Deleting 'qdec/Untitled' worked! Thanks,
Prapti -----Original Message----- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Thursday, 5 March 2009 11:10 AM To: Prapti Gautam Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] qdec error in analyze Prapti, Try deleting the directory 'qdec/Untitled' and run it again. Prior to v4.2.0, qdec did not delete that directory, which is the default working directory, so its possible some incompatible files from a prior run were lingering. Nick On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
