how_does_a_difference_in_trial_numbers_per_condition_affect_my_statistical_test +- name: Should I use t or F values for cluster-based permutation tests? + link: /faq/clusterstats_teststatistic + +- name: How can I determine the onset of an effect? + link: /faq/effectonset - name: How does ft_prepare_neighbours work? - link: /faq/how_does_ft_prepare_neighbours_work + link: /faq/neighbours_prepare -- name: How NOT to interpret results from a cluster-based permutation test - link: /faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test +- name: How can I define neighbouring sensors? + link: /faq/sensors_neighbours -- name: Should I use t or F values for cluster-based permutation tests? - link: /faq/should_I_use_t_or_F_values_for_cluster-based_permutation_tests +- name: How does a difference in trial numbers per condition affect my statistical test + link: /faq/statistics_ntrials - name: What is the idea behind statistical inference at the second-level? - link: /faq/what_is_the_idea_behind_statistical_inference_at_the_second-level - -- name: Why should I use the cfg.correcttail option when using statistics_montecarlo? - link: /faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo + link: /faq/statistics_secondlevel - name: Getting started with LIMO MEEG link: /getting_started/limo diff --git a/_data/tag/support.yml b/_data/tag/support.yml index ecaf4cdf5..e332e76c3 100644 --- a/_data/tag/support.yml +++ b/_data/tag/support.yml @@ -11,7 +11,7 @@ link: /discussion_list - name: How to ask good questions to the community? - link: /faq/how_to_ask_good_questions_to_the_community + link: /faq/emaillist_howtoask - name: Privacy Policy link: /privacy diff --git a/_data/tag/surf.yml b/_data/tag/surf.yml index 7d279e9e7..52327f089 100644 --- a/_data/tag/surf.yml +++ b/_data/tag/surf.yml @@ -1,3 +1,3 @@ - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash diff --git a/_data/tag/svn.yml b/_data/tag/svn.yml index 26b741e22..f03629d91 100644 --- a/_data/tag/svn.yml +++ b/_data/tag/svn.yml @@ -4,9 +4,9 @@ - name: Accessing the FieldTrip source code through SVN link: /development/svn -- name: How can I keep track of changes to the code? - link: /faq/how_can_i_keep_track_of_the_changes_to_the_code - - name: Why was FieldTrip maintained in SVN and not in Git? - link: /faq/why_is_fieldtrip_maintained_in_svn_and_not_in_git + link: /faq/svnversusgit + +- name: How can I keep track of changes to the code? + link: /faq/trackchanges diff --git a/_data/tag/template.yml b/_data/tag/template.yml index 6ab755c34..4daa1ae0b 100644 --- a/_data/tag/template.yml +++ b/_data/tag/template.yml @@ -1,5 +1,5 @@ - name: Why are there multiple neighbour templates for the Neuromag306 system? - link: /faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system + link: /faq/neighbours_neuromag - name: Template models and data link: /template diff --git a/_data/tag/timelock.yml b/_data/tag/timelock.yml index ddaa56de7..52f3b0287 100644 --- a/_data/tag/timelock.yml +++ b/_data/tag/timelock.yml @@ -2,7 +2,7 @@ link: /example/dipolefit_somatosensory_erf - name: What kind of filters can I apply to my data? - link: /faq/what_kind_of_filters_can_i_apply_to_my_data + link: /faq/preproc_filtertypes - name: Reference documentation link: /reference diff --git a/_data/tag/toolbox.yml b/_data/tag/toolbox.yml index 5500da6af..6e1f3fef1 100644 --- a/_data/tag/toolbox.yml +++ b/_data/tag/toolbox.yml @@ -1,12 +1,6 @@ -- name: Can I prevent "external" toolboxes from being added to my MATLAB path? - link: /faq/can_i_prevent_external_toolboxes_from_being_added_to_my_matlab_path - - name: Which external toolboxes are used by FieldTrip? link: /faq/external -- name: How to select the correct SPM toolbox? - link: /faq/how_to_select_the_correct_spm_toolbox - - name: Replacements for functions from MathWorks toolboxes link: /faq/matlab_replacements @@ -16,3 +10,9 @@ - name: What are the MATLAB and external requirements? link: /faq/requirements +- name: How to select the correct SPM toolbox? + link: /faq/spmversion + +- name: Can I prevent "external" toolboxes from being added to my MATLAB path? + link: /faq/toolboxes_legacyvsexternal + diff --git a/_data/tag/topo.yml b/_data/tag/topo.yml index 7d279e9e7..52327f089 100644 --- a/_data/tag/topo.yml +++ b/_data/tag/topo.yml @@ -1,3 +1,3 @@ - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash diff --git a/_data/tag/topoplot.yml b/_data/tag/topoplot.yml index 7d279e9e7..52327f089 100644 --- a/_data/tag/topoplot.yml +++ b/_data/tag/topoplot.yml @@ -1,3 +1,3 @@ - name: The databrowser crashes and destroys the whole MATLAB session, how can I resolve this? - link: /faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this + link: /faq/databrowser_crash diff --git a/_data/tag/trialdef.yml b/_data/tag/trialdef.yml index 98ba80713..26800fb44 100644 --- a/_data/tag/trialdef.yml +++ b/_data/tag/trialdef.yml @@ -4,11 +4,11 @@ - name: Making your own trialfun for conditional trial definition link: /example/trialfun -- name: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? - link: /faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore - - name: Is it possible to keep track of trial-specific information in my analysis pipeline? - link: /faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline + link: /faq/trialinfo + +- name: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? + link: /faq/trialinfo_trl - name: FieldTrip Walkthrough link: /walkthrough diff --git a/_data/tag/trialfun.yml b/_data/tag/trialfun.yml index 444aa3bd5..3062a8a47 100644 --- a/_data/tag/trialfun.yml +++ b/_data/tag/trialfun.yml @@ -4,21 +4,21 @@ - name: Making your own trialfun for conditional trial definition link: /example/trialfun -- name: How can I transform trigger values from bits to decimal representation with a trialfun? - link: /faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun +- name: What is the relation between "events" (such as triggers) and "trials"? + link: /faq/eventsversustrials -- name: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? - link: /faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore +- name: How can I transform trigger values from bits to decimal representation with a trialfun? + link: /faq/trialfun_bit2decimal - name: Is it possible to keep track of trial-specific information in my analysis pipeline? - link: /faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline + link: /faq/trialinfo + +- name: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? + link: /faq/trialinfo_trl - name: How can I check or decipher the sequence of triggers in my data? link: /faq/triggers -- name: What is the relation between "events" (such as triggers) and "trials"? - link: /faq/what_is_the_relation_between_events_such_as_triggers_and_trials - - name: Preprocessing of EEG data and computing ERPs link: /tutorial/preprocessing_erp diff --git a/_data/tag/trialinfo.yml b/_data/tag/trialinfo.yml index 22bb0ac15..98f8656dd 100644 --- a/_data/tag/trialinfo.yml +++ b/_data/tag/trialinfo.yml @@ -1,6 +1,6 @@ -- name: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? - link: /faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore - - name: Is it possible to keep track of trial-specific information in my analysis pipeline? - link: /faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline + link: /faq/trialinfo + +- name: I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore? + link: /faq/trialinfo_trl diff --git a/_data/tag/trigger.yml b/_data/tag/trigger.yml index 887643190..6ef25da55 100644 --- a/_data/tag/trigger.yml +++ b/_data/tag/trigger.yml @@ -1,5 +1,5 @@ - name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data + link: /faq/inspect_events - name: How can I check or decipher the sequence of triggers in my data? link: /faq/triggers diff --git a/_data/tag/type.yml b/_data/tag/type.yml index 250edb5dd..5811290ad 100644 --- a/_data/tag/type.yml +++ b/_data/tag/type.yml @@ -1,15 +1,15 @@ - name: How are the various MATLAB data structures defined? - link: /faq/how_are_the_various_data_structures_defined + link: /faq/datatype -- name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data +- name: How is the segmentation defined? + link: /faq/datatype_segmentation - name: How is anatomical, functional or statistical "volume data" described? - link: /faq/how_is_anatomical_functional_or_statistical_volume_data_described - -- name: How is the segmentation defined? - link: /faq/how_is_the_segmentation_defined + link: /faq/datatype_volume - name: What does a typical call to a FieldTrip function look like? - link: /faq/what_does_a_typical_call_to_a_fieldtrip_function_look_like + link: /faq/fieldtrip_functioncall + +- name: How can I find out what eventvalues and eventtypes there are in my data? + link: /faq/inspect_events diff --git a/_data/tag/values.yml b/_data/tag/values.yml index 3e5d21a4d..a7abbd05c 100644 --- a/_data/tag/values.yml +++ b/_data/tag/values.yml @@ -1,3 +1,3 @@ - name: How can I find out what eventvalues and eventtypes there are in my data? - link: /faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data + link: /faq/inspect_events diff --git a/_data/tag/volume.yml b/_data/tag/volume.yml index 379f49981..a6d2118fb 100644 --- a/_data/tag/volume.yml +++ b/_data/tag/volume.yml @@ -1,11 +1,11 @@ - name: How to change the MRI orientation, the voxel size or the field-of-view? - link: /faq/how_change_mri_orientation_size_fov - -- name: How is anatomical, functional or statistical "volume data" described? - link: /faq/how_is_anatomical_functional_or_statistical_volume_data_described + link: /faq/anat_reslice - name: My MRI is upside down, is this a problem? - link: /faq/my_mri_is_upside_down_is_this_a_problem + link: /faq/anat_upsidedown + +- name: How is anatomical, functional or statistical "volume data" described? + link: /faq/datatype_volume - name: Getting started with ParaView link: /getting_started/paraview diff --git a/_data/tag/warning.yml b/_data/tag/warning.yml index 457157109..0474008a1 100644 --- a/_data/tag/warning.yml +++ b/_data/tag/warning.yml @@ -1,9 +1,9 @@ - name: How can I visualize the different geometrical objects that are needed for forward and inverse computations? - link: /faq/how_can_i_visualize_the_different_geometrical_objects_that_are_needed_for_forward_and_inverse_computations + link: /faq/inspect_geometries - name: Installation and setting up the path link: /faq/installation - name: Why are there multiple neighbour templates for the Neuromag306 system? - link: /faq/why_are_there_multiple_neighbour_templates_for_the_neuromag306_system + link: /faq/neighbours_neuromag diff --git a/_data/tag/wavelet.yml b/_data/tag/wavelet.yml index e7a7693b0..1d71b1498 100644 --- a/_data/tag/wavelet.yml +++ b/_data/tag/wavelet.yml @@ -1,9 +1,9 @@ -- name: What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? - link: /faq/what_are_the_differences_between_the_old_and_the_new_implementation_of_wavelet_formerly_wltconvol_in_ft_freqanalyis +- name: Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? + link: /faq/freqanalysis_foimismatchwavelet - name: What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'? - link: /faq/what_convention_is_used_to_define_absolute_phase_in_mtmconvol_wavelet_and_mtmfft + link: /faq/freqanalysis_phasedefinition -- name: Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalyis? - link: /faq/why_does_my_output.freq_not_match_my_cfg.foi_when_using_wavelet_formerly_wltconvol_in_ft_freqanalyis +- name: What are the differences between the old and the new implementation of 'wavelet' (formerly 'wltconvol') in ft_freqanalysis? + link: /faq/freqanalysis_wavelet_new diff --git a/_data/tag/workshop.yml b/_data/tag/workshop.yml index 76206157a..d7f6330bd 100644 --- a/_data/tag/workshop.yml +++ b/_data/tag/workshop.yml @@ -1,8 +1,8 @@ - name: Can I organize my own FieldTrip workshop? - link: /faq/can_i_organize_my_own_workshop + link: /faq/workshop - name: How should I prepare for the upcoming FieldTrip workshop? - link: /faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop + link: /faq/workshop_preparation - name: FieldTrip courses and workshops link: /workshop diff --git a/tag/interpolate.md b/tag/interpolate.md deleted file mode 100644 index 2ec597840..000000000 --- a/tag/interpolate.md +++ /dev/null @@ -1,4 +0,0 @@ ---- -layout: tag -tag: interpolate ---- diff --git a/tag/label.md b/tag/label.md deleted file mode 100644 index 9b3a6e190..000000000 --- a/tag/label.md +++ /dev/null @@ -1,4 +0,0 @@ ---- -layout: tag -tag: label ----