[Freesurfer] rerunning FS data with FS 5.1.0

Dear FreeSurfer developers, We are planning to rerun previously processed data (3 waves) with the newest FS version from scratch. We have some questions before starting the pipeline. 1) to keep white matter edits is it enough to copy tmp/control.dat file or we need to copy the complete FS tree

[Freesurfer] downsampling surface in native space

Dear FS experts, I would like to downsample a subject's white surface to arrive with a smaller number of vertices in order to feed the surface into FSL's surface tracking. I tried to map the fsaverage6 onto the single subject: mri_surf2surf --hemi lh --srcsubject fsaverage6 --sval-xyz white --t

Re: [Freesurfer] Talairach Failure Detection

Hi Daniel what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion. Unfortunately it did not fix the error.  I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talaira

Re: [Freesurfer] TRACULA some fiber volumes being too small

There were recently a few messages on the list regarding this. What you should do is include "set reinit=1" in your config file, and then run trac-all -priors -c $CONFIG trac-all -path -c $CONFIG Make sure you only include the pathway of interest in the config file; otherwise, it will re-run the

[Freesurfer] visualize defects using tkmedit

It is possible to visualize topological defects in tksurfer by loading the curvature from surf/?h.defect_labels. Is there any way to visualize these defects in tkmedit? I am having trouble seeing how the defects are related to wm.mgz, etc., in tksurfer, and it would be very helpful if there were

Re: [Freesurfer] FW: TRACULA some fiber volumes being too small

Hi Fernando - Thank you for your kind words. You can indeed try the reinit option as Christofer suggested when one of the pathways looks like a single curve and not like a volume. However, because some of your other pathways in the screenshots look a bit funky too, I would also check that th

Re: [Freesurfer] downsampling surface in native space

Hi Franz, try mapping the xyz coordinates of the individual into fsaverage6 (or fsaverage5 or lower) space. This should solve both of your problems (I think). doug On 10/18/2012 07:53 AM, Franz Liem wrote: > Dear FS experts, > > I would like to downsample a subject's white surface to arrive wit

Re: [Freesurfer] Mixed-effects models for longitudinal data analysis in Freesurfer

Is training a within subject factor or between? If between, then you can do it as a two group design as I described in a post yesterday. doug On 10/17/2012 08:04 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote: > Hi Doug, > > Is it possible to add an extra factor to this repeated measures fs

Re: [Freesurfer] visualize defects using tkmedit

Try using the defect-seg script. It will create labels and segmentations of defects that you can visualize. Run it with --help to see how to run it and call tkmedit and tksurfer to visualize the defects. doug On 10/18/2012 10:41 AM, Benjamin Kay wrote: > It is possible to visualize topological d

Re: [Freesurfer] Cortical thickness percent difference surface maps howto

Hi Knut, if you have a glm analysis, set up a contrast for group1 vs 0 and group2 vs 0. This will create gamma.mgh files that are the mean thicknesses for each group. You can then compute the mean: fscalc group1/gamma.mgh add group2/gamma.mgh div 2 -o group.mean.mgh Then compute the percent diffe

Re: [Freesurfer] Probably activation due to vessels

It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data i

Re: [Freesurfer] withe matter of cortical Lables

Hi Gabriel, don't use the ASegStatsLUT.txt ctab file. It will only report the volumes of structure in the ctab, and that ctab does not have the WM parcellations. You can use FreeSurferColotLUT.txt instead. When you use --empty, this will report on *everything* in the ctab, which will probably b

Re: [Freesurfer] Talairach Failure Detection

Hi, I did recon-all -i -s and then what Nick posted. 2012/10/18 Bruce Fischl > Hi Daniel > > what was your original data format? Did you start with dicoms? > Bruce > > On Thu, 18 Oct 2012, Daniel Ferreira wrote: > > Thanks Nick very much for your suggestion. >> Unfortunately it did not fix

Re: [Freesurfer] downsampling surface in native space

Hi Doug, thanks for the answer. This works great. Franz Am 18.10.2012 um 17:37 schrieb Douglas N Greve: > Hi Franz, try mapping the xyz coordinates of the individual into > fsaverage6 (or fsaverage5 or lower) space. This should solve both of > your problems (I think). > doug > > > On 10/18/2

[Freesurfer] Cortical thickness percent difference surface maps script in matlab feedback wanted.

Dear Freesurfer expert I have produce a script to make percent difference in cortical thickens using information from the mailing list. Could you please take look if this script is correct, or if there is a better way to do it? function [ out ] = diff_map( difference, average ) %percent differ

Re: [Freesurfer] Cortical thickness percent difference surface maps script in matlab feedback wanted.

how about this instead? out = difference; out.vol = 100*difference.vol./average.vol; On 10/18/2012 04:00 PM, Knut J Bjuland wrote: > Dear Freesurfer expert > > I have produce a script to make percent difference in cortical thickens using > information from the mailing list. > Could you please