Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Fwd: [freesurfer] installation
by Ignacio Letelier 18 Aug '10

18 Aug '10

Sorry Doug I forgot to send the entire email thread. Now, could you please help me with the installation. Best regards. Forwarded conversation Subject: [freesurfer] installation ------------------------ From: *Ignacio Letelier* <nachoadress(a)gmail.com> Date: 2010/8/18 To: freesurfer(a)nmr.mgh.harvard.edu Hi all I'm a new freesurfer user and I have some troubles installing the program. after moving to cd /usr/local I typed *freesurfer-virtual:~>* tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz replacing <platform>-<release> with freesurfer-Linux-centos4-stable-pub-v4.3.1 I get the following error message Cannot >>* open: No such file or directory *>>* *>>* tar: Error is not recoverable: exiting now *>>* *>>* tar: Child returned status 2 *>>* *>>* tar: Error exit delayed from previous errors * I don´t know exactly what I'm doing wrong, this may happen because I'm not in the right directory or something? How can I get informnation about my Linux and Freesurfer software version.* * Any help will be greatly appreciated, thanks in advance -- Ignacio ---------- From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu> Date: 2010/8/18 To: Ignacio Letelier <nachoadress(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Is that file in that directory? What size is it? Do you have write permissions to that folder? doug Ignacio Letelier wrote: > ------------------------------------------------------------------------ > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ---------- From: *Ignacio Letelier* <nachoadress(a)gmail.com> Date: 2010/8/18 To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Hi Doug At least i've made sure that freesurfer location is in */usr/local/freesurfer * The Freesurfer properties tab says that it weights 3.1 GB Now, the Permissions tab says: *Owner*: freesurfer (freesurfer) *Access*: Read&Write *Group*: freesurfer *Acces*: Read only *Others* :Read only Thanks Doug -- Ignacio ---------- From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu> Date: 2010/8/18 To: Ignacio Letelier <nachoadress(a)gmail.com> So do you have write access? Also, remember to send the entire email thread in the letter. I delete emails aggressively so I won't always know what you are talking about. Also, please respond to the list. Others may be interested, and it gets saved in the archive. doug ---------- From: *Ignacio Letelier* <nachoadress(a)gmail.com> Date: 2010/8/18 To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 2010/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> I guess I do have write acces (according to with what I understood from my previous email) I'm not a Linux or Unix expert so help me please..... Thanks doug -- Ignacio ---------- From: *Douglas N Greve* <greve(a)nmr.mgh.harvard.edu> Date: 2010/8/18 To: Ignacio Letelier <nachoadress(a)gmail.com> Hi Ignacio, did you see the other requests in my email? doug Ignacio Letelier wrote: > > > 2010/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: > greve(a)nmr.mgh.harvard.edu>> > -- Ignacio

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User-defined colormaps
by Hansen, Kathleen (NIH/NIMH) [F] 18 Aug '10

18 Aug '10

Hello, If we are visualizing fmri surface data with tksurfer, how can we load our own user-defined colormaps? If this is not possible in tksurfer, is it possible using some other Freesurfer function? Thank you, Kathleen

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installation of v5.0.0 without erasing v.4.5.0
by Gonzalo Rojas Costa 18 Aug '10

18 Aug '10

Hi: Can I install freesurfer v5.0.0 without erasing v.4.5.0 ?... Because I want to test some new features but I need to continue using v.4.5.0... I installed v.4.5.0 in /usr/local/freesurfer... Sincerely, Gonzalo Rojas Costa

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[freesurfer] installation
by Ignacio Letelier 18 Aug '10

18 Aug '10

Hi all I'm a new freesurfer user and I have some troubles installing the program. after moving to cd /usr/local I typed *freesurfer-virtual:~>* tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz replacing <platform>-<release> with freesurfer-Linux-centos4-stable-pub-v4.3.1 I get the following error message Cannot >>* open: No such file or directory *>>* *>>* tar: Error is not recoverable: exiting now *>>* *>>* tar: Child returned status 2 *>>* *>>* tar: Error exit delayed from previous errors * I don´t know exactly what I'm doing wrong, this may happen because I'm not in the right directory or something? How can I get informnation about my Linux and Freesurfer software version.* * Any help will be greatly appreciated, thanks in advance -- Ignacio

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using -nuintensitycor-3T flag with v-5.0.0
by Mehul Sampat 18 Aug '10

18 Aug '10

Hi Folks, I would like to use the -nuintensitycor-3T flag as listed in the release notes (http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) I had two questions about this new option: 1. Can I just use this as follows: recon-all -s bert -autorecon1 -autorecon2 -nuintensitycor-3T (then run -autorecon3) ? 2. I don't think there are any parameters associated with this flag. is this correct ? thanks Mehul

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Curvature of the Corpus Callosum
by Alan Francis 17 Aug '10

17 Aug '10

Hi All: Does a lower score on the curvature index of the CC (as done by FreeSurfer) imply that the Corpus Callosum is more curved (smaller radius) or is it the other way around? thank you, Alan |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan Francis Brain Spectroscopy and Neuroimaging Lab Beth Israel Deaconess Medical Center Dept of Psychiatry Harvard Medical School Boston 02215

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ERROR: _FindFacePath
by Fernanda Palhano 17 Aug '10

17 Aug '10

Hello, When trying running recon-all I am getting the following error: #@# Fix Topology rh Sat Aug 14 04:15:31 BRT 2010 ERROR: _FindFacePath: could not find path! Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Sat Aug 14 04:26:14 BRT 2010 I've tryed twice, but i get the same error. Could anyone help me? Thanks in advance, Fernanda

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CUDA support in 5.0
by Gennan Chen 17 Aug '10

17 Aug '10

Hi! I will like to try the beta CUDA support in 5.0. And I have some questions here 1. Are all needed libraries bundled in the release? Or I need to go to CUDA's site to get those dependency? And if I need to, what are those dependency I need to grab and install? 2. I have RH 5 64 bit linux box with single NVIDIA FX card and macpro snow leopard box with dual NVIIDA GT 120. Does CUDA support work for both OS? If they do, any idea what the speed up will be?? Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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recon-all error
by Carl Dambkowski 17 Aug '10

17 Aug '10

Hi, again (I've emailed once before), I am trying to test my freesurfer installation and everything goes fine (tksurfer, qdec, etc). However, once I get to: recon-all -s bert -autoreco1 i get: FREESURFER_HOME: Undefined variable. However, I believe I've set it up properly with: setenv FREESURFER_HOME Desktop/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh And I get back: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR Desktop/freesurfer/subjects MNI_DIR Desktop/local/freesurfer/mni With no errors. When I give the command: echo $FREESURFER_HOME I also get back: Desktop/freesurfer Any suggestions? Thanks, Carl -- Carl Dambkowski Research Assistant Cerebral Localization Laboratory Columbia University Medical Center (212) 342-3668

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medialorbitofrontal_area
by Jose Soares 17 Aug '10

17 Aug '10

Hi all, I am doing a study about the medialorbitofrontal, and I am having some strange area results in a lot of subjects. The rh areas are much higher than the lh areas of medialorbitofrontal: Some examples: lh rh 1714.0 2822.0 1720.0 2632.0 1728.0 2675.0 1877.0 2733.0 1498.0 2719.0 2067.0 2542.0 1870.0 2666.0 1554.0 2263.0 1535.0 2566.0 1794.0 2392.0 1487.0 2547.0 Why is this happening, any idea? Should I do any correction? Thanks for the help, Miguel.

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Freesurfer