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updated sections and added subsections in the FAQ overview, see #571
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robertoostenveld committed Jul 8, 2022
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19 changes: 11 additions & 8 deletions example.md
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Expand Up @@ -13,20 +13,23 @@ See also the [tutorials](/tutorial) and [frequently asked questions](/faq).

### Reading and preprocessing data

- [Detect the muscle activity in an EMG channel and use that as trial definition](/example/detect_the_muscle_activity_in_an_emg_channel_and_use_that_as_trial_definition)
- [Fixing a missing sensor](/example/fixing_a_missing_sensor)
- [Getting started with reading raw EEG or MEG data](/example/getting_started_with_reading_raw_eeg_or_meg_data)
- [How to incorporate head movements in MEG analysis](/example/headmovement_meg)
- [Interpolating data from the CTF151 to the CTF275 sensor array using ft_megrealign](/example/megrealign)
- [Making your own trialfun for conditional trial definition](/example/making_your_own_trialfun_for_conditional_trial_definition)
- [Analyzing NIRS data recorded during unilateral finger- and foot-tapping](/example/nirs_fingertapping)
- [Analyzing NIRS data recorded during listening to and repeating speech](/example/nirs_speech)
- [The correct pipeline order for combining planar MEG channels](/example/combineplanar_pipelineorder)
- [Detect the muscle activity in an EMG channel and use that as trial definition](/example/detect_the_muscle_activity_in_an_emg_channel_and_use_that_as_trial_definition)
- [Use independent component analysis (ICA) to remove ECG artifacts](/example/ica_ecg)
- [Use independent component analysis (ICA) to remove EOG artifacts](/example/ica_eog)
- [Use denoising source separation (DSS) to remove ECG artifacts](/example/use_denoising_source_separation_dss_to_remove_ecg_artifacts)
- [Fixing a missing sensor](/example/fixing_a_missing_sensor)
- [Re-reference EEG and iEEG data](/example/rereference)

### Sensor-level analysis

- [Analyzing NIRS data recorded during unilateral finger- and foot-tapping](/example/nirs_fingertapping)
- [Analyzing NIRS data recorded during listening to and repeating speech](/example/nirs_speech)
- [The correct pipeline order for combining planar MEG channels](/example/combineplanar_pipelineorder)
- [How to incorporate head movements in MEG analysis](/example/headmovement_meg)
- [Interpolating data from the CTF151 to the CTF275 sensor array using ft_megrealign](/example/megrealign)

### Spectral analysis

- [Analysis of high-gamma band signals in human ECoG](/example/ecog_ny)
Expand Down Expand Up @@ -91,7 +94,7 @@ See also the [tutorials](/tutorial) and [frequently asked questions](/faq).
- [Plotting the result of source reconstructing on a cortical mesh](/example/plotting_source_surface)
- [Making a synchronous movie of EEG or NIRS combined with video recordings](/example/video_eeg)

## Miscellaneous
## Various other examples

- [BIDS - the brain imaging data structure](/example/bids)
- [Combining simultaneous recordings in BIDS](/example/bids_pom)
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72 changes: 40 additions & 32 deletions faq.md
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Expand Up @@ -12,36 +12,53 @@ We invite you to [add your own](/contribute) example scripts or frequently asked
See also the [tutorials](/tutorial) and [example scripts](/example).

## Reading and preprocessing data
- [How can I append the files of two separate recordings?](/faq/append_files)
- [How can I check or decipher the sequence of triggers in my data?](/faq/triggers)
- [How can I consistently represent artifacts in my data?](/faq/how_can_i_consistently_represent_artifacts_in_my_data)
- [How can I convert one dataformat into an other?](/faq/how_can_i_convert_one_dataformat_into_an_other)
- [How can I find out what eventvalues and eventtypes there are in my data?](/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data)
- [How can I import my own dataformat?](/faq/how_can_i_import_my_own_dataformat)

- [How can I use the databrowser?](/faq/how_can_i_use_the_databrowser)
- [How can I inspect the electrode impedances of my data?](/faq/how_can_i_inspect_the_electrode_impedances_of_my_data)
- [How can I interpret the different types of padding that I find when dealing with artifacts?](/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts)
- [How can I merge two datasets that were acquired simultaneously with different amplifiers?](/faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers)
- [How can I preprocess a dataset that is too large to fit into memory?](/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory)
- [How can I process continuous data without triggers?](/faq/how_can_i_process_continuous_data_without_triggers)
- [Should I rereference my EEG data prior to, or after ICA?](/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal)
- [I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore?](/faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore)

## Specific data formats
- [How can I read EGI mff data without the JVM?](/faq/how_can_i_read_egi_mff_data_without_the_jvm)
- [How can I read all channels from an EDF file that contains multiple sampling rates?](/faq/how_can_i_read_all_channels_from_an_edf_file_that_contains_multiple_sampling_rates)
- [How can I transform trigger values from bits to decimal representation with a trialfun?](/faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun)
- [How can I use the databrowser?](/faq/how_can_i_use_the_databrowser)
- [How can I extend the reading functions with a new dataformat?](/faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat)
- [How does the CTF higher-order gradiometer work?](/faq/how_does_the_ctf_higher-order_gradiometer_work)
- [How does the filter padding in preprocessing work?](/faq/how_does_the_filter_padding_in_preprocessing_work)
- [How can I extend the reading functions with a new dataformat?](/faq/how_can_i_extend_the_reading_functions_with_a_new_dataformat)
- [I have problems reading in neuroscan .cnt files. How can I fix this?](/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this)
- [I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that?](/faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that)
- [I used to work with trl-matrices that have more than 3 columns. Why is this not supported anymore?](/faq/i_used_to_work_with_trl-matrices_that_have_more_than_3_columns._why_is_this_not_supported_anymore)
- [Is it possible to keep track of trial-specific information in my FieldTrip analysis pipeline?](/faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline)
- [Why are the fileio functions stateless, does the fseek not make them very slow?](/faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow)
- [How can I import my own dataformat?](/faq/how_can_i_import_my_own_dataformat)
- [How can I deal with a discontinuous Neuralynx recording?](/faq/discontinuous_neuralynx)
- [How can I fix a corrupt CTF meg4 data file?](/faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file)
- [How can I fix a corrupt CTF res4 header file?](/faq/how_can_i_fix_a_corrupt_ctf_res4_header_file)
- [How can I read corrupted (unsaved)\_CTF_data?](/faq/how_can_i_read_corrupted_unsaved_ctf_data)
- [I am having problems reading the CTF .hc headcoordinates file](/faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file)

### Data handling

- [Reading is slow, can I write my raw data to a more efficient file format?](/faq/reading_is_slow_can_i_write_my_raw_data_to_a_more_efficient_file_format)
- [The databrowser crashes and destroys the whole MATLAB session, how can I resolve this?](/faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this)
- [What dataformats are supported?](/faq/dataformat)
- [How can I append the files of two separate recordings?](/faq/append_files)
- [How can I convert one dataformat into an other?](/faq/how_can_i_convert_one_dataformat_into_an_other)
- [How can I merge two datasets that were acquired simultaneously with different amplifiers?](/faq/how_can_i_merge_two_datasets_that_were_acquired_simultaneously_with_different_amplifiers)
- [How can I preprocess a dataset that is too large to fit into memory?](/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory)

### Trials, triggers and events

- [How can I check or decipher the sequence of triggers in my data?](/faq/triggers)
- [How can I find out what eventvalues and eventtypes there are in my data?](/faq/how_can_i_find_out_what_eventvalues_and_eventtypes_there_are_in_my_data)
- [How can I process continuous data without triggers?](/faq/how_can_i_process_continuous_data_without_triggers)
- [How can I transform trigger values from bits to decimal representation with a trialfun?](/faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun)
- [Is it possible to keep track of trial-specific information in my FieldTrip analysis pipeline?](/faq/is_it_possible_to_keep_track_of_trial-specific_information_in_my_fieldtrip_analysis_pipeline)

### Artifacts

- [What kind of filters can I apply to my data?](/faq/what_kind_of_filters_can_i_apply_to_my_data)
- [Why are the fileio functions stateless, does the fseek not make them very slow?](/faq/why_are_the_fileio_functions_stateless_does_the_fseek_not_make_them_very_slow)
- [Why is there a residual 50Hz line-noise component after applying a DFT filter?](/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter)
- [Should I rereference my EEG data prior to, or after ICA?](/faq/should_I_rereference_prior_to_or_after_ica_for_artifact_removal)
- [Do I need to resample my data, and if so, how is this to be done?](/faq/resampling_lowpassfilter)
- [I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that?](/faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that)
- [Why does my ICA output contain complex numbers?](/faq/why_does_my_ica_output_contain_complex_numbers)
- [How can I consistently represent artifacts in my data?](/faq/how_can_i_consistently_represent_artifacts_in_my_data)
- [How can I interpret the different types of padding that I find when dealing with artifacts?](/faq/how_can_i_interpret_the_different_types_of_padding_that_i_find_when_dealing_with_artifacts)
- [How does the filter padding in preprocessing work?](/faq/how_does_the_filter_padding_in_preprocessing_work)
- [Why is there a residual 50Hz line-noise component after applying a DFT filter?](/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter)

## Spectral analysis

Expand Down Expand Up @@ -136,14 +153,6 @@ See also the [tutorials](/tutorial) and [example scripts](/example).
- [How fast is the FieldTrip buffer for realtime data streaming?](/faq/how_fast_is_the_fieldtrip_buffer_for_realtime_data_streaming)
- [How should I get started with the FieldTrip realtime buffer?](/faq/how_should_i_get_started_with_the_fieldtrip_realtime_buffer)

## Questions that pertain to corrupt datafiles

- [How can I deal with a discontinuous Neuralynx recording?](/faq/discontinuous_neuralynx)
- [How can I fix a corrupt CTF meg4 data file?](/faq/how_can_i_fix_a_corrupt_ctf_meg4_data_file)
- [How can I fix a corrupt CTF res4 header file?](/faq/how_can_i_fix_a_corrupt_ctf_res4_header_file)
- [How can I read corrupted (unsaved)\_CTF_data?](/faq/how_can_i_read_corrupted_unsaved_ctf_data)
- [I am having problems reading the CTF .hc headcoordinates file](/faq/i_am_having_problems_reading_the_ctf_.hc_headcoordinates_file)

## Distributed computing

- [What are the different approaches I can take for distributed computing?](/faq/what_are_the_different_approaches_i_can_take_for_distributed_computing)
Expand Down Expand Up @@ -199,6 +208,7 @@ See also the [tutorials](/tutorial) and [example scripts](/example).
- [MATLAB does not see the functions in the "private" directory](/faq/matlab_does_not_see_the_functions_in_the_private_directory)
- [MATLAB version 7.3 (2006b)_crashes_when_I_try_to_do_...](/faq/matlab_version_7.3_2006b_crashes_when_i_try_to_do)
- [Should I add FieldTrip with all subdirectories to my MATLAB path?](/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path)
- [The databrowser crashes and destroys the whole MATLAB session, how can I resolve this?](/faq/the_databrowser_crashes_and_destroys_the_whole_matlab_session_how_can_i_resolve_this)
- [What are the MATLAB requirements for using FieldTrip?](/faq/requirements)
- [What is the relation between "events" (such as_triggers) and "trials"?](/faq/what_is_the_relation_between_events_such_as_triggers_and_trials)
- [Which external toolboxes are used by FieldTrip?](/faq/external)
Expand Down Expand Up @@ -232,7 +242,7 @@ See also the [tutorials](/tutorial) and [example scripts](/example).
## Various other questions

- [Are the FieldTrip lectures available on video?](/faq/video)
- [Can I map different Electrode position layouts?](/faq/capmapping)
- [Can I map different electrode position layouts?](/faq/capmapping)
- [Can I organize my own FieldTrip workshop?](/faq/can_i_organize_my_own_workshop)
- [How can I anonymize DICOM files?](/faq/how_can_i_anonymize_dicom_files)
- [How can I anonymize a CTF dataset?](/faq/how_can_i_anonymize_a_ctf_dataset)
Expand All @@ -243,9 +253,7 @@ See also the [tutorials](/tutorial) and [example scripts](/example).
- [How do I prevent FieldTrip from printing the time and memory after each function call?](/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call)
- [How should I prepare for the upcoming FieldTrip workshop?](/faq/how_should_i_prepare_for_the_upcoming_fieldtrip_workshop)
- [How should I specify the coordinate systems in a BIDS dataset?](/faq/bids_coordsystem)
- [I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that?](/faq/i_used_ica_on_my_meg_data_from_before_2012_and_now_fieldtrip_crashes_why_is_that)
- [What are the units of the data and of the derived results?](/faq/units)
- [What types of datasets (and their respective analyses) are used on FieldTrip?](/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip)
- [What usage information is FieldTrip tracking?](/faq/tracking)
- [Where can I find open access MEG/EEG data?](/faq/open_data)
- [Why does my ICA output contain complex numbers?](/faq/why_does_my_ica_output_contain_complex_numbers)

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