haiyangjin / fmri-matlab Goto Github PK

Labels generated by earlier versions of FS typically include the values of significance in the fifth column. But it seems that the last column of the labels generated by FS7 is all 0.

This could be "fixed" manually.

Just rename some variables within functions and probably it does not really matter.

Put surface (surface/) related functions in a separate folder. These functions should not be specific to FreeSurfer or HCP.
Put FreeSurfer-specific functions in freesurfer/.

1. remove 'mgz' from those function names.
2. remove unused codes (e.g., fsaverageLR)

To calculate the AUC for decoding (in addition to the accuracy)

[X, Y, T, AUC] = perfcurve(correctAns, probability, labelFor1);

It seems that lots of functions have to be updated to add this functionality.

Now all the codes used to identify functional ROI reply on FreeSurfer data structure. Maybe it is possible to isolate their dependency, and, therefore, data from other software (e.g., hcp, fmriPrep) can also use these codes. e.g.,

fs_neighborvtx
fs_perivtx
fs_trimlabel
...

Use the following functions to set $SUBJECTS_DIR and $FUNCTIONALS_DIR before running anything:

fs_setup('path/to/FreeSurfer');
fs_subjdir('path/to/SUBJECTS_DIR');
fs_funcdir('path/to/FUNCTIONALS_DIR');