I have now gotten this to run on 3 subjects. However I have 786 subjects and need to find the bad apple. Is there a way I can do quality checks on each subject’s difference map in fsaverage space that mris_preproc has made? Basically I want to cycle through the concatenated file in a systematic way that hopefully doesn’t involve me opening them one at a time in freeview. How could I do this?

Sara Sims

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sara Sims <snolin@uab.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 3, 2018 at 10:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mris_preproc paired diff outputs 0 values

External Email - Use Caution

Hello,

I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does indeed have values.

Here is a sample of my subject list:

100206.central

100206.far

100307.central

100307.far

100408.central

100408.far

…etc.

Here is my mris_preproc script:

mris_preproc --target fsaverage --hemi lh --isp $in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh --isp $in/FP/100307.central/lhsurf.mgh --isp $in/FP/100307.far/lhsurf.mgh --isp $in/FP/100408.central/lhsurf.mgh --isp $in/FP/100408.far/lhsurf.mgh … --out $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff

The output log shows no errors, the number of inputs equals the number in the subject list and it creates a file but it’s all zeros. I just have no idea as to why this would happen?

Thanks,

Sara Sims