External Email - Use Caution

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

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-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

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

________________________________ 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.

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-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:

External Email - Use Caution

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

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-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

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

________________________________

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.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JXE4loxoVSWvRnSvM4_y8rICe-67UpO0JMss9fbLED_T79...

External Email - Use Caution

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

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-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

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-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:

External Email - Use Caution

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

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-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

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

________________________________

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.

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nlWHpJdM869PvioMpYDMQhYq0zQ5wKb1uxHNSXE3QLKNSg...https://secure-web.cisco.com/1JXE4loxoVSWvRnSvM4_y8rICe-67UpO0JMss9fbLED_T79lF-50WppgxJvcE1HJ6g0yQ0PR9oO9w1p2pnKFxjmC9yJs_ZBFS6LZaqVw7fU5CGL_O-hxXjXy2Yei1AS-tdNCk63hcxLaAttzu8rIYlxTFgazWTeuUCznQoNThIJDnMr02QR9jlksJ3pQpRWY8dgMzVecfXsNPJUFr4e-cFP5jXDuHxgxvasMHXt2FRP9iAd_A-W9VnaaQG9xceEZfdaS9Z2qj_vrrBbvVZOS0MA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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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.

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-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

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-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

* External Email - Caution *

External Email - Use Caution 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

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-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

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-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:

External Email - Use Caution

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

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-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

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

________________________________

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.

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/17h3TvVLkgLXM2caBw5awAo7bLyCG3yA4v-X0kCOATdavdH...https://secure-web.cisco.com/1JXE4loxoVSWvRnSvM4_y8rICe-67UpO0JMss9fbLED_T79lF-50WppgxJvcE1HJ6g0yQ0PR9oO9w1p2pnKFxjmC9yJs_ZBFS6LZaqVw7fU5CGL_O-hxXjXy2Yei1AS-tdNCk63hcxLaAttzu8rIYlxTFgazWTeuUCznQoNThIJDnMr02QR9jlksJ3pQpRWY8dgMzVecfXsNPJUFr4e-cFP5jXDuHxgxvasMHXt2FRP9iAd_A-W9VnaaQG9xceEZfdaS9Z2qj_vrrBbvVZOS0MA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

________________________________

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.

________________________________ 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.

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-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

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edumailto:glasserm@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, January 26, 2021 at 11:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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: Tuesday, January 26, 2021 at 9:45 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

* External Email - Caution *

External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Tuesday, January 26, 2021 11:28 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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: Tuesday, January 26, 2021 at 9:13 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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-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 Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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-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

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-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

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

________________________________

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.

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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.

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-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 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-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

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edumailto:glasserm@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, January 26, 2021 at 11:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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: Tuesday, January 26, 2021 at 9:45 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

* External Email - Caution *

External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Tuesday, January 26, 2021 11:28 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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: Tuesday, January 26, 2021 at 9:13 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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-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 Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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-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

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-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

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

________________________________

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.

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

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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.

________________________________ 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.

________________________________ 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.

External Email - Use Caution

Sorry I’m completely confused now about what you are trying to do. The data in ${StudyFolder}/${Subject}/T1w is also in MNI space, but after only a 6 DOF rigid registration (i.e. no changes in brain shape, just a similar brain orientation and AC at 0,0,0). What does “paint surfaces” mean anyhow?

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 1:00 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution 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-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 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-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 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-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

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edumailto:glasserm@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, January 26, 2021 at 11:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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: Tuesday, January 26, 2021 at 9:45 AM 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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External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Tuesday, January 26, 2021 11:28 AM 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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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.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: Tuesday, January 26, 2021 at 9:13 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <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 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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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Hi there

As a follow-up to this, I downloaded one file to test things and it seems the .gii surface files cannot be read by Freeview 7.1:

mrisReadGIFTIfile: GIFTI file /data-01/trisanna/freesurfer/freesurfer_7.1.1/100307_from_HCP/T1w/Native/100307.R.white.native.surf.gii is invalid!

I used mris_convert to get the .white to open

Any idea why it wouldn't be able to open as a .gii? ________________________________ 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 26, 2021 6:12 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

Great, I will check out all the folders. Just made an account now. By "paint surfaces" I mean create/edit labels on the surfaces, specifically related to sulci.

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 3:06 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

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Sorry I’m completely confused now about what you are trying to do. The data in ${StudyFolder}/${Subject}/T1w is also in MNI space, but after only a 6 DOF rigid registration (i.e. no changes in brain shape, just a similar brain orientation and AC at 0,0,0). What does “paint surfaces” mean anyhow?

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 1:00 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

External Email - Use Caution

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-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 1:57 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

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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-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 12:24 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 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Glasser, Matthew" <glasserm@wustl.edumailto:glasserm@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, January 26, 2021 at 11:01 AM 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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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.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: Tuesday, January 26, 2021 at 9:45 AM 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 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Tuesday, January 26, 2021 11:28 AM 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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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.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: Tuesday, January 26, 2021 at 9:13 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <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 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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

________________________________

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.

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That’s not a good idea either.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@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-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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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

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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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-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 9:53 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Glasser, Matthew glasserm@wustl.edu Sent: Tuesday, January 26, 2021 11:45 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

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That’s not a good idea either.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@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-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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, January 25, 2021 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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-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

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-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

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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_______________________________________________

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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.

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca mailto:trisanna.sprung-much@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca mailto:trisanna.sprung-much@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

---

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.

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1ZIER8I9fCGumiTfRT5iL30YUBhJFUmWXgLeQAFdh4O0B-X_DhsgNDWG3S7WKJ5XNjiaLfBfvseF2ilWnEhpQ1eOeyG330fgXzhsSZTttwSOvRR7biHRQltTrSUCX0jJepAPQa96p-C4sulsjX1CRBCGizUC3_yJmgz4xlgkiyPAW-0W4fVsKuwTrTpSYuTywcrr3ghI9S2PDHdBdPIEItAFR4dom2r9OOH7w-CKvHzPQVeq-x8oZOyeKkmbDE6m45kfoV6J-HImkytegZl3M-Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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