It is trying to sample onto fsaverage, but the overlay is already on fsaverage. If you want to use mris_preproc in this way, then the mgx volume needs to be sampled onto the native surface. Since they are already on fsaverage, you can simple run
mri_concat C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz On 04/07/2017 12:14 PM, miracle ozzoude wrote: > 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 <http://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 <http://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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
