Hello Freesurfer, I am trying to concat my surface pet file using mris_preproc but I get this error with no output folder or files " mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz nsubjects = 2 INFO: output detected as nifti, turning on reshaping tmpdir is ./tmp.mris_preproc.20623 /net/synapse/nt/mozzoude/Analysis Log file is all.lh.mgx.ctxgm.fsaverage.sm00.mris_preproc.log Fri Apr 7 10:03:48 UTC 2017 setenv SUBJECTS_DIR /net/synapse/nt/mozzoude/Analysis cd /net/synapse/nt/mozzoude/Analysis /opt/freesurfer-6.0.0/freesurfer/bin/mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz
Linux neuron2.sri.utoronto.ca 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.20623 Src lh sphere.reg Trg lh sphere.reg
--------------------------------------------------- #@# 1/2 C6_01_001_140813 Fri Apr 7 10:03:48 UTC 2017 -------------- ----------------------- mri_surf2surf --srcsubject C6_01_001_140813 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh --sval C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --reshape --cortex ERROR: dimension inconsistency in source data Number of surface vertices = 125993 Number of value vertices = 163842 Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
setenv SUBJECTS_DIR /net/synapse/nt/mozzoude/Analysis cd /net/synapse/nt/mozzoude/Analysis mri_surf2surf --srcsubject C6_01_001_140813 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh --sval C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --reshape --cortex
sysname Linux hostname neuron2.sri.utoronto.ca machine x86_64 user mozzoude srcsubject = C6_01_001_140813 srcval = C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz srctype = trgsubject = fsaverage trgval = ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /net/synapse/nt/mozzoude/Analysis/C6_01_001_140813/surf/lh.sphere.reg Loading source data"
Below are the scripts i ran prior to mris_preproc and the mris_preproc command line: 1) mri_vol2surf --mov C6_01_001_140813.gtmpvc.output/mgx.ctxgm.nii.gz --reg C6_01_001_140813.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 --o lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage 2) mri_vol2surf --mov C6_01_003_140908.gtmpvc.output/mgx.ctxgm.nii.gz --reg C6_01_003_140908.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 --o lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage 3) mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz
Thanks. Best, Paul