Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

Hi Jun - It's failing at the point where it tries to extract the low-b images from the DWI series. I suspect that the number of frames in the 4D DWI volume that is extracted from your dicom does not match the number of frames that it expects to find based on how many gradient vectors or b-valu

[Freesurfer] Problem with mris_euler_number

Dear FS experts I am trying to reconstruct surface-based cortical models with a high resolution (0.5x0.5x0.5mm) using the ­cm flag. After topology fixing, the function mris_euler_number stops and reports the following error: mrisFindNeighbors: ../surf/lh.orig: face[324829].v[2] = 164499, but face

Re: [Freesurfer] Problem with mris_euler_number

Hi Jurgen usually that only happens if you run out of disk space or memory or something somewhere in the pipeline. If you rerun does it happen again? The other possibility is that your surfaces are too big, although we upped all the max constants a while ago. What version are you running? Bru

Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH))

Hi all, I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed? My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get t

Re: [Freesurfer] 4 groups non-linear effect

If you want to look for an interaction between two groups, then use the contrast [1 -1 -1 1] We don't have a way to fit nonlinear models, but you can apply a nonlinearity to the blood data and then include it as a linear covariate doug On 06/28/2014 06:20 PM, Jacobs H (NP) wrote: > > Dear Fre

[Freesurfer] tkmedit coronal view - y coordinate issue

Hi, In FreeSurfer 5.3, when I click around in a coronal view slice, the Talairach y coordinate changes (in both the cursor column and the mouse column). This doesn’t make sense - it’s the same coronal slice, so shouldn’t anywhere on that same plane still have the same y coordinate? When I take

[Freesurfer] Pons and midbrain segmentation....

Hi: How can I segment the pons and midbrain using freesurfer ?... or any other segmentation software that do such task ?... Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes

[Freesurfer] reading & writing surface files in python

hi freesurfers, i'm looking to read and write freesurfer surface files in python -- like MRIread.m & MRIwrite.m but for surfaces and in python. i'm happy to write the code myself, but it seems like the kind of thing that has been done before and i don't want to reinvent the wheel if i don't have

[Freesurfer] Mean diffusuvuty MD

Hi Fs Experts, In order to calculate the mean diffusivity MD in my DTI data I did the following: 1. For the Eigvals.nii (the output of dt_recon) I used the following command line: fslmaths eigvals -div 3 md.nii 2. mri_vol2vol -mov md.nii --reg register.dat --fstarg -- interp nea

Re: [Freesurfer] reading & writing surface files in python

mne-python supports this https://github.com/mne-tools/mne-python/blob/master/mne/surface.py On Mon, Jun 30, 2014 at 2:10 PM, Alex Kell wrote: > hi freesurfers, > > i'm looking to read and write freesurfer surface files in python -- like > MRIread.m & MRIwrite.m but for surfaces and in python.

[Freesurfer] problems with Surface-based Interhemispheric Registration

Hi all, I have a problem with 'Surface-based Interhemispheric Registration' I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' finish with the error below (indeed in the xhemi/label directory, there is no file) What can I do?

Re: [Freesurfer] recon-all ERROR, no idea why

Thanks Douglas, orig.mgz looks fine to me. Do you know if there is any detailed log i could look into? Or maybe process tasks one after the other? *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State Univ

[Freesurfer] Optseq2 Help!!

Hello! I am trying to use optseq to optimize my study design and cannot get it to accept the parameters I need for my task and I have officially stumped those helping me at my institution so I need your help! I am trying to run a very simple design where my stimuli are presented for 3.5 seconds a

[Freesurfer] annotation files for cortical labels?

Hi Freesurfer Team, I'd like to view a multicolored quilt of individual cortical icosahedron subdivisions. I have labels for these subdivisions stored in the SUBJECT/label folder I can also batch load all these labels and view them in Freeview but am not sure how to randomize their colors for a mu

Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

Hi Anastasia, Thank you for your e-mail. I took 65 DWIs (5 b0 volumes and 60 direction DWIs). I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images. Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts. It seems consistent. I attach bvals and bvecs. These fil

[Freesurfer] Build with CUDA 5.5?

Guys, Would it be possible to get Freesurfer 5.3.0 built with CUDA 5.5? The newest Ubuntu does not have support for 5.0. Thanks in advance, Chris Adamson. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal C

Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

Hi Jun - By a simple word count on these files: % wc -w bvals bvecs 65 bvals 198 bvecs 263 total As you can see, there are 3 extra entries in the bvecs file. If you then open the file, you'll see that there is an extra column of zeros in the end. Not sure if that's what's causing the pr