Re: [Freesurfer] Problem with visualising hippocampal subfield segmentation

Hi Koen, Thanks, this solved the problem. Ed On 4 Apr 2012, at 19:21, Koen Van Leemput wrote: Hi Ed, It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file

Re: [Freesurfer] Stylus Input for Cortical Edits

Hi Jeff: We too have found Wacom tablets are great for editing and also these are easy on the back and eyes. best, Alan On Wed, Apr 4, 2012 at 6:46 PM, Emily Rogalski erogal...@gmail.com wrote: We have found Wacom tablets are excellent for editing. On Apr 4, 2012 4:40 PM, Jeff Stout

Re: [Freesurfer] white matter hyper intensities

Hi Greg, yes, that can happen where they are hyper-intense on T2 and hypo-intense on T1 and thus look like GM on the T1. It's not that common since they are usually deeper, but we have seen it. sorry Bruce On Wed, 4 Apr 2012, Gregory Kirk wrote: a collaborator just got a grant review

Re: [Freesurfer] How to flatten time course on the cortex

Hi Kaveh, yes, you can create a 2d patch using tksurfer to cut it out, then mris_flatten to flatten it. cheers Bruce On Thu, 5 Apr 2012, Kaveh Kohan wrote: Thank you for all replies. One more question to bother you. in : http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsrecon.ppt In

Re: [Freesurfer] Qdec issue

Sonya, it looks like subject 1005 is missing its aseg.stat file for some reason. confirm that it completed its recon correctly, then run: recon-all -s 1005 -segstats which will create the stats files. then qdec should run properly. it should not be necessary to use the -skip flag (thats use

Re: [Freesurfer] lobar WM volumes

You don't need to do 2b if all you want are the lobar wm segmentations. 2b should just copy the cortical labels into the new seg. mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz

Re: [Freesurfer] Mapping pf fsaverage surface to native volume

The template specifies the output geometry. When you specify --identity, you specify a particular transformation between the volume and the surface, so you can't change the target volume without specifying a different transform. I'm at a bit of a loss as to why this is not working. What is

Re: [Freesurfer] lobar WM volumes

Thanks, Doug. I actually want lobar both GM and WM. So would this be the correct syntax to generate lobar GM and WM labels? mri_aparc2aseg --ssubject --labelwm --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe Yes, I started to do as you suggest with tkmedit using FreeView, but I thought

Re: [Freesurfer] lobar WM volumes

Yes, that looks right to me doug On 04/05/2012 11:50 AM, Irwin, William wrote: Thanks, Doug. I actually want lobar both GM and WM. So would this be the correct syntax to generate lobar GM and WM labels? mri_aparc2aseg --ssubject --labelwm --rip-unknown --ctxseg aparc+aseg.mgz --annot

[Freesurfer] TRACULA trac-all -path does not generate all the paths

Hi all, Running TRAC-ALL - PATH, I've got a error. Strangely trac-all reports all jobs done without error as last, but actually it didn't generate any reconstructed paths. When I looking through the 'trac-all.log' file, I found only one error on dmri_mergepaths saying ERROR: must specify input

Re: [Freesurfer] white matter hyper intensities

interestingly, in this case i think there may even be reason why white matter hyper intensities could be more common in our insular region of interest where we detected thinning. The disease is HIV and activated monocytes invade the perivascular spaces where they can cause inflamation, which

Re: [Freesurfer] TRACULA trac-all -path does not generate all the paths

Hi Juke - Impossible to tell without looking at the output for the specific cases. Could you send the entire trac-all.log file for one of them? Thanks, a.y On Thu, 5 Apr 2012, Juke Cha wrote: Hi all, Running TRAC-ALL - PATH, I've got a error. Strangely trac-all reports all jobs done

[Freesurfer] Cortical Thickness

Dear Freesurfer group I want to get cortical thickness, and I am confused between using these two command lines: mris_anatomical_stats -t subjid/surfhttp://ads.clicksor.com/search.php?q=surf/lh.thickness -b subjid lh that gives following information number of vertices total surface area

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - If you upload this data set I'm happy to look at it. Also, I strongly recommend getting the updated version of trac-all from the wiki (I'm guessing from the log file that you're probably not using that?) See 2012/01/09 update here:

Re: [Freesurfer] Cortical Thickness

Whu when I use mris_anatomical_stats subjid lh, I get different result? Here average CT is 2.163+-0.898, while with 2 previous commands they were zeros. number of vertices = 110852 total surface area = 71971 mm^2 total gray matter volume=

Re: [Freesurfer] Error on Step 3 of longitudinally process

Sorry accidentally found your old email now. Anyway, the problem is the -- in the subject name. Either remove those or probably easier: name the base 10022_base Best, Martin On Mon, 2012-02-27 at 15:36 -0700, Brain Apprentice wrote: Hi, I was wondering if I am doing something wrong when

Re: [Freesurfer] aseg.mgz looks worse after longitudinal processing on 5.1

Hi BA, don't really know what you mean. The slices are slightly different and there are some differences but from these images I cannot say what is more accurate and what is not. Cheers, Martin On Mon, 2012-03-12 at 10:14 -0600, Brain Apprentice wrote: Hi Surfers, I have done some