You don't need any special flags with the -hires option. Also, it is helpful to include the recon-all.log file.

On 1/22/2021 12:15 AM, Glasser, Matthew wrote:

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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

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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

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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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