Re: [Freesurfer] Processing MEMPRAGE

2019-03-05 Thread Rusche, Johann
ase, but Andre (ccd) can confirm > > cheers > Bruce > > On Tue, 5 Mar 2019, Rusche, Johann wrote: > >> >> Dear Freesurfers, >> >> >> Reading through the mailing list I understood how to >> process our nmr MEPRAGEs and I would like to &

[Freesurfer] Processing MEMPRAGE

2019-03-05 Thread Rusche, Johann
Dear Freesurfers, Reading through the mailing list I understood how to process our nmr MEPRAGEs and I would like to double-check we are using unpacksdcmdir correctly. Unpacking with unpacksdcmdir gives me two nifti files, a 4-echo nifti file (92MB) and a 1-echo nifti file (23MB). Am I correct

Re: [Freesurfer] Pial surface error (failing dura removal)

2019-01-10 Thread Rusche, Johann
Dear Douglas, This is just a friendly reminder concerning the data I send you. I'd much appreciate if there is any advice on how to advance our pial surfacing other than manual editing. Thanks! Johann From: Rusche, Johann Sent: Monday, January 07, 2019

Re: [Freesurfer] Pial surface error (failing dura removal)

2019-01-07 Thread Rusche, Johann
) Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look? On 1/6/19 6:20 PM, Rusche, Johann wrote: Dear Freesurfers, I have been processing my T1 dataset through the longitudinal pipeline with the -3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large

Re: [Freesurfer] Calculating volume using pial files

2019-01-07 Thread Rusche, Johann
Have you tried aparcstats2table? This command does not convert, but it extracts all the stats which allows you to play with the volume and any other stats. https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table Johann From: freesurfer-boun...@nmr.mgh.harva