Freesurfer November 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
73 discussions

Re: [Freesurfer] labels
by Sasha Wolosin 14 Nov '05

14 Nov '05

I looked through the recon-all.log file, but I could not find any references to mris_ca_label or mris_anatomical_stats, do you know what else I can search for? I found this warning in several places, but I don't know if it is related: INFO: Volume /tmp/mritotal_12360/orig_8_dxyz.mnc cannot be found. In the recon-all.status file there is another warning: Euler: NHoles = WARNING: Number of holes is not zero This subject was previously manually edited with an older version (oct 2003 release). I made four copies of the subject and ran each of the following in both the 2003 release and the latest stable release: recon-all -subjid subject -stage3 -stage4a -stage4b recon-all -subjid subject -all I only saw the warnings in subjects run with the stable release, (in the 2003 release NHoles =0). Could I be missing some files? Thanks, Sasha >>> Xiao Han <xhan(a)nmr.mgh.harvard.edu> >>> If you run "recon-all -all ...", then mris_ca_label and mris_anatomical_stats should be included as the final two steps. You can check the recon-all.log file under each subject's script directory to see why mris_ca_label wasn't executed in your previous run of recon-all. -Xiao On Mon, 14 Nov 2005, Sasha Wolosin wrote: > That might have been what happened. I loaded the annotation to the > other surfaces, but they also looked strange. Then I re-ran > mris_ca_label and the labels look normal. > > So are mris_ca_label and mris_anatomical_stats not part of the recon-all > script (I am using the stable release)? > > Thanks, > Sasha > > > >>>> Xiao Han <xhan(a)nmr.mgh.harvard.edu> >>> > hmm, that's wierd. > Did you recomputed the white surface after the annotation file was > generated? > You can try to load the annotation to other surfaces of the same > hemisphere, like ?h.sphere, ?h.sphere.reg, to see whether the same > scattered appearance still exists. > > -Xiao > > > On Mon, 14 Nov 2005, Sasha Wolosin wrote: > >> I double-checked, the correct hemisphere is loaded >> >>>>> Xiao Han <xhan(a)nmr.mgh.harvard.edu> >>> >> It's not normal. >> It's very likely that you load a rh annotation to a lh surface or the >> other way around. Pls double check. >> >> -Xiao >> >> On Mon, 14 Nov 2005, Sasha Wolosin wrote: >> >>> Dear all, >>> >>> When I load the ?h.aparc.annot with the ?h.white surface in > tksurfer, >>> the labels look very scattered, is this normal? (please see attached >>> jpeg) >>> >>> 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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labels
by Sasha Wolosin 14 Nov '05

14 Nov '05

Dear all, When I load the ?h.aparc.annot with the ?h.white surface in tksurfer, the labels look very scattered, is this normal? (please see attached jpeg) 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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long time to finish a case by recon-all
by tulu 12 Nov '05

12 Nov '05

Dear Freesurfer experts, First of all, I thanks for your wonderful tool. I run the recon-all -autorecon-all script and it can finish my mri data without error. The only problem is it need 3 days (about 72 hours) to finished one mri data. I wonder if anyone have same experience and how to correct it (I use P4 2.8G CPU with 2G RAM, OS is Linux Fedora Core 4). Thanks replay KL chen

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mri_surf2surf
by Irina Sigalovsky 12 Nov '05

12 Nov '05

Hello, I have a *.w file which I map onto a different subject (say, average7) using mri_surf2surf. Let's say that my original file has N vetrices equal to 100 and all other equal to 0. Is there a reason why a "new" *.w file (output of mri_surf2surf) has: - N1 vertices equal to 100 where N1 is not equal to N (not even close); - some vertices that have values that are neither 100 nor 0 (i.e., some new values are introduced). This is how I use mri_surf2surf: mri_surf2surf --hemi lh --srcsubject iss09newnew --srcsurfval iss09newnew/surf/R1map0.8LP2Thresh15-lh.w --src_type w --trgsubject average7 --trgsurfval average7/surf/iss09_R1mapThresh15-lh.w --mapmethod nnfr --trg_type w My second (unrealted) question is where I can find information about MNI Talairach coordinates for a given surface (i.e., what file contains this information). Thank you, Irina

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RE: [Freesurfer] problems with spheres
by Thomas, Adam (NIH/NIMH) 11 Nov '05

11 Nov '05

Florent, I'm using MapIcosahedron from the SUMA package to do the spherical averaging and the distortions are visually quite striking in an area that is fairly important in this study. Here's a screen shot of the smoothwm surface after recreating it with an icosahedron mesh: http://fmrif.nimh.nih.gov/~adamt/ridges.jpg Note the ridges along the gyrus. There is also a spike coming out of the sulcus nearby that is a little hard to see. Ziad (the developer for SUMA) also thought some sort of regional smoothing might be the best solution. If that's the consensus, we'll pursue that option. -Adam --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370 -----Original Message----- From: florent segonne [mailto:fsegonne@csail.mit.edu] Sent: Thursday, November 10, 2005 4:51 PM To: Thomas, Adam (NIH/NIMH) Cc: freesurfer(a)nmr.mgh.harvard.edu; fischl(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problems with spheres Dear Thomas, Looking at the file rh.sphere.asc, it seems that the problem comes from the spherical registration that generates a spherical surface with, as you said, small triangles slightly overlapping. However, these distortions should be extremely small. If you really need to get rid of them, one hacky solution would be to detect these (small) regions and to smooth them untill the overlapping edges(faces) disappear. Since these regions are small, this should not generate large metric distortions. But maybe Bruce has some other ideas. Florent ------------------------------------- Florent Segonne PhD Candidate Stata Center 32-D430 CSAIL MIT 1 617 253 2986 http://people.csail.mit.edu/~fsegonne ------------------------------------- On Thu, 10 Nov 2005, Thomas, Adam (NIH/NIMH) wrote: > > I recently noticed that some of my subject's spherical surfaces appears > to have several small, pyramid-like points on them. One example is shown > here in tksurfer: > > http://fmrif.nimh.nih.gov/~adamt/sphere.jpg > > Looking at these points in more detail in suma shows that several > triangles are folder on top of each other so that all the vertices are > on the spheres surface, but some triangles are entirely overlapped by > others. > > The spherical surface is here: > > http://fmrif.nimh.nih.gov/~adamt/rh.sphere.asc (11MB) > > And this is a close up of near node 141619 in suma: > > http://fmrif.nimh.nih.gov/~adamt/sphere_suma_zoom.jpg > > > These distortions are causing us problems with subject averaging. Is > there something we can do to fix or avoid them? > > Thanks, > -Adam > > --- > Adam Thomas adamt(a)nih.gov > Functional MRI Facility, NIMH/NIH/DHHS > 10 Center Dr, Room B1D708A > Bethesda MD. 20892-1148 > Phone:301-402-6351 Fax: 301-402-1370 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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freesurfer on debian
by Darren Weber 10 Nov '05

10 Nov '05

If freesurfer is adopting some kind of open-source license (hoorrah!), can we do away with the requirement for a license file? Are there any components/dependencies of freesurfer that are not open-source? Does anyone have detailed instructions for a) compiling freesurfer? b) installation of freesurfer on debian? Is anyone working on creating a debian package for freesurfer? For that matter, has anyone created any rpm packages for freesurfer? Debian already has a package for minc tools, see http://packages.debian.org/stable/science/minc-tools but this does not include all the MNI tools (eg, n3 and mritotal). Comments, suggestions all welcome. Thanks, Darren

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problems with spheres
by Thomas, Adam (NIH/NIMH) 10 Nov '05

10 Nov '05

I recently noticed that some of my subject's spherical surfaces appears to have several small, pyramid-like points on them. One example is shown here in tksurfer: http://fmrif.nimh.nih.gov/~adamt/sphere.jpg Looking at these points in more detail in suma shows that several triangles are folder on top of each other so that all the vertices are on the spheres surface, but some triangles are entirely overlapped by others. The spherical surface is here: http://fmrif.nimh.nih.gov/~adamt/rh.sphere.asc (11MB) And this is a close up of near node 141619 in suma: http://fmrif.nimh.nih.gov/~adamt/sphere_suma_zoom.jpg These distortions are causing us problems with subject averaging. Is there something we can do to fix or avoid them? Thanks, -Adam --- Adam Thomas adamt(a)nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370

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how do you include parietal lobe in the cut?
by Joongnam Yang 10 Nov '05

10 Nov '05

Hi, I know how to cut the occipital lobe and flatten it. You cut calcarine and pick three points and another point to select the plane and do "cut plane". Would someone let me know how to extend the cut so that the cut can include part of the parietal lobe? The menu bar has "whole brain cut" and "occipital cut" only. Thanks. Nam.

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Re: [Freesurfer] mris_fix_topology
by Sasha Wolosin 10 Nov '05

10 Nov '05

Hi Bruce, yep, the cerebellum was attatched, so I guess that must have been the problem. 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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directories needed for recon-all
by Goldman, Aaron (NIH/NIMH) 10 Nov '05

10 Nov '05

Hi, I just upgraded my freesurfer distribution (recon-all now says it's version 1.114), and am preparing to try out the creation process. Before I do that, I was wondering what I need to make sure my subjects directory contains for everything to work properly (for example, I remember the old version skipped a step if you didn't have the average7 directory in there). Also, do I need to make sure my average7, etc aren't obsolete versions? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

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Freesurfer November 2005