Hi, All,
I am trying to extract the surface normal values using mri_surf2surf: %mri_surf2surf --s subject1 --hemi lh --sval-nxyz white --tval lh.white.surfn.img --trg_type analyze4d
The error mesage is : ...... Loading source data Extracting surface normals INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Reshaping 131441 (nvertices = 131441) ANALYZE FORMAT ERROR: nslices 131441 in volume exceeds 32768
I am using FreeSurfer v303. I tested the above command on the subjects inflated by old version of FreeSurfer, and I could get the surface normals. Anything wrong with the new inflation?
Thank you for your time.
XJ Kang
You can't use analyze for this because the number of vertices is a prime number. No dimension in an analyze file can exceed 32k. Usually, we get around this by dividing up the vertices across mutiple "slices", but this is not possible when the number of vert is prime. NIFTI inherited the same problem. Try using mgh instead.
doug
On Wed, 22 Nov 2006, XJ Kang wrote:
Hi, All,
I am trying to extract the surface normal values using mri_surf2surf: %mri_surf2surf --s subject1 --hemi lh --sval-nxyz white --tval lh.white.surfn.img --trg_type analyze4d
The error mesage is : ...... Loading source data Extracting surface normals INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Reshaping 131441 (nvertices = 131441) ANALYZE FORMAT ERROR: nslices 131441 in volume exceeds 32768
I am using FreeSurfer v303. I tested the above command on the subjects inflated by old version of FreeSurfer, and I could get the surface normals. Anything wrong with the new inflation?
Thank you for your time.
XJ Kang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I got the following message when doing the skull strip:
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 71137
Find the largest 110-component... heap usage = 113392 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 22057 voxels first estimation of the COG coord: x=140 y=179 z=122 r=91 first estimation of the main basin volume: 3160802 voxelsSegmentation fault
recon-all exited with ERRORS at Wed Nov 29 15:46:36 PST 2006
Seems 71137 in "Count how many 110 voxels are present : 71137" is too small compared to other subject's. Any idea about this "Segmentation fault"? Thanks.
XJ
check to see if your talairach is ok On Wed, 29 Nov 2006, XJ Kang wrote:
Hi,
I got the following message when doing the skull strip:
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 71137
Find the largest 110-component... heap usage = 113392 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 22057 voxels first estimation of the COG coord: x=140 y=179 z=122 r=91 first estimation of the main basin volume: 3160802 voxelsSegmentationfault
recon-all exited with ERRORS at Wed Nov 29 15:46:36 PST 2006
Seems 71137 in "Count how many 110 voxels are present : 71137" is too small compared to other subject's. Any idea about this "Segmentation fault"? Thanks.
XJ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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XJ Kang