[Freesurfer] problem in running recon-all

Hi, I ran "recon-all -subjid 2144 -all" and it just got frozen after a while. I have attached the log herewith. Appreciate your help. Thanks! Shahab - Need a quick answer? Get one in minutes from people who know. Ask your question on Yahoo! Answers

[Freesurfer] error in brainmask...

Hi, Some the processed images have error in their brainmasks (e.g., partial stripping of skull, partial removing of neck and other parts etc.). Is there any way to correct them automatically? Appreciate it. Shahab - Need a quick answer? Get one in mi

[Freesurfer] problem in runnign tkmedit on linux...

Hi I am getting the following error when I run tkmedit or tksurfer: Couldn't create output file .xdebug_tkmeditfreeglut (tkmedit): OpenGL GLX extension not supported by display ':0.0' It seems X11 server configuration is not set properly to run OpenGL applications. Any ideas? Thanks Shahab

[Freesurfer] how to extract a piece of cortical surface...

Hello, I am working on nonlinear registration of cortical surface and subcortical volumes. I am able to extract individual subcortical objects from the freesurfer segmentation for registration, but don't know how to extract a patch from cortical surface. Could somebody guide me please?

[Freesurfer] is there any online resource for manual segmentations of subcortical objects...

Hello,   Is there any online resource for manual segmentations of subcorical objects, e.g. hippocampus, amygdala, caudate etc? I appreciate it.   Shahab Stay in the know. Pulse on the new Yahoo.com. Check it out. ___ Freesurfer mailing list Frees

[Freesurfer] how to save segmentation in analyze format by using command line?

Hello,   I usually open subcortical segmentations in tkmedit and save the segmentations in analyze format. Is there any command line option to do the same? Appreciate it.   Shahab Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business. ___

[Freesurfer] cotical surface labeling...

Hi,   I can extract subcorical objects from freesurfer segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.   Thanks Shahab Ge

Re: [Freesurfer] question about surface based segmentation...

ything (subcortical and cortical)BruceOn Tue, 12 Sep 2006, Shahabuddin Ansari wrote:> Hi,>> I have done volume-based segmentation using freesurfer> and now am interested in surface-based segmentation. I> have used the following set of commands in> volume-based segmentation:>&g

[Freesurfer] question about surface based segmentation...

Hi, I have done volume-based segmentation using freesurfer and now am interested in surface-based segmentation. I have used the following set of commands in volume-based segmentation: #!/bin/csh # Shahab Ansari, August 22, 2006 #The following command creates a directory structure for the subject

[Freesurfer] having problem in running recon-all...

Hello,   I am having problem in running the following command:   recon-all -i 2996926_02.img -s 2996926_02 I used to run the command before without any problem. Recently my linux has been updated to suse version, would that be a source of problem. The console display the following error:   I

[Freesurfer] need a list of segmented subcorical regions and their intensity values...

Hello, I have seen a list of 40 freesurfer-segmented subcortical objects with their respective intensity values somewhere in the documentation, but not able to locate it now. Could somebody help me please. Thanks Shahab __ Do You Yahoo!? Tired of s

Re: [Freesurfer] having problem in runing recon-all

Please disregard my previous email. The error was due to my stupid mistake. Thanks! Shahab --- Shahabuddin Ansari <[EMAIL PROTECTED]> wrote: > Hello, > > I am having a problem in running recon-all command. > I > have run this command without any problem. Today I > move

[Freesurfer] having problem in runing recon-all

Hello, I am having a problem in running recon-all command. I have run this command without any problem. Today I moved the image into another directory and getting the following error: mri_convert /ensc/IMAGE4/STUDENTS/SANSARI/freesurfer/subjects/4365 /ensc/IMAGE/opt/FREESURFER/subjects/4365/mri/o

RE: [Freesurfer] how to register subcortical segmentation with theoriginal image

Hi Valentina,   Have you tried the following command? recon-all -motioncor -s   Shahab "Durastanti, Valentina (NIH/NINDS) [F]" <[EMAIL PROTECTED]> wrote:  Hi,I'm trying to run -autorcon1 of a subject who has 3 mgz images but always came out an error about the motion correction. So I tried r

[Freesurfer] Transformation of segmenation

Hello Bruce, Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?

[Freesurfer] how to register subcortical segmentation with the original image

Hello,   I have subcortical segmentations from freesurfer. I have automatically extracted one of the segmented objects (binary). I need to get the grayscale map of the object and do not know how to register the segmented object with the original image (analyze) so it can be overlayed for masking?

[Freesurfer] want to view one segmented subcortical object at a time...

Hello, I have segmented subcortical regions of the whole brain from Freesurfer. Can somebody help me how to view one object (say right hippocampus) at a time. Thanks Shahab __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection

[Freesurfer] How to display isolated segmented object in Freesurfer viewer

Hello, Thanks for answering my previous querry. I have successfully segmented the subcortical regions of the brain. Now, my next simple question is how to display each segmented object separately? I think it is to do with masking, but not sure how to apply that in 3D. Thanks Shahab _

[Freesurfer] question about subcortical brain segmentation using Freesurfer...

Hello, I am new Freesurfer user. I need to segment subcortical regions of brain and wondering that if there is any doc or tutorial on the subject. I appreciate your comments. Thanks Shahab __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best