[Freesurfer] Running selxavg with many (~5000) different conditions

External Email - Use Caution Hi, I'm currently running an analysis that requires defining each of 5000 stimuli as a condition during processing, and for each subject, I have about 140 runs. As a result, selxavg is taking a very long time and huge amounts of memory to run.

[Freesurfer] Register individual functional volume to MNI152

External Email - Use Caution Hi all, I’m having some trouble getting an an accurate registration between an individual functional volume and MNI152 space. Presently, I’m using the commands: bbregister --s MNI152_FS --mov volumeInFunctional --reg mniDir/filename2mni.lta

[Freesurfer] Custom color map in Freeview

Hi all, I’m wondering whether there’s a way to create a custom color map in Freeview that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, Jet and GE Color options. Ideally, I could assign each number value a given color, e.g. every “0” value in an .nii file is

[Freesurfer] Reset view command in freeview

Hi all, I’m wondering whether there's a command-line equivalent to the the Reset View tool found in the Freeview GUI when you right-click a volume in 3d view. I tried using the -viewport tag (e.g. freeview -v myvolume.nii.gz -viewport coronal), but the problems with this are: (1) Though the

[Freesurfer] TRACULA error "R: Subscript out of range"

Hi all, I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is exiting with the output below. Most notably, I think, is the section of the output that says "R: Subscript out of range.” repeatedly and then the section afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8

[Freesurfer] Tracula / 0 slices processed in Bedpostx before queuing post processing stage

Hi, I’m having difficulty making BedpostX work on non-tutorial data per the tutorial located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula The preprocessing has worked without errors, but now