Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
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, preci...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
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, preci...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
On 06/07/2013 02:24 PM, preci...@nmr.mgh.harvard.edu wrote: 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? No, you have to add -autorecon3 to run autorecon3 Will running 'recon-all -make all -s subj007' do away with my manual edits? No, FS never deletes manual edits unless you explicitly tell it to. Running -make all tells it to update things that need to be based on modification dates on the file. doug -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, preci...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is
Re: [Freesurfer] FS-FAST - ERROR: mapping surfaces
Hi Ronny you should have run recon-all -autorecon2-wm -subjid subj007 -autorecon3 at this point you should be fine running -make all. It should retain all your manual edits cheers Bruce On Fri, 7 Jun 2013, preci...@nmr.mgh.harvard.edu wrote: 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, preci...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
