Dear Martin, Yes I think so, and I run the mri_glmfit with fsaverage as the subject like: mri_glmfit --glmdir lh.thickness.rmanova --y lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss --C tp1-vs-tp2.mtx --C tp1-vs-tp3.mtx --C tp2-vs-tp3.mtx --C tp-effect.mtx --C mean.mtx --surf fsaverage lh
it reports: FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Freesurfer/k/lh.thickness.sm05.mgh logyflag 0 usedti 0 FSGD rmanova.fsgd labelmask /Freesurfer//fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness.rmanova Loading y from /Freesurfer/k/lh.thickness.sm05.mgh INFO: gd2mtx_method is doss Saving design matrix to lh.thickness.rmanova/Xg.dat Normalized matrix condition is 1.73205 Matrix condition is 1.73205 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149955 voxels in mask Saving mask to lh.thickness.rmanova/mask.mgh Reshaping mriglm->mask... search space = 74612.965197 DOF = 0 ERROR: DOF = 0 It seems still something wrong was ignored. Also if I call the preproc or surf2surf commands with the base subject, i.e. k, instead of fsaverage, will it work? or even better? mris_preproc --target k --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd mri_surf2surf --s k --hemi lh --fwhm 5 --sval lh.thickness.mgh --tval lh.thickness.sm05.mgh Thanks, Kaiming On Thu, Jan 30, 2014 at 3:18 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>wrote: > Your data was probably mapped to fsaverage when you call the preproc or > surf2surf commands? If so you should specify fsaverage as the subject nane. > Best Martin > > > Sent via my smartphone, please excuse brevity. > > > -------- Original message -------- > From: Kaiming Yin > Date:01/29/2014 9:07 PM (GMT-05:00) > To: FreeSurfer Mailing List > Subject: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit > "--surf subject hemi" > > Dear FreeSurfer guys, > > I am using longitudinal processing stream and with the > RepeatedMeasuresAnova. > I follow the instruction here from > http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova > > my fsgd file is: > > GroupDescriptorFile 1 > Title k_longitudinal > Class k > Variables TP1-vs-TP2 TP1-vs-TP3 > Input k_1 k 1 1 > Input k_2 k -1 0 > Input k_3 k 0 -1 > > > contrasts is: > > tp1-vs-tp2.mtx tp1-vs-tp3.mtx tp2-vs-tp3.mtx tp-effect.mtx mean.mtx > 0 1 0 0 0 1 0 -1 1 0 1 0 > 1 0 0 > 0 0 1 > > I run the mris_preproc and mri_surf2surf commands as the same for left > hemi thickness, > > but when I run the mri_glmfit command it reports "ERROR: you must use > '--surface subject hemi' with surface data". if i add the flag as: > mri_glmfit ...(as the same before)... --surface k lh > or --surface k lh > thickness > or --surface > k_1.long.k lh > or --surface > k_1.long.k lh thickness > or --surface k_1 lh > or --surface k_1 lh > thickness > it still goes wrong and even not make an output folder. > > Any problems there? > > thanks, > Kaiming > > 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 . 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. >
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