[Freesurfer] Brain volume covariate problem in QDEC

Hello, I am using Qdec to analyze thickness (etc) using various IVs (e.g., Verbal IQ) while controlling for cortical grey matter volume (or ICV) as a nuisance factor. With the exception of the IV Sex, every time I run the analysis it goes into an endless loop, sporadically stating that the "Matri

[Freesurfer] Is this normal when importing the annotations in tksurfer?

Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurf

Re: [Freesurfer] manual editting problem

Hi Jing, You have some white matter voxels missing in the wm.mgz for the rh. You can add some wm to that volume using the edit tool or you can also try control points. If you are adding wm, make sure you select the aux volume on the brush info toolbox. Fill in wm voxels for all slices. Control po

Re: [Freesurfer] manual editting problem

Can you send an image? On Sep 15, 2011, at 6:38 PM, Sita Kakunoori wrote: > > How does the wm.mgz look. Correcting the white surface will correct the > pial surface as well. > > Sita. > > > On Thu, 15 Sep 2011, Jing Ming wrote: > >> >> Hi Surfers: >> We have been coming >> across seve

Re: [Freesurfer] FSGD Contrast Setup Question

Hi Josh, With sophisticated mixed modeling procedures that use MLE estimation (e.g., SAS's PROC MIXED) it would be possible to use all your data while still modeling the necessary covariances. If you extracted ROI-based measures that would be a possible approach you could take. However, I don't

Re: [Freesurfer] manual editting problem

How does the wm.mgz look. Correcting the white surface will correct the pial surface as well. Sita. On Thu, 15 Sep 2011, Jing Ming wrote: > > Hi Surfers: >We have been coming > across several gray matter regions that are not included within the pial > surface (red line) when it should be

Re: [Freesurfer] FSGD Contrast Setup Question

Hi Josh, there is not a way that I know of to do the paired analysis if some are missing a scan. A "real" statistician might know of a way theoretically, and I might be able to implement that theory, but I don't know myself. So does that mean you want to do an unpaired test? doug Roffman, Josh

Re: [Freesurfer] mri_glmfit simulator

Hi Antonella, have you looked at the help (--help) for the mri_glmfit and mri_glmfit-sim functions? If you still have questions after that let me know. doug ps. If you're still learning about multiple comparison correction, I would recommend reading the following papers. They discuss validatin

Re: [Freesurfer] using mri_label2label with full path

Hi Chris, I think you are a little stuck. One thing you can do is to run recon-all with the -no-ba-labels switch as the last arg. This will prevent it from running that part of the code. You might then be able to run recon-all with only the -ba-labels switch in a separate process. doug Chris w

Re: [Freesurfer] FSGD Contrast Setup Question

Hi Adam, you have a "repeated measures" design. In your case, this is best handled using a paired analysis. You can search for "paired" on the wiki to get instructions. The easiest way to do this is to run mris_preproc with the --paired-diff option, then follow the instructions for the "standar

[Freesurfer] Errors in Cortical Parcellation

Hey there, I was excited to find out that Freesurfer has two atlases built in which do cortical parcellation as I am trying to do analysis on the precentral gyrus ROI only. However, when creating a mask showing the pre-central gyrus parcellation, I noticed that in the middle of the gyrus the al

[Freesurfer] manual editting problem

Hi Surfers: We have been coming across several gray matter regions that are not included within the pial surface (red line) when it should be (e.g., very anterior parts of the temporal lobe). From my understanding of similar posts on the forum, it seems that there isn't a way to add this

[Freesurfer] mri_glmfit simulator

Dear Doug, Can you please give me some details about how the corrections by multiple comparisons are done? Which step in the following code is doing the corrections? Are the corrections for multiple comparisons done by cache or by cwpvalthresh or the corrections are done by some parts that are

[Freesurfer] tkmedit bus error

Hi FSusers I run recon-all in a patient without problems, but when I tried to view it in tkmedit, an error pops up. I appreciate your help! Best regards, Carolina recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT 2011 done cvalencia-Precision-WorkStation-T3400:~> tkmed

Re: [Freesurfer] Talairach transformation

Dear all, indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria - Original Message - From: "Avi Snyder" To: "Sita Kakunoori" , fel...@cbs.mpg.de, "Avi Snyder" Cc: