Good. I forgot to mention, the 'Design Name' entry box on the Design tab is intended for keep track of a particular analysis. For instance lets say your looking at thickness on the left hemi where you have selected diagnosis and age as factors. You might want to name the Design 'diagnosis_age_thickness_lh'. It will put the results in the $SUBJECTS_DIR/qdec/diagnosis_age_thickness_lh dir, which is handy as a way to save the results.
Nick On Thu, 2009-03-05 at 11:30 +1100, Prapti Gautam wrote: > 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
