RE: [Freesurfer] mri_vol2surf help
if the borders are jagged you could dialate then erode the label on the surface in tksurfer. Tools-Labels-Dialate Selected Label Tools-Labels-Erode Selected Label this will also close any holes in the label. -- brian On Thu, 11 Aug 2005, Fornito, Alexander wrote: That worked thanks. Wandering if I could get your advice on the best way to proceed. I'm resampling manually traced ROIs onto the surface and using custom fill to convert them to labels to obtain regional thickness. As I see it, I can do this in 2 ways: 1 - convert the ROI (which is saved as a greyscale mask in analyze format) to cor format (which puts the ROI in the same space as the orig, and therefor the surface), and load it as an overlay in tksurfer 2 - use mri_vol2surf to resample the mask to the surface Both approaches produce a pretty good result (ie., the ROI is where it should be), but there appears to be slight differences in the exact locations of the marked vertices around the ROI borders. I was wandering if there's any reason why I should prefer on approach over the other? Also, the borders of the labels are somewhat jagged when overlaid on the surface, which I presume is because the overlays are at voxel resolution, whereas the surface is smoothed at subvoxel resolution. Is there any way to correct the overlays for this discrepancy? Would it be a sin not to? Thanks for your help, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 1:42 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] mri_vol2surf help 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 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 127 --hemi lh --surf white --surfreg 127/surf/lh.white --out test/test --out_type cor srcvol = 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 127 surfreg = 127/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg - INFO: could not find 127/mri/orig/001/reg_objects/127_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 127/mri/orig/001/reg_objects/127_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/127/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 ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ 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] mri_vol2surf help
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 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 127 --hemi lh --surf white --surfreg 127/surf/lh.white --out test/test --out_type cor srcvol = 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 127 surfreg = 127/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg - INFO: could not find 127/mri/orig/001/reg_objects/127_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 127/mri/orig/001/reg_objects/127_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/127/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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2surf help
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 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 127 --hemi lh --surf white --surfreg 127/surf/lh.white --out test/test --out_type cor srcvol = 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 127 surfreg = 127/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg - INFO: could not find 127/mri/orig/001/reg_objects/127_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 127/mri/orig/001/reg_objects/127_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/127/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 ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_vol2surf help
That worked thanks. Wandering if I could get your advice on the best way to proceed. I'm resampling manually traced ROIs onto the surface and using custom fill to convert them to labels to obtain regional thickness. As I see it, I can do this in 2 ways: 1 - convert the ROI (which is saved as a greyscale mask in analyze format) to cor format (which puts the ROI in the same space as the orig, and therefor the surface), and load it as an overlay in tksurfer 2 - use mri_vol2surf to resample the mask to the surface Both approaches produce a pretty good result (ie., the ROI is where it should be), but there appears to be slight differences in the exact locations of the marked vertices around the ROI borders. I was wandering if there's any reason why I should prefer on approach over the other? Also, the borders of the labels are somewhat jagged when overlaid on the surface, which I presume is because the overlays are at voxel resolution, whereas the surface is smoothed at subvoxel resolution. Is there any way to correct the overlays for this discrepancy? Would it be a sin not to? Thanks for your help, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 1:42 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] mri_vol2surf help 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 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 127 --hemi lh --surf white --surfreg 127/surf/lh.white --out test/test --out_type cor srcvol = 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 127 surfreg = 127/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg - INFO: could not find 127/mri/orig/001/reg_objects/127_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 127/mri/orig/001/reg_objects/127_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/127/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 ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
