Re: [Freesurfer] FreeSurfer use in dogs

Thanks Nick Bruce, Nick - I have high resolution T1W 3D scans, with 1mm voxel size and pretty good grey white matter contrast. Could you put me in touch with those that have used freesurfer on canine brains please? If I had a canine brain MRI atlas, similar to the Talairach atlas, could I

Re: [Freesurfer] Retinotopy stimuli

Hi all, Thank you very much! I did 2 runs of each of the stimuli I described in one session (I previously got some pretty decent maps from these data using the mrVista package from Stanford). I followed the retinotopy instructions from the FS wiki (

Re: [Freesurfer] A question about the Freesurfer version compatibility of Tracula

Hi Shanqing - As long as you have good aparc+aseg's for your subjects, the version should not be a problem. a.y On Thu, 7 Jul 2011, Shanqing Cai wrote: Hi, I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer. However, my data set are processed with the recon-all of

[Freesurfer] Freesurfer and VBM

Hello, I'm wondering if anyone could help me out with a question I had. For a study I'm working on, I'm comparing the regional brain volumes in adolescents with and without PTSD. I ran VBM analysis and Freesurfer on my subjects and I found some significant results on VBM (however, only using

[Freesurfer] muliple fressurfer instance and cuda

Hi When I have ran two or more Freesurfer instance in pc with one geforce gtx 460. I usually get a abort or memory corruption when running two or more Freesurfer instance. I usually get trouble when two ore more Freesurfer instance is in autocon3 phase of the recon-all protocol. Cheers Knut J

Re: [Freesurfer] muliple fressurfer instance and cuda

Try running only one GPU-assisted recon-all On Fri, Jul 8, 2011 at 10:02, Knut J Bjuland knut...@hotmail.com wrote: Hi When I have ran two or more Freesurfer instance in pc with one geforce gtx 460. I usually get a abort or memory corruption when running two or more Freesurfer instance. I

[Freesurfer] Mri_glmfit ERROR: dimension inconsistency in source data

Hi, During running fixed effects glm to combine runs, the analysis of all but one subject went fine. The log file contains this error message: mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval

Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30

Good morning Bruce, And many thanks again. Yes, bert inflated looks OK on the other computer. I will try to update the video card driver and see if this will fix the problem. In the mean time I have one more question: while running the recon-all on a new computer

Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30

Hi Antonella, where did you get NPI001.nii.gz? Can you send us the output of running mri_info on it? Sounds like it has more than one frame in it. What are the multiple volumes? cheers Bruce On Fri, 8 Jul 2011, Antonella Kis wrote: Good morning Bruce, And many thanks again. Yes, bert

Re: [Freesurfer] Freesurfer and VBM

Hi Ed, Thanks for that reassurance! Nice to know I didn't do something wrong! I'll have a read through of this literature, thank you so much!!! Fatima -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ed

[Freesurfer] mri_glmfit DOF error

Hello Freesurfers, I have a problem with mri_glmfit. I performed the analysis on two FA data. My fsgd is: GroupDescriptorFile 1 Title SUBJ_FA Class PRE Class POST Input FA_1 PRE Input FA_2 POST group_difference.mtx: 1 -1 The results in cmd line DOF = 0 ERROR: DOF = 0 What does it mean this

Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30

now I'm confused. What computer are you running it on that does fail? On Fri, 8 Jul 2011, Antonella Kis wrote: Here is my results after running mri_info on the file NPI001.nii.gz (I can run recon-all for the same file on a different computer without getting this multiple frames error):

[Freesurfer] Error with multiple frames

Hi Bruce, Sorry for making you confused. The true is I have 3 computers in my office. On two of them (LNX2 and LNX3) I installed by myself the new version of the FS. LNX2 is the one on which the bert infalted surface is looking weird. LNX3 is working perfect ( I cross my fingers and hope

Re: [Freesurfer] Freesurfer and VBM

Fatima, I can't really say anything on this topic but I did want to point you to some information on FreeSurfer vs. VBM: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.WhataretheadvantagesofFreeSurferoverVBM.3F Allison On Fri, 8 Jul 2011, Ahmed, F, Me fah...@sun.ac.za wrote:

Re: [Freesurfer] cortical dysplasia

Hi Pedro, I tried to send you the image of my problem but the mailing list rejected my attachment, despite the file is only 769 k. How I can post an image in order to illustrate my problem? Thanks, Carolina 2011/7/7 Carolina Valencia cvalen...@linkdx.com.co Hi Pedro, Yes I have a case with

Re: [Freesurfer] Freesurfer and VBM

There are a couple of things that come to mind. - Are you sure you have the same GLM in both analyses? - It might not be the thickness that is changing. Try looking at the jacobian, curvature, and/or gyrfication - Examine the individual VBM results carefully to make sure that they are not being

Re: [Freesurfer] muliple fressurfer instance and cuda

2011/7/8 Knut J Bjuland knut...@hotmail.com: It work fine with just one GPU-assisted recon-all. Sorry, I messed up earlier, and didn't send my reply to the list. your experience makes sense, since the Freesurfer programs make no attempt to share the GPU beyond that which the driver imposes.

[Freesurfer] Optseq with Sparse Sampling

Hi, I'm planning to run an auditory experiment using a pseudo-sparse sampling design. Something like: 4 sec stim period + 2 sec acquisition + 4 sec stim period + 2 sec acquisition ... So for example, I'd like to find an optimal sequence for a design with a TR of 6 seconds but where the stimulus