Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Install two verson of freesurfer on one computer
by yczhang＠nlpr.ia.ac.cn 23 May '08

23 May '08

Dear Mr or Ms, I want to know whether I can install two versions of freesurfer on one computer. If I want to use one version,I just change the freesurfer home by "gedit .bashrc". If I want to use another,I change back to the former freesurfer home of another version. Whether they are compatible with each other? Thanks!

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Creating a volume with MRIS_FILL
by Cochrane Jamison 22 May '08

22 May '08

I am using mris_fill to create a volume from the lh.pial surface as well as the rh.pial surface. I have 2 questions: 1. How can I combine the 2 separate hemisphere volumes into a single full brain volume that I can export and view in analyze? I only know to use mri_convert on each one separately. Does this need to be done before I run mris_fill, or is there another combined surface that has the same resolution as the pial surfaces that I can run mris_fill on? 2. I know that when I run mris_fill, the volumes that are produced do not contain orientation information. When I load them into Analyze, the volume is mirrored and upside down. I was wondering how I can "get" orientation information back into the volume, and also correct the mirrored and upside down viewing issue. These results were produced by Freesurfer from standard dicom files from a volumetric scan. Thanks, Cochrane Jamison

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Combining two regions
by Pierson, Ronald K 22 May '08

22 May '08

I apologize if this has been asked and answered before, but I wish to combine rostral and caudal middle frontal gyri for a summary measure. To find the average thickness of the entire region, will it be weighted by the surface area or by the number of vertices? Avg_MidFront = ((CaudThick*NumVertsCaud) + (RostThick*NumVertsRost) / (NumVertsCaud + NumVertsRost)) Or Avg_MidFront = ((CaudThick*SurfAreaCaud) + (RostThick*SurfAreaRost) / (SurfAreaCaud + SurfAreaRost)) Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

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talairach_avi
by Juranek, Jenifer 22 May '08

22 May '08

Just curious... 1) was talairach_avi (or more specifically, 4dfp suite) introduced with any particular version# of freesurfer? Or has it always been the default? 2) Any comments on differences/similarities with mritotal as called by the -use-mritotal flag within freesurfer? Many Thanks, Jenifer

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Tksurfer vertex array
by Keller, Corey J. 22 May '08

22 May '08

Hi Freesurfers, I am trying to develop an accurate intracranial electrode placement visualization tool with a patient's pre-op MRI and post-op CT. With the pre-op MRI we can do a freesurfer cortical reconstruction and output that surface in talairach space. Has anyone had any luck with co-registering a cortically reconstructed surface with a CT scan with intracranial grid electrode artifacts? Sorry, this is not necessarily a freesurfer question but thought it was a good place to ask. Thanks in advance. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital Wang 735, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

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retinatopy question
by Elif SIKOGLU 21 May '08

21 May '08

Hello, I have a basic question regarding retinatopy analysis. In the paradigm files we specify whether the run was mapping eccentricity or polar angle stimulus, and we specify the number of cycles in mkanalysis. Don't we need to be more specific about the stimulus, i.e. how many wedges trace one cycle or the duration of each wedge? Thanks,

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WM parcellation regions
by Marlisa Isom 21 May '08

21 May '08

Hi everyone, Our group is interested to know whether there is a way to view the WM parcellation regions as you would gray matter. My understanding is that the viewer options are for white matter hemisphere totals, as in it's either left or right. Thanks again! Marlisa Marlisa Isom Research Coordinator Head Research Laboratory Washington University in St. Louis (314) 935-8033

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segmentation problem
by Dick, Rachel 21 May '08

21 May '08

Hello, I'm having some issues with the cortex as seen in the attached picture. I know in the more medial regions I can add control points to the white matter to help the pial line extend further out. However, laterally, I'm not sure how to include that cortex that is left out. Any help would be greatly appreciated. Thanks in advance, Rachel

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a problem
by yczhang 21 May '08

21 May '08

Using lgi or thickness,how could I know the anatomical correspondence for a statistical difference area which had been found between patients and controls. I have to report the significant regions ,for example ,postcentral sulcus or posterior cingulate Thanks! yczhang 2008-05-21

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missing libg2c.0.dylib
by Jose Miguel Selman 21 May '08

21 May '08

Hi everyone: I have run freesurfer on Centos for a while now with no problems. I installed the most recent version on a MacBook pro. Tkmedit and Tksurfer work fine, but when attempting the recon-all processing I get an error of a "missing libg2c.0.dylib". The last part of the log follows: --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin Kernel Version 9.2.2: Tue Mar 4 21:17:34 PST 2008; root:xnu-1228.4.31~1/ RELEASE_I386 i386 recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4 2008 I tried to get information on the list but could not find anything. Thanks Dr. Jose M Selman Confidencialidad: La informacion contenida en este correo y cualquier archivo adjunto es de caracter confidencial. La utilizacion, distribucion, divulgacion o reproduccion esta autorizada exclusivamente para su(s) destinatario(s). Si ha recibido este correo por error, por favor notifiquelo a su remitente y eliminelo completamente de sus recipientes. Clinica Las Condes se lo agradece.(Los acentos han sido suprimidos intencionalmente para no exponer al texto a reemplazos de los caracteres acentuados.) The information contained in this e-mail and any attached files is strictly confidential. Its use, distribution, publication or reproduction is exclusively authorized for its addressee. If you have received it by error, please notify its sender and eliminate it completely from your files. Clinica Las Condes thanks you.

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