Hello,
I have been attempting to run a between group DTI contrast using glmfit, and it could not determine how to produce the data that is given to mri_glmfit as its input. My approach below may be wrong, so if you can recommend a better way of doing it please advise. Assuming this method is a valid approach, here is my technical problem: the resampling step shown below seems to work, but glmfit reports that there is an incorrect number of rows, so I guess something goes wrong.
The first thing I do is resample from volume to surface onto average7 for each of the subjects:
cat Subject_Lists/bw-group-error-dti-5 | while read sub ; do mri_vol2surf \ --src "$sub"/dti/unwarp/maps/sreg/fa.bhdr \ --srcreg "$sub"/bold/register.dat \ --trgsubject average7 \ --out DTI_HCvASD_mriglfmit/surface/"$sub"_fa.mgh \ --hemi lh done
And then I create a final output to give to mri_glmfit:
mri_concat DTI_HCvASD_mriglfmit/surface/mano*_fa.mgh --o DTI_HCvASD_mriglfmit/all_fa.mgh
The process I'm attempting above is similar to what mris_preproc uses surf2surf to do, but I think I need to use vol2surf instead of surf2surf. As far as I can tell mris_preproc would not work, because in what I am doing I need to go from the volume to the surface. This vol2surf method "works" in that it doesn't have any errors when running (though some warnings about registration file being different from source file), and it generates the resampled surface that I concatenate at the end. So far so good but when I run mri_glmfit, I get an error message (see below).
mri_glmfit \ --really-use-average7 \ --y DTI_HCvASD_mriglfmit/all_fa.mgh \ --fsgd fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd \ --glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir \ --C fsgd_and_contrast_files/BwGroupErrorDTI5.mat sysname Linux hostname vantz machine x86_64 user levy FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh logyflag 0 usedti 0 FSGD fsgd_and_contrast_files/BwGroupErrorDTI5.fsgd glmdir DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir DoFFx 0 Creating output directory DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir Loading y from /autofs/space/ventzl_015/users/DTI_HCvASD_mriglfmit/all_fa.mgh Matrix condition is 1 Pruning voxels by frame. Found 155495 voxels in mask Saving mask to DTI_HCvASD_mriglfmit/HCvASD.fsfast.glmdir/mask.mgh search space = 155495 *ERROR: dimension mismatch between y and X. y has 23 inputs, X has 24 rows. * My .fsgd file matches the exact set of subjects that went into the aggregate .mgh file, so that isn't the reason.
What do you think might be the cause of this error?
Thanks, Rob
Also, here is some information on the environment I ran these commands in: -------- freesurfer-Linux-centos4_x86_64-dev-20070819 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/local/freesurfer/dev/fsl [vantz:SUBJECTS_DIR] (nmr-dev-env) pwd /space/ventzl/1/users/SUBJECTS_DIR