Re: [Freesurfer] Recon-all reconstructed image coordinates

2022-02-07 Thread Salar Dini, Elaheh
External Email - Use Caution Thank you so much. This actually worked well. Just two simple follow-up questions: 1. Do I assume right that this solution doesn't work on aparc+aseg? 2. If I want to run recon-all -autorecon2 -autorecon3 on a subject that I have a proper brai

Re: [Freesurfer] Using -bigventricles for infant segmentation

2022-02-07 Thread Paul Wighton
External Email - Use Caution A quick correction: The -bigventricles flag is supported in `recon-all` and in `samseg` but not in `infant_recon_all`, unfortunately. -Paul On Mon, Feb 7, 2022 at 2:17 PM Paul Wighton wrote: > Hi Fateme, > > Unfortunately, `-bigventricles` isn't sup

Re: [Freesurfer] Using -bigventricles for infant segmentation

2022-02-07 Thread Paul Wighton
External Email - Use Caution Hi Fateme, Unfortunately, `-bigventricles` isn't supported on the infant recon stream, that's a feature of the samseg stream. -Paul On Fri, Feb 4, 2022 at 1:58 PM Fateme Sadat Haghpanah wrote: > External Email - Use Caution > > Dear FreeSur

Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

2022-02-07 Thread Jennifer Bramen
External Email - Use Caution Hi Doug I think my first question should be “do I need to do KM?”. This is an amyloid scan and I want to estimate intensity within regions of interest. Do I need KM to estimate mean intensity? This is what I know about the timing of the 4 amyloid P

[Freesurfer] PhD position in Cognitive Neuroscience

2022-02-07 Thread Nicolas Langer
External Email - Use Caution PhD position in Cognitive Neuroscience Department: Department of Psychology at the University of Zurich (Switzerland), Methods of Plasticity Research (http://secure-web.cisco.com/1yrXnmcLak8VcmE09mDHZoci-sk4X3q07igz895-SUBVrvpGAg2ru7ufy8eZC02-v

[Freesurfer] Tracula prepocessing error awk: fatal: cannot open file dmri/dwi_orig_las.1.bvals

2022-02-07 Thread Vicente Ferrer
External Email - Use Caution Hi all, I was trying to run trac-all preprocessing and it seems there is a problem with eddy_openmp. The program is unable to find the dwi_orig_las.1.bvals file which makes that the index.txt is empty. see the terminal output: trac-all -prep -c trac