[Freesurfer] ICV smaller than the brain

Hello, I asked a question similar to this last year when working with FS 4.3.1, and I'm hoping that there is something new in FS 5 that can help. I am having a problem where a lot of my subjects' brains are larger than the eICV. In FS 4.3.1, it is happening in about 70/140 subjects, and in FS 5,

Re: [Freesurfer] RAS to MNI coordinates of a label

I am using the coordinates obtained with the matlab function "read_label()". I send you one of my labels. Thanks a lot, Yolanda 2011/5/3 Douglas N Greve > Which coordinates are you using? Can you send me the label? > doug > > Yolanda Vives wrote: > >> Hi Doug, >> >> The problem is that when I p

[Freesurfer] subcortical volume and qdec

Dear freesurfer experts: I had processed my data with recon-all, and also ,I had compared the cortical thickness difference between the con and pat with qdec .however,when i I try to compare the sub-cortical volume difference between con and pat ,the results were the same as the thickness,

Re: [Freesurfer] resample data to surface that is already in conformed space

Hi Greg, you can use --regheader subjectname with mri_vol2surf doug GREGORY R KIRK wrote: > I have probabilistic tractography output that is already in freesurfer > conformed space, i need to resample > it onto the cortical surface, how can I ? > > i.e. mri_vol2surf does not have an option for th

[Freesurfer] resample data to surface that is already in conformed space

I have probabilistic tractography output that is already in freesurfer conformed space, i need to resample it onto the cortical surface, how can I ? i.e. mri_vol2surf does not have an option for the data already being in registration ( requires transform. i know i can load in freesurfer and sav

Re: [Freesurfer] autorecon1 after Talairach correction: can I re-run other than with -notalairach?

aga, no, its not possible to guide (initialize) the registration with your manual one. but if recon-all -s subjid -tal-check passes, then your tal check is likely good enough. n. On Tue, 2011-05-03 at 16:56 +0200, Agnieszka Burzynska wrote: > Dear all, > For one of my subjects I had to correc

[Freesurfer] How to determine gray matter in the aseg.mgz

Dear Experts, I would like to generate a gray matter mask using the aparc+aseg.mgz file. Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to deci

Re: [Freesurfer] Openmi version of freesurfer

On Tue, 2011-05-03 at 18:08 +0200, Knut J Bjuland wrote: > is ther any plans to produce an version of freesurfer for openmpi and/or > cuda 4.0? Do Anders Dale produce an version of freesurfer for openmi > interface that enable use of freesurfer on supercomputer? I would not expect a migration

Re: [Freesurfer] unable to use cuda 4.0.13 and cuda 3.2.16 with nvidia 270.41.03, fedora 14

On Tue, 2011-05-03 at 18:05 +0200, Knut J Bjuland wrote: > I have also installed cuda 3.2 with the same results. There might be an > error in CUDA Error in file 'devicemanagement.cu' on line 46 : invalid > argument. which I got when I used the latest nvidia driver with cuda 3.2 > Could anybody

[Freesurfer] Openmi version of freesurfer

HI is ther any plans to produce an version of freesurfer for openmpi and/or cuda 4.0? Do Anders Dale produce an version of freesurfer for openmi interface that enable use of freesurfer on supercomputer? Knut J Bjuland ___ Freesurfer mailing list Fre

Re: [Freesurfer] unable to use cuda 4.0.13 and cuda 3.2.16 with nvidia 270.41.03, fedora 14

I have also installed cuda 3.2 with the same results. There might be an error in CUDA Error in file 'devicemanagement.cu' on line 46 : invalid argument. which I got when I used the latest nvidia driver with cuda 3.2 Could anybody on this list try freesurfer with cuda and the latest nvidia drive

Re: [Freesurfer] RAS to MNI coordinates of a label

Which coordinates are you using? Can you send me the label? doug Yolanda Vives wrote: > Hi Doug, > > The problem is that when I put the coordinates in a MNI altas, it says > that they correspond to the caudate and not to the cingulate and I > would like to know if the procedure that I am followi

Re: [Freesurfer] RAS to MNI coordinates of a label

Hi Doug, The problem is that when I put the coordinates in a MNI altas, it says that they correspond to the caudate and not to the cingulate and I would like to know if the procedure that I am following is correct. Regards, Yolanda 2011/5/3 Douglas N Greve > Hi Yolanda, they should already be

[Freesurfer] autorecon1 after Talairach correction: can I re-run other than with -notalairach?

Dear all, For one of my subjects I had to correct the Talairach step manually. My manual correction, however, may not be perfect. Is it possible to re-run autorecon1 using the Talairach correction to GUIDE (but not REPLACE) the automatic registration? Thank you! Aga _

Re: [Freesurfer] A problem about mri_glmfit result

sorry, I mean to do it for both the FSGD file and the matlab script. I just tried it with your data and it works. doug soft.join Huang wrote: > Hi, doug. > > Thanks for your suggestion, but it does not seem to work. > After having divided the ICV by 1e6, I reculated the betas, and got > the si

Re: [Freesurfer] RAS to MNI coordinates of a label

Hi Yolanda, they should already be in mni305 coordinates, so the identity matrix is correct. Did you find a potential problem? doug Yolanda Vives wrote: > Hi all, > > I am interested in obtaining the MNI or talairach coordinates of a > label. The procedure that I have performed is the followin

[Freesurfer] Neuroimaging position

Applications are invited for a position at a Hospital Research Center in Barcelona, Spain. The position is full-time for 15 months (with a probable extension to 18 months). It entails working mainly on neuroimaging data. The postholder will help in analyzing functional, structural, and diffusion

Re: [Freesurfer] question regarding the comparison of two methods: repost

Hi Heidi, why do they have to be in a common space? You aren't comparing across subjects, just within subject across method. Or are you trying to make maps of accuracy? That will be hard to do unless you use our coordinate system to do your segmentation, which I assume you do not. In any case,

[Freesurfer] question regarding the comparison of two methods: repost

Dear FreeSurfers, We are comparing two methods to measure the volume of a subcortical structure (our method and FreeSurfer). We want to compare them spatially, by doing a voxel-based analyses. We thought to isolate the structure from the aseg.mgh as well as our own structure. Then we smoothe

[Freesurfer] RAS to MNI coordinates of a label

Hi all, I am interested in obtaining the MNI or talairach coordinates of a label. The procedure that I have performed is the following: First of all I have performed a QDEC analysis. From the results, I have drawn a label of a significant area of the brain, that corresponds to the cingulate. Afte

Re: [Freesurfer] Smaller Virtual Machine

So... What about this? Cheers :) El 29/04/2011 16:43, Pedro Paulo de Magalhães Oliveira Junior escribió: I'll check if it's public On Fri, Apr 29, 2011 at 11:40, Fidel > wrote: Thanks PPJ, I have made a fast search in Amazon's page and via google and I

Re: [Freesurfer] A problem about mri_glmfit result

Hi, doug. Thanks for your suggestion, but it does not seem to work. After having divided the ICV by 1e6, I reculated the betas, and got the similar results as before in Matlab, just the beta4 -- correspondent to ICV -- multiplied a 10^6. And then I computed the rank of matrix X that the value is 4