Re: [Freesurfer] Binary volume to surface label

Hi Jonathan what is the label? What space is it in? If it has gray/white contrast you could try bbregister. cheers Bruce On Sat, 11 May 2013, Jonathan DuBois wrote: Hi Freesurfer Experts,  I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to regis

[Freesurfer] Still confused by group analysis..

Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg

Re: [Freesurfer] Binary volume to surface label

Hi Bruce, Thanks for the quick response. The label is a manually traced area of the cortex. It is in subject scanner space and has a single value, so it probably would not work with bbregister. I can load it in tkmedit as a segmentation and the alignment is correct. I attached a screenshot. Is the

Re: [Freesurfer] Binary volume to surface label

Hi Jonathan you don't need to register it if it's shown properly in tkmedit or freeview. Can you tell us more about what you are trying to do? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce,  Thanks for the quick response. The label is a manually traced area of the cortex. It is

Re: [Freesurfer] Binary volume to surface label

Hi Bruce, I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best, Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: > Hi Jonathan > > you don't need to register it if it's shown properly in tkmedit or > freevi

Re: [Freesurfer] Binary volume to surface label

try using --regheader cheers Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: Hi Bruce,  I would like to convert the .mgz label volume to a surface label for that subject, but mri_vol2surf requires a registration file. Best,  Jonathan On Sunday, May 12, 2013, Bruce Fischl wrote: Hi J

[Freesurfer] Restricting ROI Analysis

Hi everyone, We are trying to restrict an analysis using Qdec to a region of interest. We have successfully created the ROI mask, however the analysis continues to be run on the entire brain. Any help is greatly appreciated. Thanks, Skyler and Jon -- Skyler G. Shollenbarger Graduate Studen

Re: [Freesurfer] Binary volume to surface label

I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mgh It ran without error, but I could not open the resulting file in tksurfer as either a label or an overlay: - /Applications/freesurfer/tktools/tksurfer.bin: no data in label fi

Re: [Freesurfer] Binary volume to surface label

Hi Jonathan try -output_type mgh. It should create a "volume" that is nvertices long. Not sure if it can directly create a label file, maybe Doug knows? Bruce On Sun, 12 May 2013, Jonathan DuBois wrote: I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --m

[Freesurfer] Correction for multiple comparisons question

Hi Freesurfer experts, I was wondering about three things concerning the use of the mri_glmfit-sim command: 1) I tried running it with the --2spaces flag in order to Bonferroni correct over the two hemispheres but it tells me that the specific flag is not recognized. Is there another way to co

[Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

This is available online now: http://authors.elsevier.com/sd/article/S1053811913005053 On 5/7/13 3:10 PM, "Bruce Fischl" wrote: >actually Matt Glasser points out that a brief description is in his paper >that is coming out soon, and there is also some description in Andre's >multi-echo mprage

Re: [Freesurfer] Correction for multiple comparisons question

Hi Panagiotis, On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote: > Hi Freesurfer experts, > > I was wondering about three things concerning the use of the mri_glmfit-sim > command: > > 1) I tried running it with the --2spaces flag in order to Bonferroni correct > over the two hemispheres but it te

Re: [Freesurfer] Restricting ROI Analysis

Hi Skyler, I don't think we have the ability to restrict the analysis to an ROI in QDEC. You can do it with mri_glmfit with the --mask or --label option. doug On 5/12/13 4:25 PM, Skyler Gabriel Shollenbarger wrote: > Hi everyone, > > We are trying to restrict an analysis using Qdec to a region

Re: [Freesurfer] Binary volume to surface label

It cannot create a label file directly. What happens when you try to load it as an overlay? Make sure to set the threshold to 0.5. Also, before going to the surface load the binary volume onto the anatomical with the surfaces to make sure that the surfaces pass through the mask. doug On 5/1

Re: [Freesurfer] thickness

On 5/11/13 7:41 PM, Tudor Popescu wrote: Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while fact

Re: [Freesurfer] Usage of --area option in estimating the vertex-wise maps of surface area

Hi Xi-Nian, it does not do the same thing, but it does something similar. Anderson found that it gave similar results in a lot of cases, but he has found some differences. If he's still following the FS list, maybe he can comment. doug On 5/11/13 9:53 PM, Xinian Zuo wrote: Hello Doug,