Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

tksurfer/tkmedit tcl scripting "could not open display" error
by Avram Holmes 07 May '10

07 May '10

All, I have generated a batch script that saves out images from tkmedit and tksurfer which I would like to run on a cluster of workstations across a large dataset. However, when I run the jobs remotely tkmedit/tksurfer opens displays on my local machine. As a consequence, if I do not remain logged in than the tcl script fails with the following error: GLUT: Fatal Error in tkmedit.bin: could not open display: nccwscnl04.ncf.cbs.lsdiv.harvard.edu:12.0 GLUT: Fatal Error in tksurfer.bin: could not open display: nccwscnl04.ncf.cbs.lsdiv.harvard.edu:12.0 GLUT: Fatal Error in tksurfer.bin: could not open display: nccwscnl04.ncf.cbs.lsdiv.harvard.edu:12.0 Is there a way for me to run tkmedit/tksurfer with the display suppressed while still being about to save out *.tiff files of my slices/overlays of interest? Thanks for any help you can offer, Avram Holmes

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Fwd: tralairach error when recon-all
by elsh0029＠umn.edu 07 May '10

07 May '10

- Hello all, I had two kind of files ( img & hdr). I used fslchfiletype command to create nii.gz files. img and hdr files replaced by nii.gz files. I used mri_convert command to create 001.mgz files and I did. Now, when I'm running recon-all for my data it exits with error: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux joy 2.6.9-89.0.15.ELsmp #1 SMP Sat Oct 10 05:55:45 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed May 5 13:47:25 CDT 2010 any thoughts? Thank you Ansam

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Hippocampus volume normalization relative to what other volume ?...
by Gonzalo Rojas Costa 06 May '10

06 May '10

Hi: If we want to compare the hippocampus volume between different patients, which other volume could I use to normalize it ?... the ICV ?... the volume of each hemisphere ?... And, if I want to compare the amygdala, for example ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Santiago Chile

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Vertex numbers from RAS (or, labels + .aparc.annot = interesting points)
by Jed Singer 06 May '10

06 May '10

Hello again! I've got a bunch of brain scans, each having in the neighborhood of 100 points I'm interested in (corresponding to subdural electrode locations). I've also got an .aparc.annot file that has nicely divided up the cortex into (hopefully) meaningful regions. I also have a bunch of labels, each marking one of the interesting points. I would like to know in which region each of those labels sits. What I was hoping to do: call read_annotation on the .apparc.annot file read the vertex numbers from the labels using read_label index those vertex numbers into the label field returned by read_annotation index those label numbers into the fifth column of colortable.table index those table rows into colortable.struct_names smile happily What I have actually done: call read_annotation on the .apparc.annot file read labels using read_label notice that all the vertex numbers on all the labels that I have ever made are -1 try unsuccessfully to figure out what that means hunt unsuccessfully for any way of converting what I believe to be RAS coordinates from columns 2-4 of the read_label output into vertex numbers in desperation, throw myself upon the mercy of the wise people who frequent this mailing list. I'd be insanely grateful if someone could point me in the right direction. I bet there's something really simple and stupid and obvious, but I'm still a novice with this software and everywhere that I've even been able to think to look has come up a dead end. Thanks so much! Jed

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Invitation to connect on LinkedIn
by Luke Tseng 06 May '10

06 May '10

LinkedIn ------------Luke Tseng souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Luke Accepter l'invitation de Luke Tseng http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… Voir l'invitation de Luke Tseng http://www.linkedin.com/e/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/bl… ------------------------------------------ Quel est l' intérêt de faire partie du réseau de Luke Tseng ? Le réseau de Luke Tseng développera votre propre réseau : Si vous acceptez l'invitation de Luke Tseng, vous pourrez voir qui vous connaissez dans son réseau et demander à Luke Tseng de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. ------ (c) 2010, LinkedIn Corporation

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Re: [Freesurfer] Technical Doubts
by Nick Schmansky 06 May '10

06 May '10

hi, no, matlab is not used in the default (structural) processing stream. it is only used by the FS-FAST toolset included with freesurfer, which is used for processing fmri data. so you dont need to mention Matlab. n. On Thu, 2010-05-06 at 14:00 -0500, Dr. Luis Guillermo Almeida Montes wrote: > Dear Nick: > > I need to clarify some technical aspects about statistical calculations in FreeSurfer Software.I understood that I require MATLAB software only when I work with fMRI -is this correct?-, but as you know, I have been working only with structural MRI and their results (e.g. areas). So, I need to clarify If I need MATLAB software to realize the work for structural MRI or the installation program of FreeSurfer has the necessary utilities for these. Maybe I misundestood that FreeSurfer runs in MATLAB software to realize my work. > > I hope you can explain me the real need of MATLAB software for FreeSurfer because I need to give some of these technical details in the articles I will publish about my current work. I have been working in MacOSX Snow Leopard. > > Best Regards. > Dr. Luis G. Almeida > > >

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Group comparison
by Rajagopalan, Venkateswaran 06 May '10

06 May '10

Dear All, I am sorry to post this message again. Since i am not able to find from the tutorial and archives what i need i am posting it. I want to compare cortical thickness values in each region from aparc.stats file between control and patients. I am wondering whether it is possible to compare all the regions given in aparc.stats file and give a map showing which of these regions are significantly between the two groups (like VBM the final p map will give you regions which are significantly different). Do i need to create a separate contrast matrix for each and every regions (for eg one contrast for lh.cuneus,one for lh.temporalpole etc) or like in VBM studies you give a single contrast matrix and design matrix since you are testing the same hypothesis in different regions of the cortex. I also would like to know whether i have to do multiple comparisions when i am testing for same hypothesis in different regions or not needed. In the tutorials i find mostly regression between thickness and demographic parameters so any suggestion or guidance to where i can find tutorial or materials related to my above questions. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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GLM analysis on individual surface
by YUMI MAEDA 05 May '10

05 May '10

HI, I am trying to do GLM analysis on individual surface data. I found the online documentation about group feat on surface but I could not find how to do first-level feat on surface. Thank you for any information. YUMI

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Basal forebrain
by Kelly Silva 05 May '10

05 May '10

Hello! Is there any way to know the basal forebrain structure with the Freesurfer (aseg.stats)? Thanks in advance, Kelly

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Qdec Error Question
by blazey＠artsci.wustl.edu 05 May '10

05 May '10

Hi All, I am trying to use Qdec to analyze a dataset, and am getting the following error: ERROR: All stat files should have the same segmentations If one or more stats file have different segs from others, use --common-segs or --all-segs flag depending on the need. The problem is that I haven't been able to find any documentation about using these flags. It would be great is someone could either show me where the documentation is, or give me a brief explanation as to how to use these flags. Thanks in advance for any help. - Tyler Blazey

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Freesurfer May 2010