Re: [Freesurfer] How to calcutate Brain volume?

Dear Cedric, Thanks a bunch. I'll try with mri_label2label. From: Koolschijn, Cédric p.c.m.p.koolsch...@uva.nl To: Anupa AV av.an...@yahoo.com Sent: Monday, April 15, 2013 1:07 PM Subject: Re: [Freesurfer] How to calcutate Brain volume? Dear Anupa, The

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Looking at the image posted previously. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were missed by 5.2 in this

[Freesurfer] 32 bit ubuntu in a 64 bit workstation- Problem

Dear All, I'm working with a system, where 32 bit ubuntu is loaded on to a 64 bit computer. Previously there were graphics problem (Screen gets stuck-- So I restarts it and 'll log in again). Now I'm facing a problem where I cannot enter into ubuntu. Any solutions for this problem will be

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

The 5.2 image has been smoothed, by a small degree, relative to 5.1. Either prior to FS processing or by FS, it would seem. On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell christopherbell2...@gmail.com wrote: Looking at the image posted previously.

[Freesurfer] convert MNI152 mask to label file

Hi all, I want to convert a mask I made in MNI152 space using the Harvard-Oxford Atlas into a (subcortical) label file so that I can run an ROI analysis using func2roi-sess. Does anyone know what commands I would need to do so? Thanks! Emily___

Re: [Freesurfer] creating new curv/thick/area files using tweaked white/pial

Hi Fred mris_thickness will make thickness. Not sure we have anything to make area. I guess you could try setting -n 0 in mris_make_surfaces to it runs for 0 iterations. Or we can put something together to create area - it should be trivial cheers Bruce On Mon, 15 Apr 2013, Fred Dick wrote:

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Daniel, Unfortunately, since I run all the individuals again with FreeSurfer 5.2, I just saved from the 5.1 the info I was using for comparison between version - the aseg stats. I don't have cortical thickness information for 5.1 unless we run all the cases again in 5.1

Re: [Freesurfer] creating new curv/thick/area files using tweaked white/pial

Hey, thanks Bruce. I will let you know what happens with -n 0. Area not a big deal for this. cheers, Fred On 15 Apr 2013, at 14:32, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Fred mris_thickness will make thickness. Not sure we have anything to make area. I guess you could try

[Freesurfer] pial surface with FLAIR

Dear all, I have already run the FreeSurfer 5.2 -all, and I would like to improve the pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following syntax: recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial It

[Freesurfer] Job: Postdoc in Cognitive Neuroscience at Haskins Laboratories

Postdoctoral position in Cognitive Neuroscience at Haskins Laboratories Applications are solicited for a postdoctoral fellowship in Cognitive Neuroscience at Haskins Laboratories. Applicants should have a Ph.D. in psychology, linguistics, cognitive neuroscience, or a related field. The

Re: [Freesurfer] pial surface with FLAIR

Hi Veronica, we haven't seen that before. Can you upload your subject including the FLAIR and we'll take a look? thanks Bruce On Mon, 15 Apr 2013, Popescu, Veronica wrote: Dear all, I have already run the FreeSurfer 5.2 -all, and I would like to improve the pial surface recongition using

Re: [Freesurfer] using volume label mask in mri_vol2surf

Hi Fred, why do you want to save it as a wfile? We're trying to phase wfiles out. Can you use mgh format? doug On 4/15/13 12:56 PM, Fred Dick wrote: Hey again sorry, I seem not to be able to accomplish this very simple thing! First wrote out mask as .w file using vol2surf, but

Re: [Freesurfer] using volume label mask in mri_vol2surf

Hey I wrote out to .w since I couldn't write to curv. (And I'm old fashioned!) But actually it's because I am really behind the times and forgot that .mgh was also used for surface data. And yup, this worked fine. So in answer to my question 'Bug or stupidity' - the latter! Thanks Doug, Fred

Re: [Freesurfer] unit of corpus callosum segmentation

Hi Marie, But division by 5 would give the average area of the 5 mid slices. Maybe that is even more meaningful (reliable) than just a single slice. Best, Martin On 04/14/2013 09:05 AM, Bruce Fischl wrote: Hi Marie, no, that won't account for variability across slices in the l/r direction.

Re: [Freesurfer] pial surface with FLAIR

Veronica, Hi, can you copy me on the subject data upload? You can upload data here: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Mon, 2013-04-15 at 12:30 -0400, Bruce Fischl wrote: Hi Veronica, we haven't seen that before. Can you upload your subject including the

Re: [Freesurfer] setting thresholds in qdec

Thanks Nick -- that fixed it. -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel:

[Freesurfer] Use our own training subjects?

Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our

[Freesurfer] recon-all problems [solved]

I had several problems testing freesurfer 5.2 installation, as previously posted. Now it is all OK and I would like to share what I could learn: 1- It does not work on Fedora 18 (segfaults with all tests with tkmedit, tksurfer and recon-all) that is due to a restriction imposed by glibc (only

Re: [Freesurfer] QDEC questions

Tudor, In the recon-all.log, it has this line: ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh correctly, so this indicates to me that it might have run out of disk space. is that the case? to answer the others: 2.

Re: [Freesurfer] recon-all problems [solved]

Marcos, Thanks for looking into this. We dont have a Fedora 18 system to replicate the problem on, but we're looking at the section of code described in bugzilla report. We may need your help to test any fixes we devise. Nick On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote:

Re: [Freesurfer] recon-all problems [solved]

Marcos, Can you give this version of tkmedit a try on your Fedora 18 system? ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ you will need to copy tkmedit.bin to your freesurfer/tktools directory (not the freesurfer/bin directory). you may need to type this to

[Freesurfer] recon-all for multiple subjects using for loop

Dear FS experts, I'd like to know about the for loop command for running recon-all for multiple subjects. I went thru this link, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.html But didn't get much info. Can anyone please tell me how to run recon-all for

Re: [Freesurfer] pial surface with FLAIR

Hi Veronica, Did you try initially doing recon-all -i $FLAIR -s $SUBJECT? And then, when you do the remaining recon-all steps: recon-all -autorecon3 -s $SUBJECT -FLAIRpial It has worked for me. (And worked very well! No edits necessary for the pial surface!)

Re: [Freesurfer] recon-all for multiple subjects using for loop

Hello, In our lab, we create a txt file with all the subject names (as they appear on their respective folders). Name that txt file whatever you want (like * subs.txt*) and save it somewhere in one of the paths (we use /Users/* Home_User*). Then in terminal, after setting the environments for