Re: [Freesurfer] freesurfer for MEG/EEG source imaging
Hi Zhongming, we always generate models of the hemispheres separately. We do generate BEM surfaces, and can downsample. I'll cc Matti Hamalainen who can instruct you on how this can be done. Bruce On Tue, 9 Aug 2005, Zhongming Liu wrote: I am a new user of Freesurfer. My questions are related to the head modeling and MEG/EEG source modeling. 1. Can freesurfer generate the 3-shell boundary element model (BEM): 3 triangulated interfaces of air-scalp, scalp-skull, skull-brain? 2. Is it possible to generate a closed and folded cortical surface after the segmentation on MR images? Freesurfer seems to output two splitted hemispheres of cortex. I am particularly concerning this, because I will use the cortical surface to constrain the MEG/EEG source location and direction. 3. Is it possible to evenly (or nearly evenly) down-sample the vertices of a fine cortical surface into around 6,000 points, onto which the elementary dipole will be placed? Freesurfer generates the cortical surface with a huge number of triangles, which makes it impossible for MEG-based source imaging. Looking forward to your reply. Best regards, Zhongming Liu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer for MEG/EEG source imaging
Hello Zhongming 1. Freesurfer can do this, though it is not perfect. It is my understanding that the best (at least here at the NMR center) BEM segmentations can be obtained when running special pulse sequences called FLASH5 in the MRI to better visualize the skull boundaries. Matti can probably provide additional details. 2. The BEMs outputted are in the appropriate form for EEG/MEG source modeling. 3. The downsampling is a very serious issue that many people have brought up. If you are looking for a first approximation, you will have no problem at all. The freesurfer surfaces can simply be downsampled. However, the spacing between vertices is not uniform. Therefore, downsampling a non-uniformly spaced surface will result in another similarly non-uniformly spaced surface. If you downsample by a large number, you will become acutely aware of the problem. Conversely, if you downsample by a small number, the surface will still look very much like a surface, so perhaps you won't mind. Another possible solution to this problem, which is still not correct but may be closer, would be to establish a set of points that are uniformly distributed around a sphere, and then pick those points from the cortical surface in spherical coordinates. This solution will suffer from distortions inherent in the spherical morph. I have been in touch with the makers of SUMA, who are considering developing an option to prepare correctly down-sampled surface vertices based on surfaces Euclidean distances, and our own Doug Greve (also CCed) has also be considering options within the freesurfer environment. If you consider this issue important enough to solve, and are able to solve it, I encourage you to share it with others, because I have found that a number of people would like the correct solution available to them (myself included). Daniel On Tue, 9 Aug 2005, Zhongming Liu wrote: I am a new user of Freesurfer. My questions are related to the head modeling and MEG/EEG source modeling. 1.Can freesurfer generate the 3-shell boundary element model (BEM): 3 triangulated interfaces of air-scalp, scalp-skull, skull-brain? 2.Is it possible to generate a closed and folded cortical surface after the segmentation on MR images? Freesurfer seems to output two splitted hemispheres of cortex. I am particularly concerning this, because I will use the cortical surface to constrain the MEG/EEG source location and direction. 3.Is it possible to evenly (or nearly evenly) down-sample the vertices of a fine cortical surface into around 6,000 points, onto which the elementary dipole will be placed? Freesurfer generates the cortical surface with a huge number of triangles, which makes it impossible for MEG-based source imaging. Looking forward to your reply. Best regards, Zhongming Liu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ Mavet v'chaim b'yad halashon Life and death are in the hands of language - Proverbs 18:21 begin:vcard fn:Daniel Goldenholz n:Goldenholz;Daniel org:Mass General Hospital;MGH/MIT/HMS Martinos Center adr;dom:;;149 13th St.;Charlestown;MA;02129 email;internet:[EMAIL PROTECTED] tel;work:617-726-1223 tel;cell:617-935-9421 x-mozilla-html:FALSE url:http://www.nmr.mgh.harvard.edu/~daniel/ version:2.1 end:vcard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Editing labels
I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex Does your data have a voxel resolution different than 1mm squared? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] skull strip
Yes, skull-stripping is pretty robust. You can definitely try that on your data. -Xiao On Wed, 10 Aug 2005, Sasha Wolosin wrote: Is it possible to do skull stripping without motion correction or intensity normalization? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ 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
RE: [Freesurfer] Editing labels
Hi Kevin, It shouldn't. I created the labels by the doing the following: 1 - manully raced an ROI using another program (Analyze) in volume space and saved the ROI as a greyscale mask in analyze format 2 - used mri_convert to convert both the original T1 and ROI to COR format. 3 - Generated the surface of the T1 and loaded the ROI as an overlay in tksurfer 4 - Filled the overlay using custom fill and saved it as a label. I'm not sure how I would check the image dimensions of the label, but I assume step 2 would have put it into 1mm3, which would then convert to 1mm2 when projected onto the surface (?). -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 5:18 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] Editing labels I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex Does your data have a voxel resolution different than 1mm squared? -- Kevin Teich ___ 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
