[Freesurfer] GUI problem: Cannot open windows

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Dear Freesurfers, I have a problem with all tk* functions of FreeSurfer. It seems that whenever any of these functions try to open a window, they get stuck. Just typing tkmedit or tksurfer doesn't even show the manual entries. No error output is

[Freesurfer] Interpreting QA Tools Output -- Tal Normalization error?

Dear colleagues and experts, we would greatly appreciate any help in interpreting the results of the QA Tools. Please look at our attachments containing snapshots of the results html file after running QA Tools.

Re: [Freesurfer] FW: Re: ERROR: matrix is ill-conditioned or badly scaled

Hi Doug, I did. The email below is another FS user having the same error. Sander, I had the same problem due to having only 1 female in one of the groups (and correcting for gender). -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] FW: Re: ERROR: matrix is ill-conditioned or badly scaled

Hi both, That makes sense, however, as for my groups, all exceed 10 cases per combination for gender and scanner type (two dichotomous variables). But I also use Follow-time and age as covariate, might I need to recode those, to less unique combinations are possible? Thanks. Sander

Re: [Freesurfer] qdec table loading error

Scratch that - I simply changed the level name from blind to EB and it worked. Clearly qdec didn't like my naming assignments. Thanks anyway! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Thursday,

[Freesurfer] qdec table loading error

Hi FS experts, I'm having a really tough time trying to get my qdec.table.dat table to load into the qdec GUI. I have gone through the wiki painstakingly and have no idea why it's giving me this error message: Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using

[Freesurfer] recon-all compared to dev table

Dear freesurfer team, I'm very new to freesurfer, and I am currently working my way through the recon-all dev table functions (listed here: http://freesurfer.net/fswiki/ReconAllDevTable) step-by-step in preparation for processing a large amount of participant volumetric data. While doing so

Re: [Freesurfer] GUI problem: Cannot open windows

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Well this is a bit embarrassing: After another restart tksurfer and tkregister2 work normally. I'm a happy FreeSurfer user again. May this thread be helpful to at least one other person. Cheers, Michael On 07/05/15 11:22 , Michael Bannert wrote:

Re: [Freesurfer] mri_cvs_register using high resolution images

Oh, I see you do not have a recon for your high res volume. Could you try the below mri_vol2vol command with an additional -lta flag that has the transform that you computed to align your lowres and high res volumes? Lilla On Wed, 6 May 2015, Celine Louapre wrote: Thank you Lilla for the

Re: [Freesurfer] What to do about excessive topologic defect

Hi Bruce, The previous image I sent you was the filled.mgz image. Now, I've attached 4 more images: Using the command tkmedit sub296.fs wm.mgz -surfs -aux brain.mgz I've attached 1.) wm.mgz 2.) the image after pushing Show Aux Volume button (brain.mgz) Using the command tkmedit sub296.fs

[Freesurfer] Compute residual FWHM in GLM group analyses

Dear experts, I have run GLM group analyses on another software than FreeSurfer for personal needs. I have now beta coefficients and residual datas on fsaverage space. I'd like to use then the clusterwise correction for multiple comparisons provided by FreeSurfer. But I need for that to know the

Re: [Freesurfer] GUI problem: Cannot open windows

It s fairly common for a restart to be required after installing XQuartz (needed for the tktools). I dont know if you had just installed that package or not, but regardless Im happy its working for you now. -Zeke On 05/07/2015 09:14 AM, Michael Bannert wrote: -BEGIN PGP SIGNED

[Freesurfer] Interaction contrast setup

Hi all- I have been trying to determine the most appropriate way to set up an interaction contrast for glmfit. For my purposes I'm interested in looking at the interaction two performance variables while covarying demographics. I have 2 classes set to male and female and the first columns in my

[Freesurfer] tracking edits

Dear Freesurfer experts, I wondered how I might be able to track all the edits I make on each subject e.g., how many control points etc. But most specifically if there was a way to see how much ,numerically, the image has changed with manual correction following the initial FreeSurfer run.