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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-bounces@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

 

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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-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

 

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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-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 9:45 AM
To: Freesurfer support list <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-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.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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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.