[Freesurfer] Unknown Label in following postprocessing with mne-python

Dear fellow colleagues, in my study I use volumetric source spaces. In the process of creating them, I decided to identify all available volumelabels FreeSurfer "recognized" in the given mri image. Every single subject inherits, despite all other volumelabels, a volumelabel called "Unknown".

Re: [Freesurfer] Surface Errors

Hi Doug, Great, thank you. I sent it to you via filedrop. Best, Emily From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 4:52

Re: [Freesurfer] Problem with cortical parcellation of rh but not lh

Hi Bruce, I sent you two subject's directories through FileDrop. Thanks! Cheers Amal From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Wednesday, February 21, 2018 6:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] P

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Hi Lea, I wrote that script to simplify processing on our cluster which uses qsub PBS for submission. I have never used SLURM so far. There is two functions that you (or someone who knows this stuff) would need to modify: def submit and def wait_jobs The submit procedure basically iss

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

hi lea, in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer and then submit each subject's longitudinal pipeline as a separate slurm job. cheers, satra On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter wrote: > Hi Lea, > > > I wrote that sc

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Could be all that is needed is to add this: mycluster ='sbatch --mail-type=FAIL --mail-user= -N 1 --ntasks-per-node=10 --partition=work --export=ALL -o /%(username)s/logs/job.%J.out- e /%(username)/logs/job.%J.err "%(command)s"' and comment the lines # if queue is not None ... # pbcmd =

Re: [Freesurfer] Freesurfer equivalent to fslmaths?

Hi Jared what are the exact command lines you ran? I don't think it can be a freeview problem if the overlays are different. cheers Bruce On Wed, 21 Feb 2018, Zimmerman, Jared wrote: Hey Doug, Bruce, et al., any update on why fscalc and Matlab are not producing the same values when tryin

Re: [Freesurfer] Surface Errors

got em. can you send me coordinates (col, row,slice) where you are seeing the errors? You can also create a point set in FreeView (under File->New PointSet) On 02/22/2018 08:48 AM, Emily Schwartz wrote: > Hi Doug, > > Great, thank you. I sent it to you via filedrop. > > Best, > > Emily > __

Re: [Freesurfer] Update: asymmetric parcellation error

don't know. can you send these subjects to me through our filedrop? url below On 02/22/2018 11:39 AM, Dijkshoorn, A.B.C. (Aicha) wrote: > Dear Freesurfer developers, > > When I was troubleshooting my data I came across an odd parcellation > error that I can not place. When looking at the recons

Re: [Freesurfer] Surface Errors

Hi Doug, Attached are the point sets for the 3 subjects. For some issues, I put a range of coordinate points. Let me know if you need anything else. Thanks! Emily From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on

[Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

Hello Everyone, I would like to use the FreeSurfer labels for fMRI and DTI in graph theory analyses. I am attempting to use UMPC to generate the graphs, which requires that the diffusion tensor imaging be in .dtk form. However, I have been struggling to get the F

Re: [Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

Hi Katherine - If you mean the .trk format, that's not for storing labels, it's for storing tractography streamlines (i.e., a bunch of curves that are stored as sequences of x,y,z point coordinates). You can convert the FreeSurfer labels to nifti volumes, and see if the software that you're tryi