[Freesurfer] mirror hemispheres

Hello FreeSurfers, I wonder if it is possible to mirror my complete data, so that the right hemisphere will be the left one and the other way round. I was thinking about using this command: fslswapdim input z -x -y output and start with all the preprocessing steps afterwards. I want to use

Re: [Freesurfer] initial G-W contrast is negative

Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast. -Kathleen On 8/19/10 2:39

Re: [Freesurfer] initial G-W contrast is negative

That warning in and of itself is not critical, but it does suggest that the initial registration failed. I assume the registration still looks bad? Does this happen on a bunch of data sets or just this one? There are a couple of more steps. First, you can run with --init-fsl and check the

Re: [Freesurfer] mirror hemispheres

This does not work too well as the left hemi is registered to the right hemi atlas. This can create systematic LR differences that don't really exist. We are working on a symmetric template (and have been for a while). doug johanna feiler wrote: Hello FreeSurfers, I wonder if it is

Re: [Freesurfer] Automatic Plotting of Hemodynamic Response???

You don't have to specify a threshold at all. In that case it will average over the entire structural ROI. What you have below will average only over the positive values. What about the current stream is not streamlined? Or, how could it be improved? doug Adam Nitenson wrote: Hello

[Freesurfer] FreeSurferAlpha Label Volumes

Hello, I'd like to extract hippocampal and PHC volumes from files reconstructed with FreeSurferAlpha. Is there a command for this or would you recommend re-reconstructing to obtain label volumes? Thank you, Mona ___ Freesurfer mailing list

Re: [Freesurfer] FreeSurferAlpha Label Volumes

FreeSurferAlpha? Is this a new product? On Fri, Aug 20, 2010 at 15:08, Mona m...@nmr.mgh.harvard.edu wrote: Hello, I'd like to extract hippocampal and PHC volumes from files reconstructed with FreeSurferAlpha. Is there a command for this or would you recommend re-reconstructing to obtain

Re: [Freesurfer] FreeSurferAlpha Label Volumes

no, it's very, very old. Mona: you should definitely rerun everything On Fri, 20 Aug 2010, Pedro Paulo de Magalhães Oliveira Junior wrote: FreeSurferAlpha? Is this a new product? On Fri, Aug 20, 2010 at 15:08, Mona m...@nmr.mgh.harvard.edu wrote: Hello, I'd like to extract hippocampal and

[Freesurfer] Volume to surface dimension mismatch

I have a mask file which I need to overlay on the individual images of a group of subjects to extract thickness values within ht mask. But the mask is of dimension 2X2X2, will this be an issue? Thanks Lena ___ Lena Palaniyappan Clinical

Re: [Freesurfer] Volume to surface dimension mismatch

You'll have to sample that mask onto the surface using mri_vol2surf with the --interp nearest option. You will also have to have a registration matrix, which will depend on where the volume came from. doug Lena Palaniyappan wrote: I have a mask file which I need to overlay on the individual

Re: [Freesurfer] CUDA Error - all CUDA-capable devices are busy or unavailable

CUDA users, The problem with the _cuda binaries (message: CUDA Error in file 'devicemanagement.cu'...) has been fixed, and new binaries are available for download from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/ download the file

Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 42

Hi: Any solution for the 32 bit version ?... Sincerely, Gonzalo Rojas Costa Message: 6 Date: Fri, 20 Aug 2010 15:55:39 -0400 From: Nick Schmansky ni...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] CUDA Error - all CUDA-capable devices are busyor unavailable To:

Re: [Freesurfer] Volume to surface dimension mismatch

Doug, thanks So, is this a correct sequence: Im extracting thickness measures from VBM contrasts generated by FSL VBM analysis (this is 2X2X2): 1. To convert VBM contrast file to a binary mask: mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 (for fsl vbm generated corrp

[Freesurfer] Binary masks from aparc+aseg.mgz

Hi all, I'm creating binary mask volumes in a subject's native functional space from the segmented brain in aparc+aseg.mgz (FS v 4.5). I have found that doing this two different ways produces different results, and I'm wondering if anyone can illuminate why this might occur and which method is

Re: [Freesurfer] Volume to surface dimension mismatch

If the source is the FSL standard brain, then use $FREESURFER_HOME/average/mni152.register.dat as the registration. See if that works at stage 4. Lena Palaniyappan wrote: Doug, thanks So, is this a correct sequence: Im extracting thickness measures from VBM contrasts generated by FSL VBM

Re: [Freesurfer] Binary masks from aparc+aseg.mgz

The difference is the partial volume correction is different if there are a bunch of other labels there (aparc+aseg) vs only one label doug Timothy Vickery wrote: Hi all, I'm creating binary mask volumes in a subject's native functional space from the segmented brain in aparc+aseg.mgz (FS

[Freesurfer] IA64 release?

Hi, fsurfer team, I am just asking if there is any coming release of fs5.0 for ia64 cpu architecture? Thank you! Best, -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: (212) 263

Re: [Freesurfer] Binary masks from aparc+aseg.mgz

I see, thanks for the quick clarification. So in the Method 2 there is a chance that some voxels will show up in multiple ROIs, right? Is there a modification of Method 2 that maximizes that number of labeled voxels while ensuring that they will not show up in multiple ROIs? Thanks again, Tim

Re: [Freesurfer] Binary masks from aparc+aseg.mgz

you can play around with the fill threshold doug Timothy Vickery wrote: I see, thanks for the quick clarification. So in the Method 2 there is a chance that some voxels will show up in multiple ROIs, right? Is there a modification of Method 2 that maximizes that number of labeled voxels

Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 42

i've just posted the file 'fscudabins-linux-centos4.tgz' here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/ note that we have recently discovered a new problem with running mri_em_register_cuda on brains with skull: the results are off compared to the cpu version. so

[Freesurfer] ICV volume and 1.5T x 3.0T

Hi FS, I have two important doubts... Is it the CSF volume included in the ICV volume (aseg.stats)? Is it possible include in the same group patient acquired from 1.5T and 3.0T? Do you have an article about this topic? TK ___ Freesurfer mailing

Re: [Freesurfer] ICV volume and 1.5T x 3.0T

Thanks Doug. I'll do it! TK On Fri, Aug 20, 2010 at 7:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The ICV is not computed based on a sum of the volumes of individual structures. It is a summary measure computed from the registration to talairach space. See the wiki and Randy

Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 42

Hi Nick: I uncompress fscudabins-linux-centos4.tgz, but I continue to get the error: mri_em_register_cuda -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta Acquiring CUDA device Using default device CUDA Error in file

Re: [Freesurfer] Binary masks from aparc+aseg.mgz

Hi Doug, OK, just one last question! I've decided I'd rather use the smaller masks (generated by resampling aparc+aseg.mgz to functional space, as in my Method 1), since the difference is small (~2%), but there's absolutely no overlap in this case. Thus it's both the most conservative approach