Re: [Freesurfer] Inaccurate Surfaces Generated

Hi Bruce, Thank you very much for taking a look at this for us. I uploaded it to your ftp server under the name JeffSadino_050089_S05.tar. About 70 of our subjects are showing similar problems. It seems to be happening more frequently in fs5 as compared to fs4. If you can find anything that wi

Re: [Freesurfer] .img unsupported data type ?

Dear Freesurfers, Bruce managed to convert the files on a Linux box. I will leave the virtualbox for what it is, get Linux installed and try it again. Mark -Original message- From:Douglas N Greve To:m.vlutt...@atr.jp Cc:Freesurfer ,martijnsteenwijk Date:Wed, 05 Oct 2011 10:48:53

Re: [Freesurfer] Inaccurate Surfaces Generated

Hi jeff Sorry, this slipped through the cracks. If you upload the dataset we will take a look Bruce On Oct 5, 2011, at 8:32 PM, Jeff Sadino wrote: > Hello FreeSurfer Experts, > > Does anyone have any ideas about how to salvage this data? > > Thank you very much! > Jeff > > On Sun, Oct 2, 2

Re: [Freesurfer] qdec and maximum p-value

Thanks for the reply! Is it then possible in Qdec to compute the average thickness of the gray matter in the significant areas, and can the data be exported? Right now, I'm copying the data (for a single vertex) from the shell and parsing it in Matlab, which is cumbersome. Kind regards, Nikola

Re: [Freesurfer] bug in surface-based area and volume

Hi Tetiana, thanks for the push. I've put a new version of mris_preproc here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc This will implement the fix. To "install" make a backup of mris_preproc in $FREESURFER_HOME/bin, then move the new version. You should re-run re

Re: [Freesurfer] volume of different lobes of the brain....

You will need to run mri_aparc2aseg specifying your lobe annotation as the input (this parcellates WM based on proximity to the annotation). Then run mri_segstats on the output of that to get the WM volumes for each lobe. doug Gonzalo Rojas Costa wrote: > Hi Douglas: > > I was testing the com

Re: [Freesurfer] .img unsupported data type ?

We don't have data type 0 defined in our code. Why are you using analyze at all? The field has moved on to nifti (for good reasons). Why not convert all your data to nifti? doug m.vlutters wrote: > Thank you for the reply. > > I do have the .hdr file, but calling just the hdr doesn't do any goo

Re: [Freesurfer] cuda error...

HI Gonzalo, As Knut said, FreeSurfer is not compiled to run with CUDA 4. If you run ldd command to some freesurfer binary file you notice that the binary file links to libcudart.so.3 library. You should recompile the FreeSurfer source code. This is what I'm trying to do right now but is not easy

Re: [Freesurfer] .img unsupported data type ?

can you try running this directly on a linux box? Or upload the .img/.hdr files and we will take a look On Wed, 5 Oct 2011, m.vlutters wrote: > Thank you for the reply. > > I do have the .hdr file, but calling just the hdr doesn't do any good. > > "File not found or unknown filetype for ../.../

Re: [Freesurfer] .img unsupported data type ?

Thank you for the reply. I do have the .hdr file, but calling just the hdr doesn't do any good. "File not found or unknown filetype for ../.../ .hdr" If I specify the input again with "-it spm" it gives: "ERROR : analyzeRead(): cannot find any files for .../.../ .hdr" First moving to the corre

Re: [Freesurfer] .img unsupported data type ?

You might generate a hdr+img or nii file, and then specify the hdr or nii file to import from. Best, Martijn -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens m.vlutters Verzonden: woensdag 5 oktober 2011 7:27 Aan:

Re: [Freesurfer] BOLD time series registration to orig.mgz

Hi Tessa, you can use mri_vol2vol passing it the 4D time series volume and the BBR registration matrix and --fstarg. You will have to motion correct the time series (using the template from BBR as the target). doug On 10/5/11 6:02 AM, Tessa Dekker wrote: Hi, I have used bbregister to register

Re: [Freesurfer] bug in surface-based area and volume

Dear Doug, Just wanted to ask you when approximately the fix will be ready? I really looking forward to it, to be able to explain some results. Thank you for your time and constant help, Tanja. On Fri, Aug 19, 2011 at 4:07 PM, Douglas N Greve wrote: > > Hi Y'all, I recently found a bug in the

Re: [Freesurfer] cuda error...

Hi You should use Cuda 3.1 which is included with Freesurfer. Freesurfer is not compiled to use Cuda 4.0 or Cuda 4.1 Knut J > Date: Tue, 4 Oct 2011 11:49:50 -0400 > From: freesurfer@gmail.com > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] cuda error... > > On Tue, Oct 4

Re: [Freesurfer] BOLD time series registration to orig.mgz

Hi, I have used bbregister to register a set of partial volume fMRI time series to the subject structural (orig.mgz), which worked very well. I now want to align each volume in each given time series to the orig.mgz. However, I've only managed to get one resampled volume, the target volume, out o

[Freesurfer] Using Freesurfer reg-feat2anat registration to replace original FEAT

Dear Freesurfers, I've analyzed a run of functional data in FEAT and then used reg-feat2anat to register the FEAT results to the Freesurfer anatomicals. It turns out the original FLIRT registration was bad. When I looked at the reg-feat2anat results, images were flipped 90 degrees. I made edits