[Freesurfer] cortical parcellation in anterior cingulate region
Hello everybody, Regarding the troubles raised in the mailing list and on the release notes about the anterior cingulate being misclassified with curvature.buckner40.filled.desikan_killiany, I would like to know if you have any updated version of the atlas available? In my subjects, most of the anterior cingulate cortex is found in the frontal superior parcell. Alternatively, do I need to create my own atlas? Many thanks for your response, Marie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
phi, when I run the qdec amp; command, the error show as below:/pp[EMAIL PROTECTED]:~gt; qdec amp;br /[1] 10941br /[EMAIL PROTECTED]:~gt; qdec.bin: error while loading shared libraries: libexpat.so.0: br /cannot open shared object file: No such file or directorybr //ppnbsp;I do't knownbsp; how to deal with this problem. Could you tell me how to resolve this, Thank you!!!/p___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical parcellation in anterior cingulate region
wow, that's awful. I don't think we usually see it be this bad. If you post this subject on our website we'll take a look On Mon, 25 Jun 2007, Marie Schaer wrote: Hello Bruce Rahul, Indeed in my sample of subjects it's more the corpus callosum directly with the frontal superior, and the rostral cingulate becomes lost under the corpus callosum. I attached the image of my average subject, but each single subject looks pretty similar in that region. Many thanks, Marie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] long delay before tksurfer launches
Hello, Apologies for cross-posting (this list and martinos-tech), but I think that by posting here I might be able to reach a few more people who may have had the problem before and solved it. I have been experiencing very long load-up times, when running tksurfer. It can take up to 6 or 7 minutes to load. As far as I can tell, the application does not have any unusual or slow behaviors once it finally launches. The problem was not present until Friday, but has persisted since, and I run it the same now as I did before. Paul Raines mentioned on martinos-tech that there used to be a problem where the SUBJECTS_DIR was searched recursively and it would slow down the loading times for a comparable length of time. Can anyone confirm that this is still what tksurfer does? When I run it, I source the latest development version. If the problem is not the long search and file checks, then what could be the source of the delay? The command is: tksurfer average7 lh inflated The output is normal and I'm running it from /space/ventzl/1/users/SUBJECTS_DIR/ This is the tksurfer /usr/local/freesurfer/dev/bin/tksurfer The initial output is: surfer: current subjects dir: /space/ventzl/1/users/SUBJECTS_DIR surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/ventzl_001/users/SUBJECTS_DIR Then it hangs for 6 minutes or longer, and launches the tk gui. When I strace it, there is trace information to show initially, and then there is the text output I mentioned above, but during the waiting period there is no output from strace at all. Thanks in advance, Rob ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] long delay before tksurfer launches
strace shows you the system calls being made by the program. When it's hanging for a long time, note the last few lines of output from strace and let us know what those are. The last one will be the call that is taking so long to finish. On Mon, Jun 25, 2007 at 11:56:00AM -0400, Robert Levy wrote: Hello, Apologies for cross-posting (this list and martinos-tech), but I think that by posting here I might be able to reach a few more people who may have had the problem before and solved it. I have been experiencing very long load-up times, when running tksurfer. It can take up to 6 or 7 minutes to load. As far as I can tell, the application does not have any unusual or slow behaviors once it finally launches. The problem was not present until Friday, but has persisted since, and I run it the same now as I did before. Paul Raines mentioned on martinos-tech that there used to be a problem where the SUBJECTS_DIR was searched recursively and it would slow down the loading times for a comparable length of time. Can anyone confirm that this is still what tksurfer does? When I run it, I source the latest development version. If the problem is not the long search and file checks, then what could be the source of the delay? The command is: tksurfer average7 lh inflated The output is normal and I'm running it from /space/ventzl/1/users/SUBJECTS_DIR/ This is the tksurfer /usr/local/freesurfer/dev/bin/tksurfer The initial output is: surfer: current subjects dir: /space/ventzl/1/users/SUBJECTS_DIR surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/ventzl_001/users/SUBJECTS_DIR Then it hangs for 6 minutes or longer, and launches the tk gui. When I strace it, there is trace information to show initially, and then there is the text output I mentioned above, but during the waiting period there is no output from strace at all. Thanks in advance, Rob -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
QDEC has not been officially released yet -- soon! [EMAIL PROTECTED] wrote: hi, when I run the qdec command, the error show as below: [EMAIL PROTECTED]:~ qdec [1] 10941 [EMAIL PROTECTED]:~ qdec.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory I do't know how to deal with this problem. Could you tell me how to resolve this, Thank you!!! 我积分，我得奖，天天乐透！ http://goto.mail.sohu.com/goto.php3?code=mailadt-ta1 *用搜狗拼音写邮件，体验更流畅的中文输入 http://goto.mail.sohu.com/goto.php3?code=mailadt-ta ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Segmentation
Hi Bruce, Thank you for your quick response. Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz. Thanks, Antonio -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Hi Antonio, I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust the ?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc... Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Hi All, Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded segmented maps. Precisely - as an example - in the attached figure you can see that in the case of left insula WM, part of the tissue was classified as GM (in brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the tissue is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern. I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential errors in the generated values of thickness and volumes as well? If so, is there any way I can correct for this? Thank you in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Segmentation
Hi Antonio, that's why we we use the surfaces for white matter and cortical gray matter volume. cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Hi Bruce, Thank you for your quick response. Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure). So, even if the surfaces look good, we are worried about the effects of this misclassification on volume measurements in aseg.mgz. Thanks, Antonio -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Monday, June 25, 2007 4:10 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Hi Antonio, I wouldn't use the wm.mgz for much of anything. It's really just an intermediate step in the creation of the surfaces. In general we trust the ?h.white and ?h.pial surfaces first, then the aseg.mgz for things like hippocampus, ventricles, etc... Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Hi All, Upon reviewing subortical segmentations I see that often a mismatch exists between what appears on the wm.mgz and the color-coded segmented maps. Precisely - as an example - in the attached figure you can see that in the case of left insula WM, part of the tissue was classified as GM (in brown) in the color-coded segmented map and as WM in the wm.mgz. Contrariwise, the right temporal-parietal GM cortex part of the tissue is classified as WM (in green) the color-coded segmented map and as non-WM in the wm.mgz. The latter occurs in many regions of the brain without a clear anatomical pattern. I was wondering if this is just a display issue or it rather reflects some mismatch in actual tissue classification with consequential errors in the generated values of thickness and volumes as well? If so, is there any way I can correct for this? Thank you in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ 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] Cortical surface tessellation and smoothing
Dear list, Is there a paper or any documentation describing how freesurfer tessellate and smooth cortical surfaces? In particular, does freesurfer use any specific variety of marching cube isosurface algorithm? Regular surface smoothing (like the Laplacian smoothing) may cause undesired surface shrinking. It looks that freesurfer does a good job on surface smothing. So I'm wondering what smoothing algorithm freesurfer employ. Thanks, Kai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical surface tessellation and smoothing
Hi Kai, it was described in the Dale, et al. 1999 paper in NeuroImage, or maybe part in that and part in the 2nd part of it (Fischl et al., 1999 also NeuroImage). They are both on our wiki (surfer.nmr.mgh.harvard.edu/fswiki). We don't use marching cubes, but a custom tesselation algorithm. The surface smoothing is like a Laplacian, but the surface area of the inflated surface is constrained to be the same as the original surface. cheers, Bruce On Mon, 25 Jun 2007, Kai Li wrote: Dear list, Is there a paper or any documentation describing how freesurfer tessellate and smooth cortical surfaces? In particular, does freesurfer use any specific variety of marching cube isosurface algorithm? Regular surface smoothing (like the Laplacian smoothing) may cause undesired surface shrinking. It looks that freesurfer does a good job on surface smothing. So I'm wondering what smoothing algorithm freesurfer employ. Thanks, Kai ___ 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] problems with -clean-bm flag
Hi Antonio, What is the complete command you are using the -clean-bm flag with? Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gallo, Antonio (NIH/NINDS) [F] Sent: Monday, June 25, 2007 7:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] problems with -clean-bm flag Hi All, I'm trying to see how much my thickness measures are affected by my manual edits. When I tried to use the -clean-bm flag with autorecon2 I always got this message: -1): read error mri_em_register: could not open mask volume brainmask.mgz. It seems to me that this flag delete the brainmask.mgz file but doesn't generate a new copy of this file from the brainmask.auto.mgz file. Could you help me with that? Thank you in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
