External Email - Use Caution Thanks a lot. Now I understand what was wrong and resolve it.
Shuntaro 2020年2月29日(土) 6:20 Douglas N. Greve <[email protected]>: > > mri_vol2surf does not actually produce a surface, it produces a surface > overlay (ie, a value for each vertex). You can to run recon-all to > produce a surface > > On 2/27/2020 4:49 AM, Shuntaro Aoki wrote: > > External Email - Use Caution > > > > Dear mailing list, > > > > I was trying to convert a volume image to a freesurfer surface (as > > gii) with `mri_vol2surf` for visualization, but ended up with invalid > > surface data (i.e., a file not loadable by freeview). > > > > What I did was: > > > > --- > > % mri_vol2surf --version > > stable5 > > % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub > > --hemi lh --out ./sample_vol2surf_lh.gii > > --- > > > > Here, `sample_volume.nii.gz` is a volume image (such as a statistical > > map) registered to an individual reference T1w image of subject > > `sample-sub`, which was the input of recon-all for the subject. > > The command completed without errors: > > > > --- > > srcvol = ./sample_volume.nii.gz > > srcreg unspecified > > srcregold = 0 > > srcwarp unspecified > > surf = white > > hemi = lh > > reshape = 0 > > interp = nearest > > float2int = round > > GetProjMax = 0 > > INFO: float2int code = 0 > > Done loading volume > > Computing registration from header. > > Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz > > as target reference. > > Reading surface > > /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white > > Done reading source surface > > Mapping Source Volume onto Source Subject Surface > > 1 0 0 0 > > using old > > Done mapping volume to surface > > Number of source voxels hit = 31055 > > Writing to ./sample_vol2surf_lh.gii > > Dim: 155685 1 1 > > --- > > > > Then I tried to open the resulting surface `sample_vol2surf_lh.gii` > > with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed > > to load Surface". > > I also got the following shell output: > > > > --- > > mriseadGIFTIfile: mris is NULL! found when parsing file > > /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii > > MRISread failed > > mriseadGIFTIfile: mris is NULL! found when parsing file > > /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii > > --- > > > > The output of `mris_info` is: > > > > --- > > % mris_info sample_vol2surf_lh.gii > > ================================================== > > gifti_image struct > > version = 1.0 > > numDA = 1 > > gim->meta nvpairs struct, len = 3 : > > nvpair: 'UserName' = 'aoki' > > nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020' > > nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, > > 2010' > > > > gim->labeltable giiLabelTable struct, len = 0 : > > -------------------------------------------------- > > gim->darray[0] giiDataArray struct > > intent 0 = NIFTI_INTENT_NONE > > datatype 16 = NIFTI_TYPE_FLOAT32 > > ind_ord 1 = RowMajorOrder > > num_dim = 1 > > dims = 155685, 0, 0, 0, 0, 0 > > encoding 3 = GZipBase64Binary > > endian 2 = LittleEndian > > ext_fname = > > ext_offset = 0 > > darray->meta nvpairs struct, len = 0 : > > data = <set> > > nvals = 155685 > > nbyper = 4 > > numCS = 0 > > darray->ex_atrs nvpairs struct, len = 0 : > > -------------------------------------------------- > > gifti_image struct > > swapped = 0 > > compressed = 1 > > -- darray totals: 1 MB > > gim->ex_atrs nvpairs struct, len = 0 : > > ================================================== > > --- > > > > I checked matching between voxels in the input volume and the surface > > with the output of --srchit option and found the registration was > > fine. > > > > I also tried mgh output but got another invalid file. > > > > --- > > % mris_info sample_vol2surf_lh.mgh > > ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices! > > Probably trying to use a scalar data file as a surface! > > > > No such file or directory > > --- > > > > I would appreciate any advice on this. > > > > Regards, > > > > > > Shuntaro > > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ---------------------------------------- Shuntaro C. Aoki, Ph.D. Program-specific Researcher Neuroinformatics group Graduate School of Informatics Kyoto University [email protected] ---------------------------------------- _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
