[Freesurfer] Problem with CVS server?

Hi, I'm trying to download the source code from the cvs but it failed due to the following error: cvs [checkout aborted]: Could not map memory to RCS archive /usr/fscvsroot/dev/distribution/average/fsaverage.tar.gz,v: Cannot allocate memory Any problems with the cvs server? Your help will be ve

Re: [Freesurfer] How to get surface-based AAL template

Hi Thomas: There are no special reasons why i need the surface-based aal template. my goal is to parcellate surface into thousands of small brain areas, and construct large-scale cortical network. I have no idea how to segment the surface directly in FS. But i know the way to segment AAL t

Re: [Freesurfer] How to get surface-based AAL template

Hi Zhiliang You can use mris_make_face_parcellation Or mris_divide_parcellation directly in FreeSurfer to produce your own parcellation scheme Cheers Jürgen On [DATE], "ZhiLiangLong" <[ADDRESS]> wrote: > Hi Thomas: > There are no special reasons why i need the surface-based aal templ

[Freesurfer] MAking cuts using tksurfer

Dear All,   How to explore the "cut" tools in freesurfer using tksurfer? I'd like to make a cut along the vertex on the cortical surface (say, inflated) to divide medial and lateral components. How to do it after loading DKatlas labels and I want to cut along the vertex to divde medial and late

Re: [Freesurfer] Problem with CVS server?

I received the same error at that same file... I simply reissued the CVS checkout command and the process continued to completion. -Zeke On Apr 1, 2013, at 5:19 AM, Akio Yamamoto wrote: > Hi, > > I'm trying to download the source code from the cvs but it failed due to > the following error:

Re: [Freesurfer] MAking cuts using tksurfer

you might try using a cutting plane instead of having to draw the entire cut. cheers Bruce On Mon, 1 Apr 2013, Anupa AV wrote: Dear All,   How to explore the "cut" tools in freesurfer using tksurfer? I'd like to make a cut along the vertex on the cortical surface (say, inflated) to divide med

Re: [Freesurfer] More QDEC questions

On 03/29/2013 04:34 PM, Tudor Popescu wrote: > Thanks Doug, just to follow-up on some of these: > > > - why does QDEC only provide the volume of /subcortical/ > > structures under StatsDataImport/aseg.volume, when the automatic > > GM/WM segmentation is done for the entire brain, not j

Re: [Freesurfer] Error from mri_concat while using QDEC

Hi Tudor, That is unfortunate. You mention in the email below dated (Feb 1) that you got mri_concat working for you. If it worked for you then, but doesnt now, and nothing changed in the meantime, Im not sure there's much we can do to diagnose the issue. The mri_concat binary I sent you works in o

Re: [Freesurfer] Error from mri_concat while using QDEC

Thanks Zeke. I tried upgrading to the latest FS version, 5.2.0, but I see that the available download is only in .tar.fz format rather than in .VDI format, as v5.1.0

[Freesurfer] slice timing

Doug, I use preproc-sess 's -stc up option to time correct my slices. I only have 6 slices. Donald, I am not calculating absolute CBF values using the calibration scan. I pre-process the data and then either surround-subtract or just subtract tag from control to get CBF, would it still be a prob

[Freesurfer] slice timing

Doug, I use preproc-sess 's -stc up option to time correct my slices. I only have 6 slices. Donald, I am not calculating absolute CBF values using the calibration scan. I pre-process the data and then either surround-subtract or just subtract tag from control to get CBF, would it still be a prob

Re: [Freesurfer] slice timing

I would do the subtraction first then do the STC. On 04/01/2013 12:15 PM, Meryem Ayse Yucel wrote: > Doug, > > I use preproc-sess 's -stc up option to time correct my slices. I only > have 6 slices. > > Donald, > > I am not calculating absolute CBF values using the calibration scan. I > pre-proce

Re: [Freesurfer] slice timing

Yes. This would still be a problem. The calibration scan can either be used to get a single number or can be used to get voxel-wise values. For simplicity, lets say this is a constant across all voxels. The only thing that is a variable in the CBF equation would be the subtracted image values and d

Re: [Freesurfer] Problem with longitudinal edits

Was wondering if anyone from the Freesurfer team is looking into this issue yet. On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh wrote: > BTW, we are using Freesurfer 5.1: > freesurfer-i686-apple-darwin9.8.0-stable5-20110525 > > > On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh wrote: > >> Dear Developers

[Freesurfer] Doctoral (PhD) and Postdoctoral Position in Geneva, Switzerland

We invite applications for a Doctoral (PhD) and a Postdoctoral position at the Swiss Center for Affective Sciences (University of Geneva, Switzerland; www.affective-sciences.org/ ) and the Neuroscience of Emotions and Affective Dynamics Lab (Head: Prof. Didier Grandjean). We are seeking for high

Re: [Freesurfer] Problem with longitudinal edits

Hi Vy, not sure what it going on in your data. Surfaces are copied from the base and if they are not accurate there you need to fix it there. It seems you did that and you worked the edits in the right order. What exactly happened? You fixed cross and base and everything look fine. When you

Re: [Freesurfer] Problem with longitudinal edits

Also: brain.finalsurfs.manedit is mainly for correcting situations where the pial surface extends into the cerebellum. Did that happen in your case without editing? For other edits (e.g. pial including dura) you should fix the brainmask.mgz . Best, Martin On 04/01/2013 04:39 PM, Martin Re

Re: [Freesurfer] Problem with longitudinal edits

Hi Vy and Martin there was a bug in mri_mask that I just fixed that caused the brain.finalsurfs.mgz to be empty when the brain.finalsurfs.manedit.mgz existed. Vy: if you tell us what hardware/software platform you are using we can get you an updated version. Not sure if this will fix your prob

Re: [Freesurfer] Problem with longitudinal edits

Hi Martin, Thank you for getting back to me. To clarify what I did: 1. edited all cross-sectionals & reran until surfaces are accurate. 2. created the base from the cross-sectionals. 3. edited base & reran until surfaces are accurate 4. created longitudinal files from edited cross-sectionals & ba

Re: [Freesurfer] Problem with longitudinal edits

Hi Bruce, I just noticed this reply. Looks like you came to save the day! I am using a Mac OSX - Snow Leopard 10.6.8 (2 x 3 GHz Quad-Core Intel Xeon) Thanks, Vy On Mon, Apr 1, 2013 at 4:17 PM, Bruce Fischl wrote: > Hi Vy and Martin > > there was a bug in mri_mask that I just fixed that cause

Re: [Freesurfer] Problem with longitudinal edits

not sure it will fix your problem, but worth trying. Zeke: can you get Vy a new version of mri_mask and mris_make_surfaces. Vy: try out mri_mask first before replacing mris_make_surfaces as it's a bigger and far less tested change On Mon, 1 Apr 2013, Vy Dinh wrote: Hi Bruce, I just noticed

Re: [Freesurfer] How to get surface-based AAL template {Disarmed}

I believe that someone has created the AAL labels on the Colin 27 brain. These should be able to be transformed to the fsaverage brain. I've contacted the person who said they had the files and will let you know if I get the files and am able to transform the files. Best Regards, Donald McLaren =

[Freesurfer] qdec - 3 timepoints

Hi, I'm currently doing a long analysis of a data set that contains two groups (training and control) and 3 timepoints (baseline -BL, follow up1- FU1 follow up2-FU2) I've put it through qdec. But for the analysis qdec only gives me one measure for long.thickness-avg, rate, pc1 and spc. How do