[Freesurfer] Qdec - generate stats data table

Hello, I was running the tutorial on Qdec, when I went to generate stats data, it started running fine, and then I got the following error message: aparcstats2table --hemi rh --parc aparc.a2005s --meas area --tablefile

[Freesurfer] editing pial surface

Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can somebody please help me with that? Do I need a middle button on the mouse for it? Attached you

[Freesurfer] Robust register

Hi, I would like to use mri_robust_register to co-register b-volumes to the reference b0-volume in a DTI dataset. The documentation informs that it is not quite suitable in case of large intensity differences which apply to my case. How to proceed? Is a dev version available for this purpose?

Re: [Freesurfer] mkheadsurf and smseghead

Hi Will Doug is out of email contact until next week, and I suspect he's the best one to help you. If you haven't heard by mid week can you repost? cheers Bruce On Thu, 22 Mar 2012, Will Woods wrote: Hi, In my previous lab, which I no longer have access to, we ran mkheadsurf as part of

Re: [Freesurfer] editing pial surface

Hi Julia it's really hard to tell from just this image. If the problem is the skull strip removing voxels you can use the clone tool to paint them back in from another volume like the T1.mgz. Are you sure it's not dura or pial vessels? Where in the brain do you mean? cheers Bruce On Thu, 22

Re: [Freesurfer] mkheadsurf and smseghead

Hi Will, I noticed this as well. I don't know Doug's thinking, but I suspect it was just to avoid generating lots of files. The new script overwrites the lh.seghead, when smoothing. I would just update your script to use lh.seghead instead of lh.smseghead. HTH D Will Woods wrote: Hi, In

Re: [Freesurfer] editing pial surface

Hi Julia, Are you editing on a Mac? -Louis On Thu, 22 Mar 2012, Richter, Julia wrote: Hi freesurfer experts, I am trying to correct the pial surfaces of my data. I was able to remove voxels with the right button of my mouse, but unfortunately, it didn't work out to add voxels. Can

[Freesurfer] Displaying results from qdec on a single subject

Hi All, Is it possible to resample a .sig file from a group thickness analysis in qdec so that the results could be displayed on a single subject's anatomy rather than the fsaverage anatomy in tksurfer? Thanks, Emily -- Emily J Rogalski, PhD Assistant Research Professor Northwestern

Re: [Freesurfer] Displaying results from qdec on a single subject

Hi Emily yes, mri_surf2surf should do this for you. cheers Bruce On Thu, 22 Mar 2012, Emily Rogalski wrote: Hi All, Is it possible to resample a .sig file from a group thickness analysis in qdec so that the results could be displayed on a single subject's anatomy rather than the

[Freesurfer] Future of freesurfer

Hi all, I'm currently compiling/installing freesurfer on mac osx lion, ubuntu 12.04 (will be relased soon) and lots of packages which are required by freesurfer appear to be outdated. Is there any step-by-step installation/compilation tutorial somewhere in the web? Therefore I have a couple of

[Freesurfer] calculating DLPFC or frontal lobe grey and white matter volumes

Dear All We want to find frontal lobe grey and white matter volumes in a patient group to compare it with control group. In particular, we want to see the grey and white matter volumes in the dorsolateral prefrontal cortex (DLPFC). However we seem to

[Freesurfer] Spot Opened in Boston FreeSurfer course

Hi everyone, We had a last minute drop-out from our Boston FreeSurfer course which takes place April 2nd through the 4th. If anyone is interested in taking this spot, please let me know. Details about the course content, the registration fee, and other logistics can be found here:

[Freesurfer] Checkout release and stable branch

Hi all, I followed the instructions on the wiki but it seems impossible to checkout the stable and release branches? [toor@linux:x86_64-Linux]...or/cvsroot/test$cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r stable5 stable cvs server: cannot find module `stable'

Re: [Freesurfer] Checkout release and stable branch

the last arg should be 'dev', not 'stable'. Hi all, I followed the instructions on the wiki but it seems impossible to checkout the stable and release branches? [toor@linux:x86_64-Linux]...or/cvsroot/test$cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r

Re: [Freesurfer] Checkout release and stable branch

Thanks for the quick answer :) I'm not very familiar with cvs and was assuming 'stable' was only the name of the directory in which the code would be checked out! Thanks! Nicolas On Thu, Mar 22, 2012 at 3:09 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: the last arg should be 'dev', not

[Freesurfer] make_average_subject failure

Dear Freesurfers, Command line: make_average_subject --out average --subjects ... (n=60) . . . . . Applying LTAtransformInterp (resample_type 1) writing to /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh... ERROR: failure writing

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable: POSIXLY_CORRECT=1 It causes bc (on Debian/Ubuntu) systems to fail

Re: [Freesurfer] make_average_subject failure

did you run out of disk space? Does that path exist? On Thu, 22 Mar 2012, Klein, Holger wrote: Dear Freesurfers,  Command line: make_average_subject --out average --subjects ... (n=60)  . . . . . Applying LTAtransformInterp (resample_type 1) writing

[Freesurfer] QDEC with cluster-wise p=.1

Hello FreeSurfers, I want to do several cluster-wise corrections at a p value of .1, preferably in QDEC. To create the new template cluster, I am using this command: mri_mcsim --o test --base mc-z --surf fsaverage lh --nreps 1 --fwhm 10 Is there a way that I can tell mri_mcsim to do a

[Freesurfer] Jacobian Questions

Hello, Since the jacobian files contain only positive numbers, is there any way to make a distinction between a brain area that needs to be stretched bigger to fit the template versus a brain area that needs to be squished smaller? fsaverage is comprised of 40 subjects, but I wonder if the

[Freesurfer] Cortical Normalization Questions

Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area

Re: [Freesurfer] Jacobian Questions

Hi Jeff 1 means compressed and 1 means expanded. You can take the log if you want to turn it into the real line. I'm not sure age matters that much for the white matter surface, although it would for the pial one cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, Since the

Re: [Freesurfer] Cortical Normalization Questions

Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said

Re: [Freesurfer] Cortical Normalization Questions

Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH

Re: [Freesurfer] Cortical Normalization Questions

Yes, I think Mike's approach is a good one also, although you have to be clear about the somewhat different hypothesis you are testing On Mar 22, 2012, at 9:15 PM, Michael Harms mha...@conte.wustl.edu wrote: Hi Jeff, I personally like the idea of using average thickness as a covariate to