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Thanks for this Matt.
Just a question – is it called “MNINonlinear” because a non-linear registration
was used to MNIspace? If this is the case, I would prefer to paint in the
subject’s native space.
Best,
Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew"
<glass...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 26, 2021 at 1:57 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
External Email - Use Caution
Right just use the surfaces in ${StudyFolder}/${Subject}/MNINonLinear. These
are in MNI space and should work for you. They are in GIFTI format, which is
readable by FreeView.
In the future, it is trivial to move surfaces to MNI space after they were
computed in subject’s physical space with Connectome Workbench and FreeSurfer
probably has tools for this as well.
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 12:24 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 Bruce
Thanks for your speedy response. This would be an immense time saver if this
works. I will give this a go.
Yes, you are correct about the blurring as well!
Best
Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce"
<bfis...@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1
Hi Trisanna
Yes, I’m pretty sure that would work. That is, using the current freeview on
older versions of recon data.
Cheers
Bruce
p.s. one addendum – you should not have to blur the labels after registration,
assuming your manually labeled dataset is big enough
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 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 Matt
OK, I think there has been some confusion and I think I just realized what it
is. I am from the MNI and we are used to using the ICBM database, not HCP
database. We are also used to painting sulci in volumetric form, so we always
used to register our scans to MNI space (linear) prior to painting. We never
computed any volumetric/morphometric data of the scans, so we went ahead with
this registration to MNI space simply for painting in a common space.
What we now wish to do this year is:
Paint individual sulci directly on subject surfaces
Register the labels to fsaverage
Average and blur the labels to generate surface probability maps on fsaverage
We went the route of looking at Freesurer 7.1 because one can paint directly on
surfaces in Freeview. I therefore did not at all use the HCP pipeline but
simply tested recon-all on HCP volumes using Freesufer 7.1. We can of course
use the native scans instead of those registered to MNI152 space.
My question is the following: Could one simply use the HCP pipeline output from
the Human Connectome, convert the surfaces so they can be loaded into Freeview
7.1, and paint directly on these? This would save us from having to re-run all
HCP subjects with recon-all in 7.1….
Best,
Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 11:01 AM
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
I think it would be a good idea to take a step back and tell us what you are
trying to accomplish. This is all not the right way to go about things. The
HCP already produces surfaces registered to MNI space in the volume for example.
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: Tuesday, January 26, 2021 at 9:45 AM
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
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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-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 Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Tuesday, January 26, 2021 11:28 AM
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
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-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: Tuesday, January 26, 2021 at 9:13 AM
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
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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