Re: [Freesurfer] Fwd: trac-all -prep ERROR: Must specify input table of gradient vectors

No, there isn't. You can see available command-line options by running trac-all without arguments. On Fri, 11 Sep 2015, Katherine Damme wrote: Hey Anastasia, Is there some way to specify the in line and not by creating a configuration file? On Fri, Sep 11, 2015 at 3:46 PM, Anastasia Yendi

[Freesurfer] Registering set of extracted hippocampus

Dear experts, I look like to register a set of extracted hippocampus to a common atlas. Here is my workflow: I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocamp

Re: [Freesurfer] Fwd: trac-all -prep ERROR: Must specify input table of gradient vectors

Hi Katherine - Currently the gradient table is not read from the dicom header, so you have to specify it. This will hopefully change in the next version. Best, a.y On Thu, 10 Sep 2015, Katherine Damme wrote: -- Forwarded message -- From: Katherine Damme Date: Thu, Sep 10,

[Freesurfer] Postdoc, PhD and RA positions available at the Montreal Neurological Institute

We are currently looking for 3 enthusiastic and skilled team players (1 PhD student, 1 Postdoc, 1 RA) to join the Neuroimaging of Epilepsy Laboratory at the Brain Imaging Center (BIC) of the Montreal Neurological Institute (McGill University, Montreal, Canada) http://www.bic.mni.mcgill.ca/~noel

[Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation

Hi, I tried running the Hippocampal Segmentation using the Dev version, I get the following error (running on a mac os x Yosemite): I just downloaded the dev version a couple of days ago. Recon-all -all runs fine, but it's unable to run the hippocampals segmentation component. recon-all -s

Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly

Not the first time I guessed wrong then. Unfortunately, it does not seem to be an artefactual impression of a particular 2D projection, as I see it on multiple slices in all 3 orthogonal slice dimensions. I thought I did provide you with the dataset in previous emails, but here it is again any

[Freesurfer] cortical thickness of a volume-defined ROI

Dear Experts, I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm analysis using the commands below but it didn't work.. please could you kindly assist (log attached)? [spjwker@nanlnx2 FSL]0% cd $SUBJECTS_DIR/fsaverage/surf [spjwker@nanlnx2 surf]0% fslregister --s fsave

Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly

Hi Sebastien that isn't how the algorithm works. If I had to guess, I would guess that what you are seeing is locations with high through-plane curvature so even though a voxel looks like it is all CSF in fact the surface cuts through it. You can see this by moving back and forth a few slices.

Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly

Hello Bruce, I ran some tests overnight. By cranking up the memory of my virtual machine to its maximum (close to the 16GB of my actual machine), mri_compute_volume_fractions could run through at resolutions of -r 0.333 and -r 0.25 :-) FYI, it took 13min at the default resolution of 0.5, 50min

Re: [Freesurfer] Excluded medial white and grey matter

Hi Bronwyn I think that means that the aseg failed in that region since it is caudate and would have been filled if it had been correct. Can you check the aseg? I'm pretty surprised as I don't think I've ever seen us mislabel caudate there. You can upload it and we will take a look if you like.