Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Using qdec
by John Fredy 07 May '10

07 May '10

Hello All, We are using qdec for the analysis of relation between thickness, two roi: par Opercularis, par triangularis; two test: fmri broca and edinburgo. When I make a design with thickness, one roi and one test in Qdec appears one question like: Does the correlation between X and Y, accounting for Z, differ from zero? And a surface of one hemisphere is colored with hot colors for correlation and cold colors for anticorrelation for a relation between variables defined like X = aY + bZ + intercept. Is that the correct interpretation, thinking in correlation and anticorrelation? Regards

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merge cortical and subcortical labels
by Stefan Brauns 07 May '10

07 May '10

Dear Freesurfer experts, I want to create a medial temporal lobe label. Is it possible to merge subcortical and cortical labels? Do I therefore need to use the --regmethod volume flag of mri_label2label for cortical labels? Many thanks in advance, Stefan

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Talairach x MNI 152
by Tadeu Kubo 07 May '10

07 May '10

Hi, I've been using FS, in which the Talairach transform is applied as a standard space for registration. Instead of the Talairach transformation i would like to use the MNI 152 as it is done in FSL and SPM. Does anybody have some experience with this? What would be the impact on the results of the cortical or subcortical structures? I would appreciate it if somebody could help me out with this. Thanks in advance, Tadeu Kubo

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fsgd file creation
by Rajagopalan, Venkateswaran 07 May '10

07 May '10

Dear All, I am new to freesurfer, i am sorry i am confused so i am posting this message. I have two groups i want to compare cortical thickness values in all the areas reported in aparc.stats file between these two groups. So i started creating my fsgd file the problem i have is with the contrast matrix for instance i have 35 regions where thickness values are reported so i have 2*(35+1)=72 contrasts so do i need to specify each of them individually what i mean iS for instance if i am comparing lh.temporalpole (let us assume this is my first variable) so my contrast is 0 0 1 -1 0 0 0 0 ........(72 numbers) and i name this contrast as group-x-tempole.mtx then my second variable is lh.cuneus then my contrast matrix is 0 0 0 0 1 -1 0 0 0 .....(72 numbers) then i name it as group-x-cuneus.mtx. Is this the way to create or is there a simple way to this. Bottomline is i want to compare the differences in cortical thickness values between two groups in all the regions reported in aparc.stats. 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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fsgd file from qdec
by Rajagopalan, Venkateswaran 07 May '10

07 May '10

Dear All, I am new to freesurfer. I am wondering is it possible to save the fsgd created automatically by qdec. 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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merging lh and rh white and pial surfaces
by Alexander Opitz 07 May '10

07 May '10

Hi I would like to have a single white and pial surface for FEM based field calculation in the brain. I got these surfaces by tesselating from filled.mgz and ribbon.mgz by changing the values in the volume files. Unfortunately the surfaces don't have the acquired quality I need. They show some topological inaccuracies. Is there a way to use the freesurfer tools for topology fixing from starting with a single white matter surface? Cheers Alex -- Alexander Opitz Magnetic Resonance Center Max Planck Institue for Biological Cybernetics Tübingen

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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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