If you just want to look at the difference maps, you can load the mris_preproc output stack as an overlay, then scroll through each one of them. You're still looking at each one of them, but you don't have to open them up one-by-one.
On 12/05/2018 02:21 PM, Sims, Sara A wrote:
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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
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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
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