Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

Re: Installation Question
by DG MCLAREN 13 Nov '06

13 Nov '06

Whom should I contact with installation questions? Specifically: I am running RHEL 3 and tried to install CentOS4, which was recommended for RHEL 4. However, the libglut.so.3 library can't be found. Is there an older version of Freesurfer that would run on RHEL 3 or can that library be installed? Any thoughts would be appreciated. Best Regards, Donald McLaren ===================== D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (773) 406 2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406 2464 or email. ----- Original Message ----- From: freesurfer-owner(a)nmr.mgh.harvard.edu Date: Friday, November 10, 2006 3:43 pm Subject: Installation Question To: dmclaren(a)wisc.edu > You are not allowed to post to this mailing list, and your message has > been automatically rejected. If you think that your messages are > being rejected in error, contact the mailing list owner at > freesurfer-owner(a)nmr.mgh.harvard.edu. > >

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surface based cortical volume estimates
by Paul Greenberg 09 Nov '06

09 Nov '06

Hello, When viewing cortical surfaces and labeled volumes (aseg) with TK medit, the cortical surface runs through about 1/2 of the hippocampal volume in each hemisphere. Will this partial hippocampal volume be included in any of the surface based estimates of cortical volume found in the [?h.aparc.stats] file? Thanks very much! Paul

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white matter segmentation
by Jenny Kirchner 09 Nov '06

09 Nov '06

Hi, I am working on a case for which I have run autorecon 2. Edits seem necessary on both the pial surface and the white matter segmentation. I am now wondering if it is better to first do the white matter edits and then run autorecon 2 again to see if the pial surface errors improved or if it is more economic to do the pial surface edits in the same step. I also have a question concerning the differences in segmentation between the wm.mgz and the ?h.white. I am attaching two screenshots for you to be able to see it. The wm.mgz is showing white matter, which in the lh.white (loaded on top of the brainmask.mgz) is not defined as white matter as shown by the yellow line. (See temporal pole of the left hemisphere). I am wondering which of the both segmentations is correct, the wm.mgz version or the lh.white version and where exactely I have to do the edits. Thanks a lot for your help! Best, Jenny

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editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

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Addendum: Surface-Based Group Analysis Results --> MNI coordinate space
by emoulton＠mclean.harvard.edu 08 Nov '06

08 Nov '06

Had made a slight error in my previous request. Here it is, clarified: Is there a straightforward way to convert Surface-based Group Analysis results (e.g. sig.mgh) to ANALYZE format in conventional MNI coordinate space (i.e. viewable with FSL)? What steps, and what tools, should I use to perform such a conversion? Thanks, Eric Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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Surface-Based Group Analysis Results --> Original coordinate space
by emoulton＠mclean.harvard.edu 08 Nov '06

08 Nov '06

Hello, Is there a straightforward way to convert Surface-based Group Analysis results (e.g. sig.mgh) to ANALYZE format in conventional coordinate space (i.e. viewable with FSL)? It seems to require a bit more gymnastics than a simple mri_convert command to properly convert these surface maps. What steps, and what tools, should I use to perform such a conversion? Thanks, Eric Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

1 0

3D visualisation
by Nicolas Cherbuin 07 Nov '06

07 Nov '06

Hello, I would like to visualize subcortical structures, particularly the hippocampus, in 3D. Is there an available function to display a glass brain with solid internal structures and/or is it possible to extract this information from the freesurfer files? If yes where could I find the file format to extract the info? Also, is it possible to perform surface analyses on the subcortical structures (e.g. hippocampus) instead of on the inflated brain, for example to show differences in volume related to memory measures? Thanks Nic

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Re: [Freesurfer] is this ok?
by Chacko Cherian 06 Nov '06

06 Nov '06

Thanks Bruce. I Am using version 3.0.3,..wat can i do to to get better pial surface images? IS it something to do with the skull stripping stage or is it the motion artifacts which cause a reduction in the overall resoution of the image? Chacko. ----- Original Message ---- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Chacko Cherian <chacko_cherian(a)yahoo.com> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Monday, November 6, 2006 4:25:05 PM Subject: Re: [Freesurfer] is this ok? Hi Chako, I wouldn't worry too much about the inflated - it looks okay. Probably a result of the large motion artifact in your data. The pial surface is more worrisome - what version are you running? They are usually *much* better than this. Bruce On Mon, 6 Nov 2006, Chacko Cherian wrote: > Hello freesurer users, > > Is it ok to have such edges on the inflated surface?Is there something I can do to rectify this? > THe second image is the brainmask and wm volume as seen using tkmedit. > > (tkmedit subj1 brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white) > > THanks in advance > > Best, > > Chacko Cherian > > > >

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is this ok?
by Chacko Cherian 06 Nov '06

06 Nov '06

Hello freesurer users, Is it ok to have such edges on the inflated surface?Is there something I can do to rectify this? THe second image is the brainmask and wm volume as seen using tkmedit. (tkmedit subj1 brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white) THanks in advance Best, Chacko Cherian

2 1

Scan quality
by Derin Cobia 06 Nov '06

06 Nov '06

Should I expect this kind of quality/resolution from my FS images based on the original scan (see attached images)? These are older scans that I've been given, and I just want to make sure that the image quality isn't introducing any unnecessary error, or is not "good enough" for FS. Thanks. -Derin

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