Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

recon-all
by antao＠itsa.ucsf.edu 15 Aug '05

15 Aug '05

Hi, After processing the data in recon-all stage2, I don't want to repeat stage2 in recon-all stage3. Is there any way to do that? Thx, Antao

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mgz conversion
by David Soscia 15 Aug '05

15 Aug '05

Hey Guys, I have been converting dicom files to COR for the past month and all has been working fine. Now I am trying to convert dicom files to mgz format and I am getting an error every time. I type in the same thing I did for the COR conversion, except I replace "-ot cor" with "-ot mgz." The error is get is "mri_convert: unknown output volume type mgz" (or seomthing along those lines). I think my computer isn't recognizing the mgz format because I've never used it for anything before. Anyone know how I can fix this so it works properly? thanks, Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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mri_convert dicom
by Sasha Wolosin 15 Aug '05

15 Aug '05

I'm having some trouble running mri_convert. I keep getting an error message, do you know what this means (see below)? Thanks. [root@localhost FreeSurferPractice]$ mri_convert -it dicom -ot cor CRSG_2332/001 2332_skullstrip/mri/orig/001 mri_convert -it dicom -ot cor CRSG_2332/001 2332_skullstrip/mri/orig/001 reading from CRSG_2332/001... 124 DICOM 3.0 files in list Found 124 DICOM Files reading DICOM image... FreeElementData: 137302584 unrecognizedSegmentation fault Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 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.

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mri_convert
by Sasha Wolosin 12 Aug '05

12 Aug '05

Does mri_convert cause any loss in resolution when converting from DICOM to COR format? What about from DICOM to MGZ? Thanks, Sasha 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.

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RE: [Freesurfer] Editing labels
by Fornito, Alexander 11 Aug '05

11 Aug '05

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:kteich@nmr.mgh.harvard.edu] Sent: Thu 8/11/2005 5:18 AM To: Fornito, Alexander Cc: freesurfer(a)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

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RE: [Freesurfer] mri_vol2surf help
by Fornito, Alexander 11 Aug '05

11 Aug '05

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:greve@nmr.mgh.harvard.edu] Sent: Thu 8/11/2005 1:42 PM To: Fornito, Alexander Cc: freesurfer(a)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 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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mri_vol2surf help
by Fornito, Alexander 10 Aug '05

10 Aug '05

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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skull strip
by Sasha Wolosin 10 Aug '05

10 Aug '05

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.

3 2

Editing labels
by Fornito, Alexander 10 Aug '05

10 Aug '05

Hi, 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

2 1

freesurfer for MEG/EEG source imaging
by Zhongming Liu 10 Aug '05

10 Aug '05

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

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