Unfortunately, when the NIFTI standard was set up, they copied a shortcoming from ANALYZE, namely that each dimension is encoded by a short int, meaning that a dimension cannot have more than 32k elements. This is a problem when you have surfaces with 100k+ nodes. One work-around is to break up the 100k nodes into a number of "columns" and "rows" so that the product equals the number of nodes, but the number of cols and rows does not exceed 32k. This is what probably was done for the left hemi. For the right, you have 131876 nodes, which can only be broken down into 65938x2. I've implemented a NIFTI work-around, but only FreeSurfer knows about it (thus the warning). Unfortunately, FSL does not support this work-around.
doug Gregory Dierksen wrote: > Hi, > > I'm trying to paint functional data onto a cortical "midgray" surface. > The surface was generated using mris_expand to expand the WM surface to > 50% of the pial surface. > > The data I want to paint onto this surface is in a 96 x 96 x 17 x 512 > dimension NIFTI file generated using the feat command (the volume is the > resulting "filtered_func_data.nii.gz"). When using this command: > > mri_vol2surf --mov filtered_func_data.nii.gz \ > --reg register.dat \ > --hemi rh \ > --surf midgray.05 \ > --nvox NonZero_voxels.txt \ > --out Total_TimeSeries_RHsurface.nii.gz > > I get the following error message: > > NIFTI FORMAT WARNING: ncols 65938 in input exceeds 32768. > So I'm going to put the true ncols in glmin and set dim[1]=-1. > This should be ok within FreeSurfer, but you will not be > able to use this volume with other software. > > And an output volume with dimensions 65938 x 1 x 2 x 512 which does not > work with FSL commands. > > This is a problem since the next thing I want to do is to use fslmaths to > collapse the surface in the X, Y, and Z dimensions to obtain a mean for > the surface. > > Also confusing is the fact that the above command works fine for the left > hemisphere. > > What's going on? Am I doing something wrong? > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
