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

> <greve@nmr.mgh.harvard.edu <mailto:greve@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
>     >
>     >
>     >
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358 <tel:617-724-2358>
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>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
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