mri_concat does not take the fsgd file
On 04/07/2017 12:25 PM, miracle ozzoude wrote: > Thanks doug. Can I include fsgd file in mri_concat or use it during > the mri_glmfit stage? > Best, > Paul > > On Fri, Apr 7, 2017 at 12:18 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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> > <http://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> <http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > > > > _______________________________________________ > 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
