From a139ebd79129e73bb7da5f3bd3738c314286e52b Mon Sep 17 00:00:00 2001 From: Robert Oostenveld Date: Tue, 24 Sep 2024 10:35:25 +0200 Subject: [PATCH] added tags, see #810 --- faq/can_i_organize_my_own_workshop.md | 2 +- faq/how_can_i_distribute_a_batch_of_jobs.md | 1 + ...s_between_two_different_representations.md | 2 +- ...ime_and_memory_after_each_function_call.md | 6 ++-- faq/how_does_ft_prepare_neighbours_work.md | 2 +- ...lines_of_code_does_fieldtrip_consist_of.md | 31 ++++++++++--------- faq/timefreqtradeoff.md | 1 + ..._neuromag_and_yokogawa_layouts_good_for.md | 4 +-- ..._for_later_processing_in_other_software.md | 22 ++++++++----- 9 files changed, 41 insertions(+), 30 deletions(-) diff --git a/faq/can_i_organize_my_own_workshop.md b/faq/can_i_organize_my_own_workshop.md index d979c8854..23b892096 100644 --- a/faq/can_i_organize_my_own_workshop.md +++ b/faq/can_i_organize_my_own_workshop.md @@ -1,6 +1,6 @@ --- title: Can I organize my own FieldTrip workshop? -tags: [workshop] +tags: [faq, workshop] --- # Can I organize my own FieldTrip workshop? diff --git a/faq/how_can_i_distribute_a_batch_of_jobs.md b/faq/how_can_i_distribute_a_batch_of_jobs.md index 1a53d773a..49f143034 100644 --- a/faq/how_can_i_distribute_a_batch_of_jobs.md +++ b/faq/how_can_i_distribute_a_batch_of_jobs.md @@ -1,5 +1,6 @@ --- title: How can I distribute a batch of jobs? +tags: [faq, distcomp] --- # How can I distribute a batch of jobs? diff --git a/faq/how_can_i_map_source_locations_between_two_different_representations.md b/faq/how_can_i_map_source_locations_between_two_different_representations.md index a57473466..988730592 100644 --- a/faq/how_can_i_map_source_locations_between_two_different_representations.md +++ b/faq/how_can_i_map_source_locations_between_two_different_representations.md @@ -1,6 +1,6 @@ --- title: How can I map source locations onto an anatomical label in an atlas? -tags: [source, interpolate, atlas, label] +tags: [faq, source, interpolate, atlas, label] --- # How can I map source locations onto an anatomical label in an atlas? diff --git a/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md b/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md index a56de7908..302ece3d5 100644 --- a/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md +++ b/faq/how_do_i_prevent_fieldtrip_from_printing_the_time_and_memory_after_each_function_call.md @@ -31,8 +31,8 @@ You can also pass it as a general option to all functions like this: global ft_default ft_default.showcallinfo = 'no'; -The configuration options in the `ft_default` global variable are (in general) on startup of each FieldTrip function merged with the cfg options that you pass to that function. +The configuration options in the `ft_default` global variable are (in general) on startup of each FieldTrip function merged with the configuration options that you pass to that function. -Of course you can add this general setting to your startup.m file so that you don't have to type it each time that you start MATLAB. +Of course you can add this general setting to your `startup.m` file so that you don't have to type it each time that you start MATLAB. -\*) Note that the memory estimate is currently not yet available on windows. +\*) Note that the memory estimate is currently not yet available on Windows. diff --git a/faq/how_does_ft_prepare_neighbours_work.md b/faq/how_does_ft_prepare_neighbours_work.md index 6a2b9a2a5..7e0b65740 100644 --- a/faq/how_does_ft_prepare_neighbours_work.md +++ b/faq/how_does_ft_prepare_neighbours_work.md @@ -1,6 +1,6 @@ --- title: How does ft_prepare_neighbours work? -tags: [statistics, cluster] +tags: [faq, statistics, cluster] --- # How does ft_prepare_neighbours work? diff --git a/faq/how_many_lines_of_code_does_fieldtrip_consist_of.md b/faq/how_many_lines_of_code_does_fieldtrip_consist_of.md index db2fb4f00..2f29e5ca4 100644 --- a/faq/how_many_lines_of_code_does_fieldtrip_consist_of.md +++ b/faq/how_many_lines_of_code_does_fieldtrip_consist_of.md @@ -1,21 +1,21 @@ --- title: How many lines of code does FieldTrip consist of? -tags: [faq] +tags: [faq, matlab] --- # How many lines of code does FieldTrip consist of? You can count that using the following commands - roboos@mac001> cat `find . -name \*.m` | grep -v ' *%' | grep -v '^ *$' | wc -l - 366391 + roboos@mac001> cat `find fieldtrip-20221223 -name \*.m` | grep -v ' *%' | grep -v '^ *$' | wc -l + 493168 or excluding the external toolboxes with - roboos@mac001> cat `find . -name \*.m | grep -v external` | grep -v ' *%' | grep -v '^ *$' | wc -l - 187938 + roboos@mac001> cat `find fieldtrip-20221223 -name \*.m | grep -v external` | grep -v ' *%' | grep -v '^ *$' | wc -l + 237209 -So the answer is approximately 187938 lines of code, excluding comments and empty lines. +So the answer is approximately 237209 lines of code, excluding comments and empty lines. To provide some historical perspective here is the number of lines in older FieldTrip releases (also only counting lines of code). @@ -23,18 +23,21 @@ To provide some historical perspective here is the number of lines in older Fiel | -------- | ------------- | | 2003 nov | 3441 | | 2004 jun | 11735 | -| 2005 jun | 16969 | | 2005 dec | 19235 | -| 2006 jun | 24410 | | 2006 dec | 27507 | -| 2007 jun | 30306 | | 2007 dec | 32057 | -| 2008 jun | 37963 | | 2008 dec | 66581 | -| 2009 jun | 87756 | | 2009 dec | 89983 | -| 2010 jun | 95049 | | 2010 dec | 92192 | -| 2011 jun | 103813 | | 2011 dec | 114642 | -| 2016 oct | 187938 | +| 2012 dec | 125116 | +| 2013 dec | 128477 | +| 2014 dec | ? | +| 2015 dec | ? | +| 2016 dec | 184322 | +| 2017 dec | 198553 | +| 2018 dec | 205290 | +| 2019 dec | 215759 | +| 2010 dec | 226194 | +| 2021 dec | 234054 | +| 2022 dec | 237209 | diff --git a/faq/timefreqtradeoff.md b/faq/timefreqtradeoff.md index 29400fb2a..79dad6e8f 100644 --- a/faq/timefreqtradeoff.md +++ b/faq/timefreqtradeoff.md @@ -1,5 +1,6 @@ --- title: What is meant by time-frequency trade off? +tags: [faq, freq] --- # What is meant by time-frequency trade-off? diff --git a/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md b/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md index bc7e04253..b36b32fea 100644 --- a/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md +++ b/faq/what_are_the_different_neuromag_and_yokogawa_layouts_good_for.md @@ -1,10 +1,10 @@ --- title: What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for? -tags: [faq] +tags: [faq, layout, plotting] --- # What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for? -The Neuromag/Elekta/Megin and Yokogawa MEG systems use two different kind of sensors, gradiometers and magnetometers. Gradiometer consists of two coils, and the data recorded of such a pair reflects the gradient of the magnetic field, measured in Tesla per distance unit. In contrast, magnetometers measure the magnetic field using one coil only, resulting in a measure in Tesla. Since the two type of sensors measure in different units, data obtained from these two types of sensor cannot be easily compared directly. Therefore FieldTrip features layouts for gradiometer and magnetometer sensor positions separately, so that the user can visualize either the magnetometer data or the gradiometer data. +The Neuromag/Elekta/Megin and some Yokogawa MEG systems use a combination of two different kind of sensors within one system: (planar) gradiometers and magnetometers. Gradiometer consists of two coils, and the data recorded of such a pair reflects the gradient of the magnetic field, measured in Tesla per distance unit. In contrast, magnetometers measure the magnetic field using one coil only, resulting in a measure in Tesla. Since the two type of sensors measure in different units, data obtained from these two types of sensor cannot be easily compared directly. Therefore FieldTrip features layouts for gradiometer and magnetometer sensor positions separately, so that the user can visualize either the magnetometer data or the gradiometer data. For more information, please consult the manual of the MEG system of your choice or see [Hämäläinen, Hari, Ilmoniemi, Knuutila, Lounasmaa (1993) Magnetoencephalography—theory, instrumentation, and applications to noninvasive studies of the working human brain. Rev. Mod. Phys. 65 (2), 413-497](http://rmp.aps.org/abstract/RMP/v65/i2/p413_1) diff --git a/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md b/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md index 5840645e7..ec651bac0 100644 --- a/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md +++ b/faq/what_is_a_good_way_to_save_images_for_later_processing_in_other_software.md @@ -1,20 +1,26 @@ --- title: What is a good way to save images for later processing in other software? +tags: [faq, plotting] --- # What is a good way to save images for later processing in other software? -This is a question with many possible answers. Below is a list of tips from various users/developers: +Here are some tips from various users/developers: -- Save in .eps format, these can be easily edited in Adobe Illustrator etc. +- Save in `.eps` format, these can be easily edited in Adobe Illustrator etc. - Use the function [saveSameSize](http://www.mathworks.com/matlabcentral/fileexchange/17868-savesamesize) from the MathWorks File Exchange. This function saves the the figure like it looks on-screen. - Use the function [export_fig](http://www.mathworks.com/matlabcentral/fileexchange/23629-exportfig) from the MathWorks File Exchange for advanced saving options. -- When processing an exported .eps file in Adobe Illustrator, remember the following things/bugs about MATLAB's figure export - - MATLAB usually creates invisible 'boxes/objects' around plot-elements like axes, text, etc. To make it easier to work with the objects that are actually important, delete all these superfluous and invisible objects by selecting everything (ctrl+a), or selecting 'empty space' and deleting the ones that contain none of the elements that you want, or look unimportant (there are ALWAYS many of these annoying objects). A 'clean' figure is always easier for a Journal copy-editor to work with. - - MATLAB usually creates white squares as background of axes, deleting these makes handling the plots a lot easier. - - In a regular `plot(x,y)` figure, many additional x,y-axes are often placed on top of each other and are 'invisible' which makes foreground/background transfers problematic, delete these x,y-axes. - - When plotting several lines in as `plot(x,y,etc)`, the output is usually read as a 'grouped' object by Illustrator. Ungrouping these objects (i.e. right click --> ungroup) makes handling/editing these lines much easier. - - Whenever you notice that elements of plots were not exported as objects, but as horizontal bars of a bitmap image, or anything else that is weird, it is usually a MATLAB openGL bug. Doing `set(gcf,'renderer','painters')` usually fixes this. +When processing an exported `.eps` file in Adobe Illustrator, remember the following things/quirks about MATLAB's figure export: + +- MATLAB usually creates invisible 'boxes/objects' around plot-elements like axes, text, etcetera. To make it easier to work with the objects that are actually important, delete all these superfluous and invisible objects by selecting everything (ctrl+a), or selecting 'empty space' and deleting the ones that contain none of the elements that you want, or look unimportant (there are ALWAYS many of these annoying objects). A 'clean' figure is always easier for a Journal copy-editor to work with. + +- MATLAB usually creates white squares as background of axes, deleting these makes handling the plots a lot easier. + +- In a regular `plot(x,y)` figure, many additional x,y-axes are often placed on top of each other and are 'invisible' which makes foreground/background transfers problematic, delete these x,y-axes. + +- When plotting several lines in as `plot(x,y,etc)`, the output is usually read as a 'grouped' object by Illustrator. Ungrouping these objects (i.e. right click --> ungroup) makes handling/editing these lines much easier. + +- Whenever you notice that elements of plots were not exported as objects, but as horizontal bars of a bitmap image, or anything else that is weird, it is usually a MATLAB openGL bug. Doing `set(gcf,'renderer','painters')` usually fixes this.