You have to specify that this is a DOSS analysis with --fsgd CMTX_b.fsgd doss
On 10/31/19 12:38 PM, Georgina Angelopoulou wrote: > > External Email - Use Caution > > Dear Douglas, > > Thank you once again for your reply and your help. > > Attached please find the fsgd file (CMTX_b.fsgd) including age row > scores and the contrast file. The command line I used is the following: > - mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C > Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir > lh.CMTX_b_thickness.glmdir > > The output is the following: > > georgias-mbp:CMTX georgina$ mri_glmfit --y lh.CMTX_b.thickness.10.mgh > --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh > --cortex --glmdir lh.CMTX_b_thickness.glmdir > gdfRead(): reading CMTX_b.fsgd > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > 0 age 45.2083 12.1603 > Class Means of each Continuous Variable > 1 patientmale 38.7778 > 2 patientfemale 53.0000 > 3 controlmale 40.1667 > 4 controlfemale 51.8462 > INFO: gd2mtx_method is dods > Reading source surface > /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/surf/lh.white > Number of vertices 163842 > Number of faces 327680 > Total area 65416.984375 > AvgVtxArea 0.399269 > AvgVtxDist 0.721953 > StdVtxDist 0.195470 > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ > cwd /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX > cmdline mri_glmfit.bin --y lh.CMTX_b.thickness.10.mgh --fsgd > CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex > --glmdir lh.CMTX_b_thickness.glmdir > sysname Darwin > hostname 192.168.1.32 > machine x86_64 > user georgina > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y > /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh > logyflag 0 > usedti 0 > FSGD CMTX_b.fsgd > labelmask > /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/label/lh.cortex.label > maskinv 0 > glmdir lh.CMTX_b_thickness.glmdir > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory lh.CMTX_b_thickness.glmdir > Loading y from > /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh > ... done reading. > INFO: gd2mtx_method is dods > Saving design matrix to lh.CMTX_b_thickness.glmdir/Xg.dat > Computing normalized matrix > Normalized matrix condition is 160.248 > Matrix condition is 182721 > Found 149955 points in label. > Pruning voxels by thr: 1.175494e-38 > Found 148239 voxels in mask > Saving mask to lh.CMTX_b_thickness.glmdir/mask.mgh > Reshaping mriglm->mask... > search space = 73702.448371 > ERROR: dimension mismatch between X and contrast Contrasts/age_sim.mtx > X has 8 cols, C has 5 cols > > > Please note that an equivalent error appears with grey matter volume > and surface area. > Thank you once again, > > Best, > Georgina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
