Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30129 discussions

Tutorial
by Michael Ryan Haynes 02 Jun '05

02 Jun '05

In FreeSurferTutorial.pdf, starting on page 27 for examples on correcting holes and handles, why do the images in the original bert file appear as right hemisphere on left while the images in the tutorial appear as right hemisphere on right side? Thanks.

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skull stripping
by Fornito, Alexander 02 Jun '05

02 Jun '05

Hi all, The page about using FSL with freesurfer on the FSL website recommends using BET to skull strip the images before feeding them into freeusrfer. I've had a bit of play with this, and have noticed some marginal improvements. Would you generally recommed this practice? Are there any reasons not to? Also, what exactly does the -atlas option do? Thanks, Alex

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pictures of MRI image segmentation
by Bagnato, Francesca (NIH/NINDS) 01 Jun '05

01 Jun '05

Hi: I am having troubles in preparing a picture showing MR image segmentation in the coronal, axial and sagittal planes. Any light on that? Thanks, --francesca Francesca Bagnato, 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 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question Hi Wan, they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy. cheers, Bruce On Tue, 31 May 2005, Wan Park wrote: > Hi, I have a question. I am getting the gray volume for a standard area > (G_subcallosal) in different brains (male and female) with different > conditions. > > If I want to compare these volumes, should I normalize them with the total > brain (or hemisphere) volume or can I use these results directly? I > understand that the FS fills the volume from a particular brain into a > standard brain. So, are the volumes already normalized? Thanks, > > Wan > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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occipatal cuts
by Joongnam Yang 31 May '05

31 May '05

Hi all, I did the occipital cut for the right brain and flattened it. When I opened it with Tksurfer of csurf, the flattened surface showed up on the right edge of the display window of Tksurfer, instead of being in the center of the window. (The left flattened surface came out in the center, and I did similarly for the left and right brains.). Has anyone had this problem? or how can I fix it? Thanks always for the great help that I get from this listing. Nam.

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Gray Volume question
by Wan Park 31 May '05

31 May '05

Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions. If I want to compare these volumes, should I normalize them with the total brain (or hemisphere) volume or can I use these results directly? I understand that the FS fills the volume from a particular brain into a standard brain. So, are the volumes already normalized? Thanks, Wan

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RE: [Freesurfer] questions on check_subject
by Bruce Fischl 31 May '05

31 May '05

is this only on Tiger? And does it happen with all your subjects now that you have upgraded? On Tue, 31 May 2005, Jia Liu wrote: > Hi, Bruce- > > Thanks for your reply. I re-did morph for the right hemisphere, and the > problem persists. > > CHECKING SUBJECT ttt > WARN: time for rh.orig is older than rh.qsphere > WARN: file rh.sphere.reg is not equal in size to rh.smoothwm > > -rw-rw-r-- 1 jliu jliu 4853285 May 31 12:45 rh.sphere.reg > -rwxrwxr-x 1 jliu jliu 4853068 May 31 09:43 rh.smoothwm > -rwxrwxr-x 1 jliu jliu 4853068 May 31 09:43 rh.orig > > The log file is attached. What should I do to correct this problem? Thanks > again for your help! > > Best, > > jia > >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Sunday, May 29, 2005 9:42 PM >> To: Jia Liu >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] questions on check_subject >> >> you will need to rerun the morph. >> On Sun, 29 May 2005, Jia Liu wrote: >> >>> Hi, Bruce- >>> >>> No, the ?h.sphere.reg files are slightly larger than the orig files. > Below >>> is the list of files in the surf directory. >>> >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.inflated >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.orig >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.pial >>> -rw-rw-r-- 1 app app 4858721 Mar 16 23:46 lh.rh.sphere.reg >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.smoothwm >>> -rw-rw-r-- 1 app app 4858504 Mar 16 20:35 lh.sphere >>> -rw-rw-r-- 1 app app 4858721 Mar 16 22:14 lh.sphere.reg >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.white >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.inflated >>> -rw-rw-r-- 1 app app 4853285 Mar 16 18:54 rh.lh.sphere.reg >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.orig >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.pial >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.smoothwm >>> -rw-rw-r-- 1 app app 4853068 Mar 16 15:17 rh.sphere >>> -rw-rw-r-- 1 app app 4853285 Mar 16 16:59 rh.sphere.reg >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.white >>> >>> Will this affect the surface-based group analysis? >>> >>> Thanks again for your help! >>> >>> Best, >>> >>> jia >>> >>>> -----Original Message----- >>>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>>> Sent: Friday, May 27, 2005 8:10 PM >>>> To: Jia Liu >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] questions on check_subject >>>> >>>> not sure why the smoothwm would be different size. Is it the same size > as >>>> the orig? How about the rest of the surfaces for each hemis (sphere, >>> white, >>>> pial) >>>> >>>> On Fri, 27 May 2005, Jia >>>> Liu wrote: >>>> >>>>> Hi, >>>>> >>>>> I used check_subject and found following error message on all my >>> subjects: >>>>> >>>>> Zion:/nfs/home/Subjects> check_subject subKL >>>>> CHECKING SUBJECT subKL >>>>> WARN: file rh.sphere.reg is not equal in size to rh.smoothwm >>>>> WARN: file lh.sphere.reg is not equal in size to lh.smoothwm >>>>> WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm >>>>> Exit 3 >>>>> >>>>> However, I looked through recon-all log files and found no error >>> messages. >>>>> So what does the error message above mean? How to correct this > problem? >>> Is >>>>> there any document on check_subject? Thanks a lot for your help! >>>>> >>>>> Best, >>>>> >>>>> Jia >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >

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mesh decimation
by Alex Wade 26 May '05

26 May '05

I am trying to reduce the number of vertices in a freesurfer mesh. I am having some difficulty when I go through matlab using the 'reducepatch' command : some of the surface normals end up being scrambled resulting in strange transparent holes in the mesh. I wonder if there is some command-line routine that will directly take, say, rh.pial , decimate it and write out another mesh, say, rh.pial_dec I see that tksurfer has a write_decimation option and this works in that it generates a file but I don't know what format the output is. It doesn't seem to be a valid surface file and tksurfer will crash when I try to load it. Thanks in advance for your help Alex A.R. Wade Ph.D. Associate Scientist Brain Imaging Center The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

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parcellated areas
by Wan Park 26 May '05

26 May '05

Hi, when I do parcellate_subject, I received this message with one of my brains: 2816 1563 3354 2.147 +- 0.645 0.190 0.071 58.221 6.689 ** annotation 003c148c 1449 858 2052 2.369 +- 0.688 0.191 0.055 26.557 2.772 ** annotation 003cdc14 1996 1206 2429 2.019 +- 0.567 0.221 0.085 48.606 6.389 ** annotation 001414b4 Instead of showing the area names, it shows "annotation ..." Do you know where the problem is? Thanks, Wan

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running Freesurfer on a Linux cluster
by Renat Yakupov 26 May '05

26 May '05

Hello. Does Freesurfer run on Linux cluster really taking advantage of it? Is it, what it is called, cluster-aware? What about running on a multi-processor workstation? Up to how many CPU's can it handle? Thank you. Regards, Renat.

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BRIK and tkregister
by Joongnam Yang 24 May '05

24 May '05

Hi, I am using an old version of Freesurfer where retinotopy-analysis is enabled. If anyone having such experience, please help me. I am having trouble with csurf, and here is what I did. (1) changed Analyze file (*.hdr, *.img) into *.BRIK and *.HEAD using to3d (2) in csurf, under "session tools", I did "setup align/func scan" and it opens a window where I do "align scan dir" and it only accepts AFNI's *.BRIK and *.HEAD file. (that's why I did the conversion above). When I choose "align=>subj" to do the tkregister registration, it gives me the following error window. AFNI BRIK byte order (determined "only" from BYTEORDER_STRING parameter in this HEAD file): /............/bob+orig.HEAD is INTEL (LSB first) not SUN/SGI/MAC (MSB first) Change to MSB first? This error message was followed by either "cancel" or "force BRIK to MSB, Fix HEAD", but neither option worked, meaning the image shown on "tkregister" was all gobbled. The "subj" image is OK, but the "align" image is screwed. Could anyone give me a hint on where I should go from here? Thanks. Nam.

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