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. > Linux neuron2.sri.utoronto.ca <http://neuron2.sri.utoronto.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
>
ca >
> hostname neuron2.sri.utoronto.ca <http://neuron2.sri.utoronto.> 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
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
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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