But the question I have is why you want to do that?
On 1/26/2021 10:48 AM, Trisanna Sprung-Much wrote:
External Email - Use Caution
Hi Doug
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 I remember you saying at a workshop
a few years ago is what FreeSurfer does.
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Tuesday, January 26, 2021 11:30 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:
External Email - Use Caution
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
* 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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