External Email - Use Caution
Please explain what you are doing that requires this. There are many good
reasons why this is not the approach FreeSurfer or the HCP have taken. Not the
least of which is that all volumetrics and morphometrics will be invalid if not
measured in the subject’s own physical space.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Trisanna
Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 26, 2021 at 9:53 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
External Email - Use Caution
Hi Matt
We want the surfaces to be extracted from volumes that have been registered to
MNI152, rather than extracting the surfaces in the native space of the subject,
which is what FreeSurfer does.
I have done this for 2 other projects in the past for ICBM data (not HCP) and
it worked fine.
What would be the concern with the HCP data?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew
<glass...@wustl.edu>
Sent: Tuesday, January 26, 2021 11:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
External Email - Use Caution
That’s not a good idea either.
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve"
<dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 26, 2021 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
Why are you registering it to the MNI prior to FS analysis?
On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Trisanna Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca><mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Trisanna Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca><mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto: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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