Thanks Doug, I did make some manual edits to wm.mgz and brainmask.mgz then reran the subject a couple times using: recon-all -autorecon2-wm -subjid subj007
Shouldn't -autorecon2-wm run through -autorecon2 and -autorecon3? Will running 'recon-all -make all -s subj007' do away with my manual edits?
-Ronny
Hi Ronny, there is a dimension mismatch which usually means that the surfaces for that subject are out of synch, ie, it has not been run through to the end. This often happens when a subject is run all the way through, then edited and re-run but the re-run only runs autorecon1 and autorecon2 but not autorecon3. Try running recon-all -make all -s subj007. You can also just check if the subject is out of synch with vno_match_check subj007
doug
On 06/07/2013 11:03 AM, preciado@nmr.mgh.harvard.edu wrote:
I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is:
preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated.
-Ronny
1/1 subj007 1/1 subj007 008 lh --------- Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 -> fsaverage) ERROR: mapping surfaces
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