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Hi Matt
The sole purpose of using 7.1 is to be able to create labels directly on the surfaces (painting sulci). For the 1 subject that I ran successfully - the surfaces are decent, although a bit bumpy, perhaps because it is -hires. See images attached.
I will test another few subjects today and get back to this email.
Best, Trisanna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Glasser, Matthew glasserm@wustl.edu Sent: Tuesday, January 26, 2021 11:28 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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You are likely to get significantly worse results by reprocessing the HCP subjects with FreeSurfer 7.X. Unfortunately it has issues with HCP data that haven’t been addressed yet.
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: Tuesday, January 26, 2021 at 9:13 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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Hi Doug and Matt
So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and have been registered to our 0.5mm MNI152 template, to avoid losing data by registering to the 1mm template. That's all.
As for the recon-all.log, unfortunately I deleted it when I re-ran the same subject this weekend using an -expert file to specify the number of inflations and it worked. It took 24 hrs.
I will try to run another subject without the expert file, since Doug says this should not be necessary, and get back to you ASAP.
Best
Trisanna
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, January 21, 2021 at 12:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca Sent: Tuesday, January 19, 2021 6:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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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