External Email - Use Caution
What scans are these? I wasn’t aware of any 0.5mm scans.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, January 21, 2021 at 12:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
External Email - Use Caution Hi there
As a follow-up to this question, I tried the flags as stated and the recon-all seems to have failed at the inflation stage:
/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts
mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 version: 7.1.1 available threads: 1 scaling brain by 0.274... inflating... Command terminated by signal 11 @#@FSTIME 2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00 @#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00 Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021
Any advice would be greatly appreciated,
Trisanna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Sent: Tuesday, January 19, 2021 6:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
External Email - Use Caution Hi there
If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in FreeSurfer 7.1, would I simply use the following flags, or am I missing something?
-3T -MPRAGE -hires
Do we need an expert file with version 7.1 to specify the number of iterations for surface inflation or is this now done automatically?
Thank you Trisanna
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