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 mreuter@nmr.mgh.harvard.eduwrote:
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
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