Can you check the modification time of ~/audio/all/audio.lh/tones/ces.nii.gz ? Try deleting it and rerunning isxconcat-sess. The only other thing that I can think of is that some of the individual ces files have multiple frames. You can check that with mri_info --nframes */bold/audio.lh/tones/ces.nii.gz If the problem persists, send the terminal output of isxconcat-sess
On 4/5/19 8:05 AM, Keri Woods wrote: > > External Email - Use Caution > > Hi Freesurfer experts > > I'm having a problem running an FSFAST group analysis. When I try to > run the second level GLM, I get the following error: > > keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y > ~/audio/all/audio.lh/tones/ces.nii.gz --wls > ~/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C > groupdiff.mtx --surface fsaverage lh --glmdir > all_tones_left_glm.wls --nii.gz > gdfRead(): reading 2groups.fsgd > INFO: gd2mtx_method is dods > Reading source surface > /home/keri/recon_all/subjects/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 /home/keri/audio_108_no_stc_tau1,5 > cmdline mri_glmfit.bin --y > /home/keri/audio/all/audio.lh/tones/ces.nii.gz --wls > /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd > --C groupdiff.mtx --surface fsaverage lh --glmdir > all_tones_left_glm.wls --nii.gz > sysname Linux > hostname buddha > machine x86_64 > user keri > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y /home/keri/audio/all/audio.lh/tones/ces.nii.gz > logyflag 0 > usedti 0 > FSGD 2groups.fsgd > labelmask /home/keri/recon_all/subjects/fsaverage/label/lh.cortex.label > maskinv 0 > glmdir all_tones_left_glm.wls > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > wFile /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz > weightinv 1 > weightsqrt 1 > Creating output directory all_tones_left_glm.wls > Loading y from /home/keri/audio/all/audio.lh/tones/ces.nii.gz > ... done reading. > INFO: gd2mtx_method is dods > Saving design matrix to all_tones_left_glm.wls/Xg.dat > Computing normalized matrix > Normalized matrix condition is 1 > Matrix condition is 1.34783 > Found 149955 points in label. > Pruning voxels by thr: 1.175494e-38 > Found 66097 voxels in mask > Saving mask to all_tones_left_glm.wls/mask.nii.gz > Reshaping mriglm->mask... > search space = 31233.070725 > ERROR: dimension mismatch between y and X. > y has 116 inputs, X has 108 rows. > > > 108 is the number of subjects that I have. I can see that the y file > with 116 inputs is /home/keri/audio/all/audio.lh/tones/ces.nii.gz , > and checking the dimension of it, it confirms that it is a 4D matrix > with the 4th dimension of 116. It seems as if this file is created > during isxoconcat-sess, and I have checked and the session ID file > being used here has only 108 entries. It appears that 108 subjects are > being used in this step, as part of the output is: > > ninputs = 108 > Checking inputs > nframestot = 108 > Allocing output > Done allocing > nframes = 108 > > > I think that a source of the error could be the fact that at one time > I did have 116 subjects. I've created a new folder, copying in the > unpacked files for each subject, and repeating from the preprocessing > step, but this doesn't make any difference. Is there are chance that > there's a file outside the functional directory that has stored this 116? > > Any help is greatly appreciated. > > Best wishes, > Keri > > > > _______________________________________________ > 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
