Hi, I'm trying to resample a volume (representing a subregion of the subjects T1) onto the surface using mri_vol2surf. When I try to load the output as an overlay in tksurfer, nothing appears. The output is below. Any help would be appreciated (note, I;ve also tried to output in analyze format with no success) Thanks, Alex
mri_vol2surf --src 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 1000027 --hemi lh --surf white --surfreg 1000027/surf/lh.white --out test/test --out_type cor srcvol = 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 1000027 surfreg = 1000027/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg ----------------------------------------------------------------- INFO: could not find 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 63 INFO: chaning type to float Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /data/flanders/work/alex/freesurfer/subjects/1000027/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 148018/148018 Done mapping volume to surface Number of source voxels hit = 92960 Reshaping 2 (nvertices = 148018) Writing non-standard value for imnr1 (2, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (74009, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
Definitely do not use cor as the output. Use "paint" format (also known as .w). See the examples.
doug
On Thu, 11 Aug 2005, Fornito, Alexander wrote:
Hi, I'm trying to resample a volume (representing a subregion of the subjects T1) onto the surface using mri_vol2surf. When I try to load the output as an overlay in tksurfer, nothing appears. The output is below. Any help would be appreciated (note, I;ve also tried to output in analyze format with no success) Thanks, Alex
mri_vol2surf --src 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 1000027 --hemi lh --surf white --surfreg 1000027/surf/lh.white --out test/test --out_type cor srcvol = 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 1000027 surfreg = 1000027/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg
INFO: could not find 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in 1000027/mri/orig/001/reg_objects/1000027_lh_cog_limbic_surfreg.mat file
INFO: analyzeRead(): min = 0, max = 63 INFO: chaning type to float Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /data/flanders/work/alex/freesurfer/subjects/1000027/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 148018/148018 Done mapping volume to surface Number of source voxels hit = 92960 Reshaping 2 (nvertices = 148018) Writing non-standard value for imnr1 (2, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (74009, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure
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Doug Greve -
Fornito, Alexander