Dear all, I've come across a similar problem to the one described before in qdec, but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run it again I get the following error. I've checked to make sure my subject is named correctly and I am in the correct subject directory. Any help will be great appreciated, gdfReadHeader: reading /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd ERROR: gdfRead: /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd is not formatted properly. The first string is 'q&@', should be 'GroupDescriptorFile' Error in Analyze: command failed: mri_glmfit --y /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m gh --fsgd /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd --glmdir /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled --surf fsaverage lh --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-Intercept.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-dig_back-Cor.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-educ-Cor.mat Thanks, Prapti ---------- Message: 7 Date: Mon, 08 Dec 2008 11:43:28 -0500 From: Nick Schmansky <ni...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec message To: juliaaltenb...@yahoo.de Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu> Message-ID: <1228754609.6864.17.ca...@minerva.nmr.mgh.harvard.edu> Content-Type: text/plain Julia, Does it give any further details in the error message? It would be in the terminal output (the popup box would not have the full message). Do all of those files in the command line exist and are readable? You can also try copy-and-pasting that command directly to the terminal (outside of qdec) to see what error message it displays. Nick On Mon, 2008-12-08 at 10:57 +0000, Julia Altenburg wrote: > Hey all, > > I'm getting the following message while using qdec > > Error in Analyze: command failed: mri_glmfit --y /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh --fsgd /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec. fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-thickness-alter-Cor.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat > > I've a qdec.table and a fsgd.file included in my subject folder. > Do I have to type a command to get the fsgd. file connected? > I'm not really sure what causes the error. While using an older freesurfer version on a different mac this (but some other) error doesn't show up. > > > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0 > > Kernel info: Darwin 8.11.1 i386 > > > Thank you in advance > Cheers Julia > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ------------------------------ Message: 8 Date: Mon, 08 Dec 2008 12:51:32 -0500 From: Doug Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Statistic analysing for a mask To: Alexandru Hanganu <hanganu.alexan...@yahoo.de> Cc: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu> Message-ID: <493d5ea4.5050...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines. doug Alexandru Hanganu wrote: > Dear Freesurfer users, > > We have an MNI mask and we want to apply this mask on a group of > subjects for small volume correction. > so we did the following steps: > > 1. cd $SUBJECTS_DIR/fsaverage/surf > fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg > TT_avg152T1_to_fsaverage.dat > > 2. cd $SUBJECTS_DIR/fsaverage/surf > mri_vol2surf --mov /path/to/ROI5.nii --reg > TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest > --hemi lh --out lh.fsaverage.ROI5.mgh > > 3. cd $SUBJECTS_DIR/subjid/surf > mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval > lh.thickness --tval lh.thickness.fsaverage.mgh > . > . > . > Surf2Surf: Dividing by number of hits (163842) > INFO: nSrcLost = 0 > nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 > nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits = > 2.31875 > Saving target data > > > > 4. Next step was just for verifying, but we received an error (maybe > it's not so important): > cd $SUBJECTS_DIR/subjid/surf > mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh > --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt > > Loading > /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh > Loading lh.thickness.fsaverage.mgh > ERROR: dimension mismatch between input volume and seg > > We want to determine the statistics only for this mask for the whole > group of subjects (qdec, or mri_glmfit). > If the mapping of our subjects thickness data was good, what should we > do next in order to achieve our goal ? > > Thank you. > > Best regards, > Dr. Alexandru Hanganu > ___________________________________ > Department of Neurology, > Schleswig-Holstein University Hospital, Kiel Campus > Arnold-Heller-Str. 3, building no. 41 > D-24105 Kiel, Germany. > >----------------------------------------------------------------------- - > >_______________________________________________ >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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2008120 8/381b1a32/attachment.html ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 58, Issue 16 ****************************************** _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
