Re: [Freesurfer] define four major fiber tracts

Dear Anastasia Yendiki , Thanks so much, I will read them. Yours, Lulu 2013/10/15 Anastasia Yendiki > > Hi Lulu - We actually have an automated method to do this. You can read > about it in our paper: > http://www.frontiersin.org/**Neuroinformatics/10.3389/** > fninf.2011.00023/abstrac

Re: [Freesurfer] Tracula configuration error

Hi Michael - It doesn't look like the configuration file is the problem, or at least I cannot replicate it. I ran "trac-all -c dmrirc.txt -prep" on a mac and a linux machine and the only error I got was that the SUBJECTS_DIR doesn't exist (as expected since I don't have your directory structu

Re: [Freesurfer] bvecs and bvals don't have the same number of entries

Hi Laura - I don't think the error "bvecs and bvals don't have the same number of entries" should have to do with interspersed zero b-values. When you run "wc -l" on the bvecs and bvals files, what do you get? a.y On Mon, 14 Oct 2013, Laura Christine Anderson wrote: > Hi Anastasia, the bval/b

Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Hi Vincent, 3. It's a pain, isn't it? I sympathize but looking at the data is always a good idea. Since you'll see all 3 views in fslview, the dark slices will look like dark lines in two of these views, so you don't have to scroll through slices. There's a couple of things you can do about mo

Re: [Freesurfer] TRACULA statistics

Hi Anastasia, thanks for you answer. Now I have understood the meaning of that parameter. Best regards Lucia On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: > > Hi Lucia - It's how many sample paths were drawn to produce the probability > distribution of the path (path.pd.nii.gz). It

Re: [Freesurfer] TRACULA statistics

Hi Lucia - It's how many sample paths were drawn to produce the probability distribution of the path (path.pd.nii.gz). It depends on the configuration parameters (nsample, nkeep), so it'll be the same if these configuration parameters are the same. Hope this helps, a.y On Mon, 14 Oct 2013,

Re: [Freesurfer] Tracula configuration error

Hi Michael - It's hard to tell at which point it fails. Is there any output, is there a trac-all.log? If so, can you please attach the entire file, as well as the entire configuration file? Thanks, a.y On Sat, 12 Oct 2013, Michael Datko wrote: Hello,I have been trying to set up a working T

Re: [Freesurfer] define four major fiber tracts

Hi Lulu - We actually have an automated method to do this. You can read about it in our paper: http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract And you can learn how to use it here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula If you wanted to do this manually

Re: [Freesurfer] QA in Tracula

Hi Gari - What you're describing is something that may happen if the initialization of the tract fails. You can repeat with a different initialization by adding "set reinit = 1" and rerunning the -prior and -path parts. You should do this only for the subject and tract that has this issue, so

Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Hi Anastasia! I will go backwards with increasing difficulty for me to understand everything: 4. I see, yes this would not make sense. Thank you for the explanation! 3. With fslview I will have to run through 393,120 slices, then. (72 slices in z-direction for our 70 DWI scans for tp1 and tp2 fo

Re: [Freesurfer] Qdec taking a very long time

Did you run recon-all with -qcache? If not, then it is having to preprocess all the data (ie, sample to common space and smooth). It will take the same amount of time with -qcache, but it will store (ie, cache) the results so that it will only take a few minutes if/when you run it again. Still

[Freesurfer] Fwd: OHBM 2014 Call for Council Nominations

Original Message Subject:OHBM 2014 Call for Council Nominations Date: Mon, 14 Oct 2013 09:50:14 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear OHBM Mem

[Freesurfer] TRACULA statistics

Dear all, I noticed that in the TRACULA statistics output files (pathstats.overall.txt) the variable "Count" that should indicate the number of sample paths in the WM tract is the same for all the computed tract. Could anyone tell me why this happen? Thanks a lot Regards Lucia _ _ _ _ _ _ _

Re: [Freesurfer] regions in FreeSurferColorLUT.txt and the atlas

Hi Xinyang left/right vessel are I believe small labels that the CMA includes for vessels in the basal ganglia that would otherwise be labeled lesion. The gca is an internal format, but you can view the contents using freeview. Something like: freeview -v # where the 'frames' show you dif

[Freesurfer] Qdec taking a very long time

Hi FreeSurfers I am quite new to freesurfer. I am trying to run a GLM analysis on some FreeSurfer data. I am analysing volume (surface based) with a smoothing of 5mm, using one discrete factor and one covriate on 252 subjects. I started the analysis on Friday 4th October. Its now been 8 days a