you only have two inputs and yet trying to estimate 4 unknowns. You need more subjects
On 04/07/2017 01:45 PM, miracle ozzoude wrote:
Thanks doug. Also, I encountered another error while performing mri_glmfit. Below are the command line, fsgd, matrice and error output. a) mri_glmfit --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd Pet.fsgd dods --C edu.mtx --surf fsaverage lh --cortex --glmdir lh.pet.glmdir b) GroupDescriptorFile 1 Title Surfaced Based Pet Class Main Variables Age Education MMSE Input C6_01_001_140813 Main 71 12 6 Input C6_01_003_140908 Main 89 18 4 c) 0 1 0 0 = for age d) 0 0 1 0 = for edu e) ERROR " gdfRead(): reading Pet.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 80.5 5.5 1 Education 14.5 2.5 2 MMSE 26 4 Class Means of each Continuous Variable 1 Main 80.5000 14.5000 26.0000 INFO: gd2mtx_method is dods Reading source surface /net/synapse/nt/mozzoude/Analysis/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /net/synapse/nt/mozzoude/Analysis cmdline mri_glmfit.bin --y all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz --fsgd Pet.fsgd dods --C edu.mtx --surf fsaverage lh --cortex --glmdir lh.pet.glmdir sysname Linux hostname neuron2.sri.utoronto.ca http://neuron2.sri.utoronto.ca machine x86_64 user mozzoude FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /net/synapse/nt/mozzoude/Analysis/all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz logyflag 0 usedti 0 FSGD Pet.fsgd labelmask /net/synapse/nt/mozzoude/Analysis/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.pet.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.pet.glmdir Loading y from /net/synapse/nt/mozzoude/Analysis/all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to lh.pet.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 97.3827 Matrix condition is 184.445 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 66312 voxels in mask Saving mask to lh.pet.glmdir/mask.mgh Reshaping mriglm->mask... search space = 33150.306332 DOF = -2 ERROR: DOF = -2
Thanks, Paul
On Fri, Apr 7, 2017 at 12:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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> <mailto: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>> > <http://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>> <http://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> > <mailto: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> > <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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer