Re: [Freesurfer] Question about editing topology errors

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there, just following up on this. Thank you!

___
Trisanna Sprung-Much, PhD
Research Associate
Montreal Neurological Institute
[Logo  Description automatically generated]

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Trisanna Sprung-Much 

Date: Wednesday, March 2, 2022 at 11:07 AM
To: Freesurfer support list 
Subject: [Freesurfer] Question about editing topology errors

External Email - Use Caution
Hi there

I have this issue occurring in several hemispheres (See images attached) where 
a “sulcus” is created because the pial crosses where it shouldn’t, and am 
wondering what the best way to edit this is. I don’t think it is a matter of 
adding WM control points as it is not the WM that needs to be corrected but 
rather the pial. My 2nd image shows how the sulci should look in the pial.

Should it be just a matter of removing voxels in the brainmask.mgz and doing

recon-all -autorecon-pial -subjid

I tried this for one subject and it was not happy. Is there a way to add 
control points for the pial?

Thank you!

Trisanna Sprung-Much, PhD
McGill University
Montreal Neurological Institute
--

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[Freesurfer] Question about editing topology errors

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I have this issue occurring in several hemispheres (See images attached) where 
a “sulcus” is created because the pial crosses where it shouldn’t, and am 
wondering what the best way to edit this is. I don’t think it is a matter of 
adding WM control points as it is not the WM that needs to be corrected but 
rather the pial. My 2nd image shows how the sulci should look in the pial.

Should it be just a matter of removing voxels in the brainmask.mgz and doing

recon-all -autorecon-pial -subjid

I tried this for one subject and it was not happy. Is there a way to add 
control points for the pial?

Thank you!

Trisanna Sprung-Much, PhD
McGill University
Montreal Neurological Institute
--

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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] question about surface registration to an average surface

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Bruce

So I have 77 chimp scans reconstructed in FS (NOT registered to MNI space, but 
rather a chimp volume template, to avoid scaling). After a lot of trial and 
error, we got some really nice surfaces.

I tried to use make_average_surface this summer and I was running into one 
problem after the next and unfortunately no one answered my questions. So, we 
have a new MNI chimp average surface and I would like to know if I can somehow 
implement this average surface into FS to perform surface registration of my 
individual labels to the average surface.

Thanks!
Trisanna

--



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Sunday, December 5, 2021 12:03 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about surface registration to an average 
surface


I’m not really sure what you are trying to do, but I guess you will want to 
make your own average. I think there is a new script for this, so someone else 
will have to comment



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Saturday, December 4, 2021 10:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about surface registration to an average 
surface



External Email - Use Caution

Thanks Bruce  Yes I am working with chimp data.

Any other things I could try?



Trisanna







Sent from my Galaxy







 Original message 

From: "Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>>

Date: 2021-12-04 11:12 a.m. (GMT-05:00)

To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Subject: Re: [Freesurfer] question about surface registration to an average 
surface



Oh, then no, that won’t work



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Trisanna Sprung-Much
Sent: Saturday, December 4, 2021 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] question about surface registration to an average 
surface



External Email - Use Caution

Hi Bruce, I will try mris_sphere! But since this is a chimp average, when you 
say then register it to your atlas- is this something I should do?



Trisanna







Sent from my Bell Samsung device over Canada's largest network.







 Original message 

From: "Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>>

Date: 2021-12-04 10:27 a.m. (GMT-05:00)

To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Subject: Re: [Freesurfer] question about surface registration to an average 
surface



Hi Trisanna



Can you run mris_sphere on it to create a spherical surface? You could then 
register that to our atlas using mris_register. You will need to create a bunch 
of files that we expect though like ?h.curv, ?h.sulc, etc…  You might also need 
to specify a volume, but I expect any conformed one will be ok



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Trisanna Sprung-Much
Sent: Friday, December 3, 2021 6:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] question about surface registration to an average surface



External Email - Use Caution

Hi there



I have a bunch of labels on individual subjects and would like to register them 
to an average surface that we have created here at the MNI. So, this average 
has not gone through recon-all and there are no freesurfer recon-all files 
associated with it. There is no volume associated with it to run in recon-all.



According to the instructions for mri_surf2surf I need the sphere.reg file, 
which is generated during recon-all. I wonder if there is a way to undergo 
surface registration in my situation? I found the following documentation, but 
this seems to be for creating a new average. I have the average already.



MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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Re: [Freesurfer] question about surface registration to an average surface

[Trisanna Sprung-Much]

External Email - Use Caution

Thanks Bruce  Yes I am working with chimp data.
Any other things I could try?

Trisanna



Sent from my Galaxy



 Original message 
From: "Fischl, Bruce" 
Date: 2021-12-04 11:12 a.m. (GMT-05:00)
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about surface registration to an average 
surface

Oh, then no, that won’t work

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Saturday, December 4, 2021 10:48 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about surface registration to an average 
surface


External Email - Use Caution
Hi Bruce, I will try mris_sphere! But since this is a chimp average, when you 
say then register it to your atlas- is this something I should do?

Trisanna



Sent from my Bell Samsung device over Canada's largest network.



 Original message 
From: "Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>>
Date: 2021-12-04 10:27 a.m. (GMT-05:00)
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] question about surface registration to an average 
surface

Hi Trisanna

Can you run mris_sphere on it to create a spherical surface? You could then 
register that to our atlas using mris_register. You will need to create a bunch 
of files that we expect though like ?h.curv, ?h.sulc, etc…  You might also need 
to specify a volume, but I expect any conformed one will be ok

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Trisanna Sprung-Much
Sent: Friday, December 3, 2021 6:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] question about surface registration to an average surface


External Email - Use Caution
Hi there

I have a bunch of labels on individual subjects and would like to register them 
to an average surface that we have created here at the MNI. So, this average 
has not gone through recon-all and there are no freesurfer recon-all files 
associated with it. There is no volume associated with it to run in recon-all.

According to the instructions for mri_surf2surf I need the sphere.reg file, 
which is generated during recon-all. I wonder if there is a way to undergo 
surface registration in my situation? I found the following documentation, but 
this seems to be for creating a new average. I have the average already.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1JoFFWUwURIT9QWgPmGPEnw6MLYHphGQE-pZ0Cqw9PL8mIDJwWrWVXdJpLl00mmSsNbmVvr5MWs_tavnTIIPWeUA2U5Ohh5M5pFToTeoHDSAcs88JgwCuN5dz-XvTQr3lAXN1iQeDYv-I9WVnThT2xknN1pwPoj9xA9Q12yHZuW1LDAfqQpREioGkrlcREjR7iVI_WGmHBYLUnW3q5HNiEjSsdd9rwgzy-LsYrOkTa32dkXjRXx6E1S-oQXePAgw1KNn3m_j3KHiHHY8hpfj6KSpmntB9A4AX7UR8ve5OkV-GoYPaBhmC4Cu4q9AOasVI/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates<https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
SurfaceRegAndTemplates - Free Surfer 
Wiki<https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
The output from registration is yet another version of the subject's surface 
mesh, typically named ?h.sphere.reg, with the x,y,z vertex positions still on a 
sphere, but warped so that the subject's curvature pattern best aligns with the 
template data.Here is the same convexity data, now plotted on the lh.sphere.reg 
surface. Similar pattern, but "stretched around".
surfer.nmr.mgh.harvard.edu

Thank you,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] question about surface registration to an average surface

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Bruce, I will try mris_sphere! But since this is a chimp average, when you 
say then register it to your atlas- is this something I should do?

Trisanna



Sent from my Bell Samsung device over Canada's largest network.



 Original message 
From: "Fischl, Bruce" 
Date: 2021-12-04 10:27 a.m. (GMT-05:00)
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about surface registration to an average 
surface

Hi Trisanna

Can you run mris_sphere on it to create a spherical surface? You could then 
register that to our atlas using mris_register. You will need to create a bunch 
of files that we expect though like ?h.curv, ?h.sulc, etc…  You might also need 
to specify a volume, but I expect any conformed one will be ok

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Friday, December 3, 2021 6:42 PM
To: Freesurfer support list 
Subject: [Freesurfer] question about surface registration to an average surface


External Email - Use Caution
Hi there

I have a bunch of labels on individual subjects and would like to register them 
to an average surface that we have created here at the MNI. So, this average 
has not gone through recon-all and there are no freesurfer recon-all files 
associated with it. There is no volume associated with it to run in recon-all.

According to the instructions for mri_surf2surf I need the sphere.reg file, 
which is generated during recon-all. I wonder if there is a way to undergo 
surface registration in my situation? I found the following documentation, but 
this seems to be for creating a new average. I have the average already.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1Xi2lcpZACDikuDU8pSzKMt-Dtjs_Y2CYuQRXl20Tw2-Jmf0wKphogkszaGyohgF1-8glVslbw-7ycE60Off45do7CV75zBRWC7R99jj4-kmb52aQ7g0KXQPwhDucaVb5fAVVU5Qtiic_QCk2B1da9xVrnoqIeuGCw7-x084rQ-mqtaEbqsk7QMrmpntlJDhExNZqe4BGEWLsV76rQ9yOKUm-JXvXojeyvuvwFdiEwbgj4b_C2w_EwkxnxPtJWmOlnzv6F-jRgqlH5MYbQ38XaXlshLX_GWhfi-V2PNKIvdhGIrSz3H9xpBXZEc91Zf80rFgDPf32OkOc7vy9A2tXSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates<https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
SurfaceRegAndTemplates - Free Surfer 
Wiki<https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
The output from registration is yet another version of the subject's surface 
mesh, typically named ?h.sphere.reg, with the x,y,z vertex positions still on a 
sphere, but warped so that the subject's curvature pattern best aligns with the 
template data.Here is the same convexity data, now plotted on the lh.sphere.reg 
surface. Similar pattern, but "stretched around".
surfer.nmr.mgh.harvard.edu

Thank you,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] question about surface registration to an average surface

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I have a bunch of labels on individual subjects and would like to register them 
to an average surface that we have created here at the MNI. So, this average 
has not gone through recon-all and there are no freesurfer recon-all files 
associated with it. There is no volume associated with it to run in recon-all.

According to the instructions for mri_surf2surf I need the sphere.reg file, 
which is generated during recon-all. I wonder if there is a way to undergo 
surface registration in my situation? I found the following documentation, but 
this seems to be for creating a new average. I have the average already.

https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates
SurfaceRegAndTemplates - Free Surfer 
Wiki<https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates>
The output from registration is yet another version of the subject's surface 
mesh, typically named ?h.sphere.reg, with the x,y,z vertex positions still on a 
sphere, but warped so that the subject's curvature pattern best aligns with the 
template data.Here is the same convexity data, now plotted on the lh.sphere.reg 
surface. Similar pattern, but "stretched around".
surfer.nmr.mgh.harvard.edu

Thank you,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] turning a surface label into 3d object

[Trisanna Sprung-Much]

External Email - Use Caution

thanks Doug - I will give this a try! Appreciate it.

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 4:00 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] turning a surface label into 3d object

You can create a "patch" with something like
label2patch -surf white  fsaverage lh  lh.V1_exvivo.label ./lh.patch
then load it with
tksurferfv fsaverage lh white -patch ./lh.patch
When you load a patch, you will only be able to see the patch of the surface 
that you loaded it on
If you want to be able to toggle the whole surface on and off you can add -f 
fsaverage/surf/lh.white to the command line
It would be nice to be able to do this on-the-fly in freeview... someday



On 11/11/2021 10:33 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

Hi there

I realize this may be a bit of a stretch, but I wonder if there is any way to 
turn a surface label into its own 3D object that can then be examined on its 
own (to observe morphology) in Freeview? Similar to, for example, the sulcal 
skeletons that can be extracted in BrainVisa?

Many thanks~
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute



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[Freesurfer] turning a surface label into 3d object

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I realize this may be a bit of a stretch, but I wonder if there is any way to 
turn a surface label into its own 3D object that can then be examined on its 
own (to observe morphology) in Freeview? Similar to, for example, the sulcal 
skeletons that can be extracted in BrainVisa?

Many thanks~
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
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Re: [Freesurfer] mri_label2label issues

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Doug

THIS WORKED!!! Thank you so much for all your help!

Trisanna

--




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, November 8, 2021 1:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_label2label issues

Try this: register the old/1st recon to the second with
bbregister --mov old/mri/nu.mgz --targ newsubject --t1 --reg reg.lta
Map the old surface into the new space
mris_apply_reg --lta reg.lta old/surf/lh.white newsubject/surf/lh.white.old
Verify that the old surface overlays on the new volume
Map the old labels onto the new volume with
mris_apply_reg --src-label old/label/lh.your.label --streg 
newsubject/surf/lh.white.old newsubject/surf/lh.white --o 
newsubject/label/lh.your.label




On 11/3/2021 10:17 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution

Hi Doug

I did and I responded with the following:

that is correct Doug - the 2nd recon-all batch had a better set of scans 
(intensity wise). For some reason the T1.mgz volumes are slightly translated 
from one another, as are the surfaces (in that image I attached) and it is 
creating the same issue with the labels when I use mri_label2label. Why would 
mri_label2label with registration method as surface be having this issue? How 
might I overcome this to avoid redrawing my labels?

Thank you,

Trisanna


--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, November 3, 2021 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2label issues

Did you see this response from a few days ago?

On 10/27/2021 11:26 AM, Douglas N. Greve wrote:
I'm not sure what you did or how to interpret that pic. If I understand, you 
ran a case through recon-all and created labels on that case. You then 
recon-all again using a totally different output where you improved the 
homogeneity. You now want to map the labels you created on the 1st run to the 
2nd run. Is that right?

On 10/22/2021 4:58 PM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution

Hi there

I created labels on surfaces of subjects (chimp) registered to a particular 
volumetric template. The labels were created on the surfaces in Freeview using 
Freesurfer 7.1.

Since creating these labels, I improved the intensity inhomogeneity in the 
scans and re-ran the surfaces. When I try to use mri_label2label to transpose 
the labels to the new surfaces of each subject, the labels do not fall exactly 
where they should. In fact, the surfaces themselves have a slight translation 
in them (see snapshot). I assume this is because my registration to the 
template that I did prior to running recon-all is differing somehow between the 
2 groups. However, I thought that this should not matter since mri_label2label 
--regmethod surface is using the sphere.reg to fsaverage.

I am wondering if there is anything I can do to improve mri_label2label to 
avoid editing the labels manually?

Thank you for your time,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute



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Re: [Freesurfer] mri_label2label issues

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Doug

I did and I responded with the following:

that is correct Doug - the 2nd recon-all batch had a better set of scans 
(intensity wise). For some reason the T1.mgz volumes are slightly translated 
from one another, as are the surfaces (in that image I attached) and it is 
creating the same issue with the labels when I use mri_label2label. Why would 
mri_label2label with registration method as surface be having this issue? How 
might I overcome this to avoid redrawing my labels?

Thank you,

Trisanna


--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, November 3, 2021 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_label2label issues

Did you see this response from a few days ago?

On 10/27/2021 11:26 AM, Douglas N. Greve wrote:
I'm not sure what you did or how to interpret that pic. If I understand, you 
ran a case through recon-all and created labels on that case. You then 
recon-all again using a totally different output where you improved the 
homogeneity. You now want to map the labels you created on the 1st run to the 
2nd run. Is that right?

On 10/22/2021 4:58 PM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution

Hi there

I created labels on surfaces of subjects (chimp) registered to a particular 
volumetric template. The labels were created on the surfaces in Freeview using 
Freesurfer 7.1.

Since creating these labels, I improved the intensity inhomogeneity in the 
scans and re-ran the surfaces. When I try to use mri_label2label to transpose 
the labels to the new surfaces of each subject, the labels do not fall exactly 
where they should. In fact, the surfaces themselves have a slight translation 
in them (see snapshot). I assume this is because my registration to the 
template that I did prior to running recon-all is differing somehow between the 
2 groups. However, I thought that this should not matter since mri_label2label 
--regmethod surface is using the sphere.reg to fsaverage.

I am wondering if there is anything I can do to improve mri_label2label to 
avoid editing the labels manually?

Thank you for your time,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute



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Re: [Freesurfer] mri_label2label issues

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

Just wanted to follow up on this as I am still dealing with this issue and 
would love to avoid having to edit all labels.

Thank you!
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Trisanna Sprung-Much 

Sent: Wednesday, October 27, 2021 12:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_label2label issues


External Email - Use Caution

that is correct Doug - the 2nd recon-all batch had a better set of scans 
(intensity wise). For some reason the T1.mgz volumes are slightly translated 
from one another, as are the surfaces (in that image I attached) and it is 
creating the same issue with the labels when I use mri_label2label. Why would 
mri_label2label with registration method as surface be having this issue? How 
might I overcome this?

Thank you,

Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, October 27, 2021 12:26 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_label2label issues

I'm not sure what you did or how to interpret that pic. If I understand, you 
ran a case through recon-all and created labels on that case. You then 
recon-all again using a totally different output where you improved the 
homogeneity. You now want to map the labels you created on the 1st run to the 
2nd run. Is that right?

On 10/22/2021 4:58 PM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution

Hi there

I created labels on surfaces of subjects (chimp) registered to a particular 
volumetric template. The labels were created on the surfaces in Freeview using 
Freesurfer 7.1.

Since creating these labels, I improved the intensity inhomogeneity in the 
scans and re-ran the surfaces. When I try to use mri_label2label to transpose 
the labels to the new surfaces of each subject, the labels do not fall exactly 
where they should. In fact, the surfaces themselves have a slight translation 
in them (see snapshot). I assume this is because my registration to the 
template that I did prior to running recon-all is differing somehow between the 
2 groups. However, I thought that this should not matter since mri_label2label 
--regmethod surface is using the sphere.reg to fsaverage.

I am wondering if there is anything I can do to improve mri_label2label to 
avoid editing the labels manually?

Thank you for your time,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute



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Re: [Freesurfer] mri_label2label issues

[Trisanna Sprung-Much]

External Email - Use Caution

that is correct Doug - the 2nd recon-all batch had a better set of scans 
(intensity wise). For some reason the T1.mgz volumes are slightly translated 
from one another, as are the surfaces (in that image I attached) and it is 
creating the same issue with the labels when I use mri_label2label. Why would 
mri_label2label with registration method as surface be having this issue? How 
might I overcome this?

Thank you,

Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, October 27, 2021 12:26 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_label2label issues

I'm not sure what you did or how to interpret that pic. If I understand, you 
ran a case through recon-all and created labels on that case. You then 
recon-all again using a totally different output where you improved the 
homogeneity. You now want to map the labels you created on the 1st run to the 
2nd run. Is that right?

On 10/22/2021 4:58 PM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution

Hi there

I created labels on surfaces of subjects (chimp) registered to a particular 
volumetric template. The labels were created on the surfaces in Freeview using 
Freesurfer 7.1.

Since creating these labels, I improved the intensity inhomogeneity in the 
scans and re-ran the surfaces. When I try to use mri_label2label to transpose 
the labels to the new surfaces of each subject, the labels do not fall exactly 
where they should. In fact, the surfaces themselves have a slight translation 
in them (see snapshot). I assume this is because my registration to the 
template that I did prior to running recon-all is differing somehow between the 
2 groups. However, I thought that this should not matter since mri_label2label 
--regmethod surface is using the sphere.reg to fsaverage.

I am wondering if there is anything I can do to improve mri_label2label to 
avoid editing the labels manually?

Thank you for your time,
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute



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Re: [Freesurfer] Converting volume to annotation

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there,

I think a somewhat similar question was posted last week - does this help?

You can also run recon-all on the mni152, then run. Load it with your 
volume-based atlas to make sure that the alignment is good and that the 
surfaces surround your labels, then run
mri_vol2surf (--projfrac 0.5) on your volume-based atlas to create a 
surface-based atlas, then run mris_seg2annot to create the annotation (run with 
--help to get more docs)

On 10/11/2021 10:09 AM, Fischl, Bruce wrote:

Hi Paul



mri_vol2label maps the volume into an ascii label structure but has no 
knowledge of surfaces. You then need to run mri_label2label with options like 
–sample to sample it onto a surface



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>On
 Behalf Of Paul Dhami
Sent: Sunday, October 10, 2021 6:53 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Creating a surface parcellation from a volume atlas



External Email - Use Caution

Dear Freesurfer community,



I have a .nii volume atlas (CAREN), defining 5 networks, in MNI (ICBM152) space.



However, I wish to do my analysis in surface rather than volume space, and for 
the software I am using, that means I need to load in a .annot file.



For the first step, I used:



mri_vol2label --c CAREN_5networks.nii --id 1 --l 1.label



and did this for values 1 to 5 (for each of the networks). However, looking at 
the resulting label file, the first column is nothing but -1 values. I believe 
this should be the vertex number, and trying to combine these labels into an 
.annot file is not working.



Apologizes for the naive question, but can anyone share as to how I can 
ultimately create a surface atlas when I have the volume.nii atlas file? Was I 
wrong with mri_vol2label as my first step?



I am using Freesurfer version 7.2.0.



Thank you, Paul


--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lorenzo Pini 

Sent: Monday, October 25, 2021 8:49 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Converting volume to annotation


External Email - Use Caution

Dear experts,

I created a modified version of aparc+aseg.mgz files. Values now represent the 
functional connectivity strength of each parcel in the Desikan-Killiany atlas 
(ranging from -0.2 to 1 - rvalues).

I would like to represent these new parcellation r-values over the native 
inflated surface (with freeview maybe?). How can I convert this volume 
(modified aparc+aseg - in orig.mgz space) to label/annotation to be represented 
on the surface?

Thanks!

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Re: [Freesurfer] FW: make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

Could I get some input on this?

Thanks,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Monday, April 26, 2021 at 11:56 AM
To: Freesurfer support list 
Subject: [Freesurfer] FW: make_average_subject without Talairach transform


External Email - Use Caution
Hi there

Still hoping for some help on this.

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 20, 2021 at 10:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there,

Still wondering if we can get some help with this. Our update is the following:


  1.  When we run make_average_subject with some chimp scans, with default 
settings, it runs but the average surfaces are inflated compared to the 
individual subjects, presumably because the Talairach.xfm is being used.
  2.  When we replace the ?h.sphere.reg of each subject with one that was 
generated by registering each subject’s surfaces to those of the average chimp 
template, it runs as well, but the average surfaces are still inflated, again I 
presume because it is using Talairach.xfm.
  3.  When we insert an .xfm of each subject to the average chimp template into 
each subject/mri/transforms and use make_average_subject with –-xform flag, it 
crashes at the same spot every time. (See below for where it crashes)
  4.  If I try to start from mris_make_average_surface with –x transform.xfm, I 
get the output “don’t know what to do with transform.xfm” and it crashes.


#@# Making average lh.white surface -
Tue Apr 20 10:31:38 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/avgtest
mris_make_average_surface -X 2GabrielApril15.xfm -i 7 -o white -sdir-out 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/
 lh white sphere.reg avgtest Abby Agatha
using xform 2GabrielApril15.xfm...
reading vertex positions from white...
---
hemi= lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname   = avgtest
xform   = 2GabrielApril15.xfm
---


mris_average_surface failed



Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Wednesday, April 14, 2021 at 7:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there

As a follow-up, we realized that we had to also replace the lh.sphere.reg and 
rh.sphere.reg in the subject folders with new ones that were created by 
registering each subject lh and rh.sphere to those of the average chimp 
template. Once we did this, the script ran. However, as you can see, some 
serious scaling took place, I presume because it is still incorporating 
somewhere MNI space. I can see in the log that MNI305 seems to be called.

Any thoughts?

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 13, 2021 at 3:47 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi Doug

I did try as you suggested and no matter what I do, I get the following error 
after about 10 seconds of make_average_subject. The transforms to the average 
chimp template are in .xfm format and are in the subject/mri/transforms folder. 
These subjects were created with --hires, could that be creating a problem?


trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_7.1.1$ 
make_average_subject --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_subject --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_subject 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)
make_average_surface --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_surface --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_surface 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer

[Freesurfer] FW: make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

Still hoping for some help on this.

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 20, 2021 at 10:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there,

Still wondering if we can get some help with this. Our update is the following:


  1.  When we run make_average_subject with some chimp scans, with default 
settings, it runs but the average surfaces are inflated compared to the 
individual subjects, presumably because the Talairach.xfm is being used.
  2.  When we replace the ?h.sphere.reg of each subject with one that was 
generated by registering each subject’s surfaces to those of the average chimp 
template, it runs as well, but the average surfaces are still inflated, again I 
presume because it is using Talairach.xfm.
  3.  When we insert an .xfm of each subject to the average chimp template into 
each subject/mri/transforms and use make_average_subject with –-xform flag, it 
crashes at the same spot every time. (See below for where it crashes)
  4.  If I try to start from mris_make_average_surface with –x transform.xfm, I 
get the output “don’t know what to do with transform.xfm” and it crashes.


#@# Making average lh.white surface -
Tue Apr 20 10:31:38 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/avgtest
mris_make_average_surface -X 2GabrielApril15.xfm -i 7 -o white -sdir-out 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/
 lh white sphere.reg avgtest Abby Agatha
using xform 2GabrielApril15.xfm...
reading vertex positions from white...
---
hemi= lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname   = avgtest
xform   = 2GabrielApril15.xfm
---


mris_average_surface failed



Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Wednesday, April 14, 2021 at 7:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there

As a follow-up, we realized that we had to also replace the lh.sphere.reg and 
rh.sphere.reg in the subject folders with new ones that were created by 
registering each subject lh and rh.sphere to those of the average chimp 
template. Once we did this, the script ran. However, as you can see, some 
serious scaling took place, I presume because it is still incorporating 
somewhere MNI space. I can see in the log that MNI305 seems to be called.

Any thoughts?

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 13, 2021 at 3:47 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi Doug

I did try as you suggested and no matter what I do, I get the following error 
after about 10 seconds of make_average_subject. The transforms to the average 
chimp template are in .xfm format and are in the subject/mri/transforms folder. 
These subjects were created with --hires, could that be creating a problem?


trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_7.1.1$ 
make_average_subject --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_subject --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_subject 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)
make_average_surface --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_surface --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_surface 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)

make_average_surface

Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
/usr/local/freesurfer-7.1.1//bin

Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there,

Still wondering if we can get some help with this. Our update is the following:


  1.  When we run make_average_subject with some chimp scans, with default 
settings, it runs but the average surfaces are inflated compared to the 
individual subjects, presumably because the Talairach.xfm is being used.
  2.  When we replace the ?h.sphere.reg of each subject with one that was 
generated by registering each subject’s surfaces to those of the average chimp 
template, it runs as well, but the average surfaces are still inflated, again I 
presume because it is using Talairach.xfm.
  3.  When we insert an .xfm of each subject to the average chimp template into 
each subject/mri/transforms and use make_average_subject with –-xform flag, it 
crashes at the same spot every time. (See below for where it crashes)
  4.  If I try to start from mris_make_average_surface with –x transform.xfm, I 
get the output “don’t know what to do with transform.xfm” and it crashes.


#@# Making average lh.white surface -
Tue Apr 20 10:31:38 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/avgtest
mris_make_average_surface -X 2GabrielApril15.xfm -i 7 -o white -sdir-out 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/
 lh white sphere.reg avgtest Abby Agatha
using xform 2GabrielApril15.xfm...
reading vertex positions from white...
---
hemi= lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname   = avgtest
xform   = 2GabrielApril15.xfm
---


mris_average_surface failed



Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Wednesday, April 14, 2021 at 7:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi there

As a follow-up, we realized that we had to also replace the lh.sphere.reg and 
rh.sphere.reg in the subject folders with new ones that were created by 
registering each subject lh and rh.sphere to those of the average chimp 
template. Once we did this, the script ran. However, as you can see, some 
serious scaling took place, I presume because it is still incorporating 
somewhere MNI space. I can see in the log that MNI305 seems to be called.

Any thoughts?

Trisanna
--


From:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, April 13, 2021 at 3:47 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution
Hi Doug

I did try as you suggested and no matter what I do, I get the following error 
after about 10 seconds of make_average_subject. The transforms to the average 
chimp template are in .xfm format and are in the subject/mri/transforms folder. 
These subjects were created with --hires, could that be creating a problem?


trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_7.1.1$ 
make_average_subject --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_subject --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_subject 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)
make_average_surface --out avgApril13 --subjects Abby Agatha Amanda Artemus 
Arthur --xform 2GabrielApril13

setenv SUBJECTS_DIR 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_surface --out avgApril13 
--subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13

make_average_surface 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)

make_average_surface

Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
/usr/local/freesurfer-7.1.1//bin/make_average_surface
--out avgApril13 --subjects Abby Agatha Amanda Artemus Arthur --xform 
2GabrielApril13
input subjects: Abby Agatha Amanda Artemus Arthur
output subject: avgApril13
mri_add_xform_to_header -c auto 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13/mri/mni305.cor.mgz
 
/data-01/trisanna

Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

 = -0.083, std = 4.140
curvature mean = -0.029, std = 0.297
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.inflated.H...
curvature mean = -0.042, std = 1.033
computing parameterization for surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.sulc...
computing parameterization for surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.smoothwm...

processing subject Arthur (5 of 5)
reading spherical surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.sphere.reg...
curvature mean = -0.077, std = 4.286
curvature mean = -0.024, std = 0.300
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.inflated.H...
curvature mean = -0.007, std = 0.961
computing parameterization for surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.sulc...
computing parameterization for surface 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.smoothwm...
writing updated template with 5 subjects to rh.reg.template.tif...
curvature mean = -0.020, std = 4.236
curvature mean = -0.034, std = 0.297

#@# Making average lh.white surface -
Tue Apr 13 15:31:11 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
mris_make_average_surface -X 2GabrielApril13 -i 7 -o white -sdir-out 
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster lh white 
sphere.reg avgApril13 Abby Agatha Amanda Artemus Arthur
using xform 2GabrielApril13...
reading vertex positions from white...
---
hemi= lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname   = avgApril13
xform   = 2GabrielApril13
---


Segmentation fault (core dumped)
mris_average_surface failed
ERROR: make_average_surface

--


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 11:36 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you have the transform in the form of an LTA file, I think all you need to 
do is put it in the subject/mri/transforms folder, then spec --xfrom your.lta 
when running make_average_subject
On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi Doug

The scans were registered (6 parameter) to a common chimp template prior to 
input to recon-all. The surfaces have reconstructed nicely and match the input 
volumes.
I would now like to create an average surface from these surfaces that are “in 
the space of the average chimp volume”.

Trisanna
--


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, March 25, 2021 at 11:24 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you don't have a transform, how will you align the subjects into a common 
space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--





___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://secure-web.cisco.com/16zPDKjU1a1lBvaTLKh6JSovN0ea4oGDlAFLs_z_geY9DffTDSugJmWlDRCiTO3L0XNejkcGl6w10oDJyjLNw_nlGCTSpPgelODOxaca9dRysWrH5kqlRKb3i9W7qrbLMAvwFl8611lM61aCWL8yVEmYSX1C26xJCLKfcBANlYyY0PUuo1DHFz3iWPp4vLRyQhQF7Sx8UrUsDQcfzwyBpNjPgJrWTaPOFmxkBlxawotxw4vRsswf0-AFBXXmK09sztYwAWXUXdOzdQqy8bFCigw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer






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Freesurfer mailing list

Freesurfer@nmr.mgh.harv

Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Ah, neat! Ok, will give this a go!
Thanks a bunch

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 11:36 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you have the transform in the form of an LTA file, I think all you need to 
do is put it in the subject/mri/transforms folder, then spec --xfrom your.lta 
when running make_average_subject
On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi Doug

The scans were registered (6 parameter) to a common chimp template prior to 
input to recon-all. The surfaces have reconstructed nicely and match the input 
volumes.
I would now like to create an average surface from these surfaces that are “in 
the space of the average chimp volume”.

Trisanna
--


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, March 25, 2021 at 11:24 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you don't have a transform, how will you align the subjects into a common 
space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--





___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Doug

The scans were registered (6 parameter) to a common chimp template prior to 
input to recon-all. The surfaces have reconstructed nicely and match the input 
volumes.
I would now like to create an average surface from these surfaces that are “in 
the space of the average chimp volume”.

Trisanna
--


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 11:24 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

If you don't have a transform, how will you align the subjects into a common 
space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Thanks Bruce for your speedy response.

I am dealing with chimp scans and therefore am trying to avoid anything to do 
with Talairach. The surfaces have reconstructed pretty nicely using recon-all, 
but I’d like to create an average surface now.

I will try as you suggest

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Thursday, March 25, 2021 at 10:59 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] make_average_subject without Talairach transform

Sure, I guess you can just run mri_average. I think also if you specify the 
file name for the transform as identity.nofile to any binary that takes an lta 
file, the code will internally create an identity transform.

I won’t look pretty though….
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Thursday, March 25, 2021 10:19 AM
To: Freesurfer support list 
Subject: [Freesurfer] make_average_subject without Talairach transform


External Email - Use Caution

External Email - Use Caution
Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] make_average_subject without Talairach transform

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I’d like to know if it is possible to create an average volume and average 
surface of several subjects without having to incorporate the Talairach 
transform and no transform at all.

Thank you,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--

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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] What exactly are the BA_exvivo.thresh label and annotation files?

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Julien

In researching this a few years ago I asked the question

What exactly has been
>> done to change the .label
>> (e.g. lh BA44.label) to
>> .thresh.label (e.g. lh
>> BA44.thresh.label?

And was told

The .thresh labels have been
>> thresholded with a p-value
>>   threshold that is "best" on our
>> training set of
>>   manually/architectonically defined
>> labels.

I then looked into this a bit further and found the following explanation:

On 14-09-08 12:39 PM, Anastasia Yendiki wrote:
> On the difference between .thresh and "not .thresh" labels: The
> BA labels come from averaging histologically derived labels from a set of
> post mortem brains. The non-thresholded version is just the sum of the
> corresponding labels from the different brains in fsaverage space. So
> vertices are included even if only one of the brains had their BA in that
> vertex, which means that these labels are going to be rather large. In the
> thresholded version, a threshold has been applied to the average BA label,
> to make it have an area as close as possible to the average area of the
> individual BA labels. I hope this makes sense.


I hope this helps!

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
-- 
 

On 2021-02-18, 3:27 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
julienbesle"  wrote:

External Email - Use Caution

Hello,

The ex-vivo BA label and annotation files named 
?h.BA??_exvivo.thresh.label and BA_exvivo.thresh.annot seem to be 
thresholded versions of the corresponding probabilistic BA labels. Was a 
simple threshold on the probability used and if yes, what was the value?

In addition the annotation files, whether thresholded or not, only have 
one label per vertex. Are the labels based on the maximum probability 
across all BA labels?

Thanks

Julien

-- 
--
Julien Besle
Assistant Professor
Department of Psychology
Faculty of Arts and Sciences
American University of Beirut
Riad El-Solh / Beirut 1107 2020
Lebanon

Jesup Hall, Room 103E
Tel: +961 1 350 000 ext. 4927
-


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https://secure-web.cisco.com/1XQKd9pXAr8qUGqeGMndR3TJOl3i07YuFeBt8v6LPq0Ro62i6h-ivXgLE85MdCQy_C9CD3rVltO97GONz3BNW3rblKwSS2Ve88Pc8LZmlHrJKU2H0Bxx4KA2gZDrgSrpyTJ6rKDfwa1Ooqb8k_mekLQN8Jy2TO8jA7BLe4YkwwoliTBMfhn5k3YGSkpwixody3rFZvZ8vp1QZwZItV_nZFkSrO7aSNXgJwgfDnsRBin97WVFydnfBO3ZYqsWiVTpmAkPZaY-ypSATaVJPP7NZmw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer



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Re: [Freesurfer] overlap/intersection of labels?

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Cornelius

I found something that computes the overlap of labels across the same vertex 
when doing some research about this, not sure if this is what you mean:

https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4rsX6beTdCfGCkpiAyjUuMFA31V5ClU95ErPkQPZP8TKRthymZKTmx9z4NZ-1Q_VMNlPzPJ7PZG4H-wntegGfigUm5R6ocjIe4fS6bL4_82SxATBarpW8b6rv_vC1VPBn1ZM4Hj4ld7D7l3hMWkgB8zNZaHVjFrDQM4so73Mk3cuFXo4uZfnmiBKYK9XTJlzfFP24H6-tsGIkT4ka-7BQxMKOmF6bzTYzRo0tE8HTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_label2annot

See specifically:
--nhits

This option creates a diagnostic file showing whether the cumulative effect of 
all the label files happens to assign more than one label to each vertex. The 
output file is a 
FreeSurfer<https://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8fE_QRjLZ5IwPbIC4gnKD6g26N7TVbaIwYLg5BdgQSCFY1LmWY1cDfBL-R49zhRDt-6TzW_S84l6Z-4U3QS-SBlj8HR82qBl0HjcfjS2buz3mtuIQomiilbbafLXzRw1wQSaUnmj1OITA84m-fC1C8HrL430p2kCyyotFmJGKKwiiXBgMYlYljQIFiqINhAJFUVeI9kbMvioqTgmQZvjStJ8ARcmqHgrk_981OzG8NQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurfer>
 'overlay' format file, in which each vertex has an associated value, in this 
case the count of labels assigned to that vertex. This can be displayed in 
tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices 
(count<=1) from bad (count>=2).

I know there is also a command merge_labels that may help?

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Dr. Cornelius 
Kronlage" 
Reply-To: Freesurfer support list 
Date: Tuesday, February 16, 2021 at 11:19 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] overlap/intersection of labels?


External Email - Use Caution

Dear freesurfers,



is there an elegant way of computing the intersection or overlap of different 
labels or - which would be even more useful for my application - annotations?



I only managed to find labels_intersect (which appears to be from MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnwCugW0W6FhO8wM0TL2oLO5bi9fjIhtPrBDzhbCqKzcbupsD5PFcOSeF5Q0Rs_J3sJoI9lWbxxbrYbzUv7-bxMiuXfAqo77oTh3OfNCeUFmsk9uuSK8z0-kYvPRfV89c3qUMvDGvWaz4sAtwVH3FXBf11T46qVKtA6pTCyt2sx-P4ee8nfAHn8Aoz2sdWCcPJLXcMFrrUBot8VS3a2wmrELeIOWXwLg6zxRoTGxpHCw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html<https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naUegbdbmI9Bk7UNIwOTDDV40505y4xUMucZzUUWAKig63gNPrAZl0JMYNPDR9rlE4fUcOuQETynMWSKJG67sRNzzZQq8VF7AEsupWpjkrPP17ola-zMVT-3GDtM_dSs0-j76spejYlLevtumd4uKC8BNXwnxiW47uZxy5cBV4IPlI1yL8DP4GKO7QCjCWHuSjiE1xMapPwxOxVnVfHUKM/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html>
 ) which is awfully slow. In case this is of use for anyone else, I attached a 
modified version using 'join' that runs much faster, only has some 
compatibility issues with Mac.




>time labels_intersect precentral.label frontal.label out1.label > /dev/null

real1m41.862s
user0m31.052s
sys0m30.757s
>time bash bash_labels_intersect.sh precentral.label frontal.label out2.label

real0m0.193s
user0m0.118s
sys0m0.015s
>diff -w out1.label out2.label
>





Thank you and best wishes

Cornelius



--
Cornelius Kronlage
Assistenzarzt
Klinik für Neurologie | Neurologie mit Schwerpunkt Epileptologie
Universitätsklinikum Tübingen
Hoppe-Seyler-Str. 3 | 72076 Tübingen





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Re: [Freesurfer] mincRead error

[Trisanna Sprung-Much]

External Email - Use Caution

Hi All

As a frequent user of minctools, I know I’ve had problems in the past if I 
source minctools before sourcing freesurfer in the same terminal, because 
freesurfer uses an older version of minctools.
Also, freesurfer uses minc1 format not minc2.

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Wednesday, February 10, 2021 at 9:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mincRead error

Can you send the `mri/mri_nu_correct.mni.log` file as well? Have you installed 
minc tools separately on your local machine and do you have any of these 
variables set in your default environment?

MNI_DIR
MINC_BIN_DIR
MINC_LIB_DIR

It’s possible there’s another install of MNI that’s interfering with the 
freesurfer one.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Michele Valotti 

Date: Monday, February 8, 2021 at 9:53 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mincRead error

External Email - Use Caution
attached is the log for the run, the version of mri_convert is the same version 
on my local machine (where the command runs) and in the cloud instance

On Fri, 5 Feb 2021 at 18:02, Michele Valotti 
mailto:michele.valo...@gmail.com>> wrote:
Hi all,
I am running long FreeSurfer and after successfully testing it on my local 
machine I tried to run it on a server (which should however have the same 
FreeSurfer version and setup), but I am getting this error

mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz 
--conform
mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like 
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc...
Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 
UTC 2020 x86_64 GNU/Linux

recon-all -s base_freesurfer exited with ERRORS at Fri Feb  5 17:45:34 UTC 2021


Any idea what the cause of this might be?
Thank you!
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Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Trisanna Sprung-Much 

Sent: Tuesday, January 26, 2021 6:12 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Tuesday, January 26, 2021 3:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:00 PM
To: Freesurfer support list 
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:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:57 PM
To: Freesurfer support list 
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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 12:24 PM
To: Freesurfer support list 
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:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



Hi Trisanna



Yes, I’m pretty sure that would work. That is, using the current freeview on 
older versions of recon data.



Cheers

Bruce



p.s. one addendum – you should not have to blur the labels after registration, 
assuming your manually labeled dataset is big enough



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list 
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 o

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Tuesday, January 26, 2021 3:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:00 PM
To: Freesurfer support list 
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:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:57 PM
To: Freesurfer support list 
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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 12:24 PM
To: Freesurfer support list 
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:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



Hi Trisanna



Yes, I’m pretty sure that would work. That is, using the current freeview on 
older versions of recon data.



Cheers

Bruce



p.s. one addendum – you should not have to blur the labels after registration, 
assuming your manually labeled dataset is big enough



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list 
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: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list 
mailto:freesurfer@nmr

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

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:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:57 PM
To: Freesurfer support list 
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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 12:24 PM
To: Freesurfer support list 
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:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Hi Trisanna

Yes, I’m pretty sure that would work. That is, using the current freeview on 
older versions of recon data.

Cheers
Bruce

p.s. one addendum – you should not have to blur the labels after registration, 
assuming your manually labeled dataset is big enough

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list 
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: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
I think it would be a good idea to take a step back and tell us what you are 
trying to accomplish.  This is all not the right way to go about things.  The 
HCP already produces surfaces registered to MNI space in the volume for example.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 9:45 AM
To: Freesurfer support list 
mailto: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 wi

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

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:  on behalf of "Fischl, Bruce" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Hi Trisanna

Yes, I’m pretty sure that would work. That is, using the current freeview on 
older versions of recon data.

Cheers
Bruce

p.s. one addendum – you should not have to blur the labels after registration, 
assuming your manually labeled dataset is big enough

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Tuesday, January 26, 2021 1:13 PM
To: Freesurfer support list 
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: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution
I think it would be a good idea to take a step back and tell us what you are 
trying to accomplish.  This is all not the right way to go about things.  The 
HCP already produces surfaces registered to MNI space in the volume for example.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 9:45 AM
To: Freesurfer support list 
mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Tuesday, January 26, 2021 11:28 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution

You are likely to get significantly worse results by reprocessing the HCP 
subjects with FreeSurfer 7.X.  Unfortunately it has issues with HCP data that 
haven’t been addressed yet.



Matt.



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 9:13 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP T1w sca

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

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:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 11:01 AM
To: Freesurfer support list 
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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:45 AM
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Tuesday, January 26, 2021 11:28 AM
To: Freesurfer support list 
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:  on behalf of Trisanna 
Sprung-Much 
Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:13 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi Doug and Matt



So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.



As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.



I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.



Best

Trisanna



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, January 25, 2021 11:22 PM
To: 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: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<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/scrip

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Matt

We want the surfaces to be extracted from volumes that have been registered to 
MNI152, rather than extracting the surfaces in the native space of the subject, 
which is what FreeSurfer does.

I have done this for 2 other projects in the past for ICBM data (not HCP) and 
it worked fine.

What would be the concern with the HCP data?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Glasser, Matthew 

Sent: Tuesday, January 26, 2021 11:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1


External Email - Use Caution

That’s not a good idea either.



Matt.



From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, January 26, 2021 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1



Why are you registering it to the MNI prior to FS analysis?

On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

Hi Doug and Matt



So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.



As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.



I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.



Best

Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<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: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<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,

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Doug

We want the surfaces to be extracted from volumes that have been registered to 
MNI152, rather than extracting the surfaces in the native space of the subject, 
which I remember you saying at a workshop a few years ago is what FreeSurfer 
does.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, January 26, 2021 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

Why are you registering it to the MNI prior to FS analysis?

On 1/26/2021 10:13 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

Hi Doug and Matt

So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.

As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.

I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.

Best
Trisanna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, January 25, 2021 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<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: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<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.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fra

Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Doug and Matt

So the HCP scans are at 0.5mm resolution because they were originally 0.7mm and 
have been registered to our 0.5mm MNI152 template, to avoid losing data by 
registering to the 1mm template. That's all.

As for the recon-all.log, unfortunately I deleted it when I re-ran the same 
subject this weekend using an -expert file to specify the number of inflations 
and it worked. It took 24 hrs.

I will try to run another subject without the expert file, since Doug says this 
should not be necessary, and get back to you ASAP.

Best
Trisanna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, January 25, 2021 11:22 PM
To: 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: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 21, 2021 at 12:21 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1





External Email - Use Caution

Hi there



As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:



/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts



 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix



doing quick spherical unfolding.

limitting unfolding to 6 passes

using n_averages = 128

setting seed for random number genererator to 1234

version: 7.1.1

available threads: 1

scaling brain by 0.274...

inflating...

Command terminated by signal 11

@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00

@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00

Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021







Any advice would be greatly appreciated,



Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Trisanna Sprung-Much 
<mailto:trisanna.sprung-m...@mail.mcgill.ca>
Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
<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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Re: [Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

As a follow-up to this question, I tried the flags as stated and the recon-all 
seems to have failed at the inflation stage:

/data-01/trisanna/freesurfer/freesurfer_7.1.1/TEST2/scripts

 mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix 
../surf/lh.qsphere.nofix

doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
version: 7.1.1
available threads: 1
scaling brain by 0.274...
inflating...
Command terminated by signal 11
@#@FSTIME  2021:01:21:08:13:01 mris_sphere N 9 e 4.07 S 0.18 U 3.72 P 95% M 
281092 F 17 R 136514 W 0 c 337 w 22 I 4312 O 0 L 1.00 1.00 1.00
@#@FSLOADPOST 2021:01:21:08:13:06 mris_sphere N 9 1.00 1.00 1.00
Linux kaplan 4.15.0-132-generic #136~16.04.1-Ubuntu SMP Tue Jan 12 18:22:20 UTC 
2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s TEST2 exited with ERRORS at Thu Jan 21 08:13:06 EST 2021



Any advice would be greatly appreciated,

Trisanna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Trisanna Sprung-Much 

Sent: Tuesday, January 19, 2021 6:05 PM
To: Freesurfer support list 
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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[Freesurfer] HCP T1w scans on FreeSurfer 7.1

[Trisanna Sprung-Much]

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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Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

[Trisanna Sprung-Much]

External Email - Use Caution

thank you for your speedy response, Bruce!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Monday, January 18, 2021 6:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1


Yes, that should work

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trisanna Sprung-Much
Sent: Monday, January 18, 2021 5:01 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1



External Email - Use Caution

Hi there



There is likely a silly question but if one were to create a label on a white 
surface and wants to view it on the pial surface of the same subject, do we 
simply load the pial surface and the label? Does this give a precise 
visualization of the label on the pial surface, considering that the vertex 
number is the same across surfaces?



many thanks,

Trisanna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Wednesday, January 6, 2021 12:43 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1



If you just need one label you can create a label instead of annotations. You 
can click “Path/Custom Fill” icon on the left panel, draw a closed path and use 
custom fill tool to draw a label.  Just like in TkSurfer if you have used it 
before.



[cid:image001.jpg@01D6EDBE.8C46FD00]



On Jan 6, 2021, at 11:32 AM, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:



External Email - Use Caution

Hi there



As a follow-up to my earlier email, I figured it out. I can create 1 label in 
an annotation and simply have to assign an "index" value before saving.



Could you please confirm that this is the best way to go about create a new 
label on a surface?



Many thanks,

Trisanna

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Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

There is likely a silly question but if one were to create a label on a white 
surface and wants to view it on the pial surface of the same subject, do we 
simply load the pial surface and the label? Does this give a precise 
visualization of the label on the pial surface, considering that the vertex 
number is the same across surfaces?

many thanks,
Trisanna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Sent: Wednesday, January 6, 2021 12:43 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

If you just need one label you can create a label instead of annotations. You 
can click “Path/Custom Fill” icon on the left panel, draw a closed path and use 
custom fill tool to draw a label.  Just like in TkSurfer if you have used it 
before.

[cid:15CC1D35-3F5C-4946-A2BE-C6B73EBEC9EF@lan]

On Jan 6, 2021, at 11:32 AM, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:

External Email - Use Caution

Hi there

As a follow-up to my earlier email, I figured it out. I can create 1 label in 
an annotation and simply have to assign an "index" value before saving.

Could you please confirm that this is the best way to go about create a new 
label on a surface?

Many thanks,
Trisanna
___
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Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi Ruopeng

This makes a lot more sense! And I figured out how to erase parts and add parts 
to the same label.

Many thanks!

Trisanna Sprung-Much, PhD
McGill University
Montreal Neurological Institute
--


From:  on behalf of "Wang, Ruopeng" 

Reply-To: Freesurfer support list 
Date: Wednesday, January 6, 2021 at 11:44 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1

If you just need one label you can create a label instead of annotations. You 
can click “Path/Custom Fill” icon on the left panel, draw a closed path and use 
custom fill tool to draw a label.  Just like in TkSurfer if you have used it 
before.

[cid:15CC1D35-3F5C-4946-A2BE-C6B73EBEC9EF@lan]


On Jan 6, 2021, at 11:32 AM, Trisanna Sprung-Much 
mailto:trisanna.sprung-m...@mail.mcgill.ca>>
 wrote:

External Email - Use Caution
Hi there

As a follow-up to my earlier email, I figured it out. I can create 1 label in 
an annotation and simply have to assign an "index" value before saving.

Could you please confirm that this is the best way to go about create a new 
label on a surface?

Many thanks,
Trisanna
___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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[Freesurfer] making labels in Freeview/Freesurfer 7.1.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

As a follow-up to my earlier email, I figured it out. I can create 1 label in 
an annotation and simply have to assign an "index" value before saving.

Could you please confirm that this is the best way to go about create a new 
label on a surface?

Many thanks,
Trisanna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] creating labels on surfaces with Freeview 7.1.1

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there,

I am looking for instructions on how to create/edit my own labels directly on 
surfaces using the latest version of Freesurfer/Freeview but I cannot seem to 
find this documentation. My understanding is that an annotation file has 
multiple labels and a look up table. What if I want to just create 1 label?

When I go to Annotation --> New and create a label and assign a name and 
colour, I get the following msg when I try to save:

"There are unassigned labels in the annotation. Please assign all the labels 
first"

Any help would be greatly appreciated,

Trisanna

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Re: [Freesurfer] Fwd: vertex MNI305

[Trisanna Sprung-Much]

External Email - Use Caution

thanks Ruopeng for your speedy response! And this are indeed in MNI305?
Bruce was fairly certain but I just wanted to confirm.

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Aug 21, 2018 at 11:13 AM Ruopeng Wang 
wrote:

> I think the coordinate circled in the picture is the exact coordinate of
> the vertex, also in surface ras. The coordinate under "SurfaceRAS" is the
> coordinate of the current cursor location in surface ras. The slight
> difference is because the cursor is not exactly on the vertex, but close
> enough so that the vertex number is shown.
>
> Best,
> Ruopeng
>
> On 08/21/2018 10:10 AM, Trisanna Sprung-Much wrote:
>
> External Email - Use Caution
> Hi there
>
> Doug can you please confirm? Bruce said you would be the best to answer
> and I've got revisions that are due. Please see the image attached. In my
> manuscript I report the x,y,z next to the vertex number in Freeview for MNI
> coordinates (MNI305) of that vertex. These only different very slightly
> from the RAS and SurfaceRAS coordinates above the vertex number in the
> panel but I'd like confirmation I am reporting the correct x.y,z.
>
> best
> Trisanna
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
> -- Forwarded message -
> From: Trisanna Sprung-Much 
> Date: Thu, Jul 26, 2018 at 7:35 PM
> Subject: vertex MNI305
> To: Freesurfer support list 
>
>
> Hi there
>
> This might be a very silly question but I actually cannot find the answer
> in the email archive:
>
> Assuming I have loaded a label onto fsaverage in Freeview and want to get
> the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z
> in brackets in the panel? I attach a photo of what I mean.
>
> Best wishes
> Trisanna
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
>
> ___
> Freesurfer mailing 
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] Fwd: vertex MNI305

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

Doug can you please confirm? Bruce said you would be the best to answer and
I've got revisions that are due. Please see the image attached. In my
manuscript I report the x,y,z next to the vertex number in Freeview for MNI
coordinates (MNI305) of that vertex. These only different very slightly
from the RAS and SurfaceRAS coordinates above the vertex number in the
panel but I'd like confirmation I am reporting the correct x.y,z.

best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology



-- Forwarded message -
From: Trisanna Sprung-Much 
Date: Thu, Jul 26, 2018 at 7:35 PM
Subject: vertex MNI305
To: Freesurfer support list 


Hi there

This might be a very silly question but I actually cannot find the answer
in the email archive:

Assuming I have loaded a label onto fsaverage in Freeview and want to get
the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z
in brackets in the panel? I attach a photo of what I mean.

Best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: vertex MNI305

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

Could I get a confirmation on this?

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jul 31, 2018 at 10:41 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> sorry, I think this came during Doug's vacation. I believe that those
> coords in fsaverage are MNI ones, but he can confirm
>
> cheers
> Bruce
>
>
> On Tue, 31 Jul 2018, Trisanna Sprung-Much wrote:
>
>
>> External Email - Use Caution
>>
>> Hi there
>> Still waiting for an answer to this!
>>
>> Thanks!
>> Trisanna
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> -- Forwarded message --
>> From: Trisanna Sprung-Much 
>> Date: Thu, Jul 26, 2018 at 7:35 PM
>> Subject: vertex MNI305
>> To: Freesurfer support list 
>>
>>
>> Hi there
>> This might be a very silly question but I actually cannot find the answer
>> in the email archive:
>> Assuming I have loaded a label onto fsaverage in Freeview and want to get
>> the MNI305 coordinate of
>> that labelled vertex, am I simply using the x,y,z in brackets in the
>> panel? I attach a photo of what
>> I mean.
>>
>> Best wishes
>> Trisanna
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Fwd: vertex MNI305

[Trisanna Sprung-Much]

External Email - Use Caution

thanks Bruce! I will wait for Doug's response.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jul 31, 2018 at 10:41 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> sorry, I think this came during Doug's vacation. I believe that those
> coords in fsaverage are MNI ones, but he can confirm
>
> cheers
> Bruce
>
>
> On Tue, 31 Jul 2018, Trisanna Sprung-Much wrote:
>
>
>> External Email - Use Caution
>>
>> Hi there
>> Still waiting for an answer to this!
>>
>> Thanks!
>> Trisanna
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> -- Forwarded message --
>> From: Trisanna Sprung-Much 
>> Date: Thu, Jul 26, 2018 at 7:35 PM
>> Subject: vertex MNI305
>> To: Freesurfer support list 
>>
>>
>> Hi there
>> This might be a very silly question but I actually cannot find the answer
>> in the email archive:
>> Assuming I have loaded a label onto fsaverage in Freeview and want to get
>> the MNI305 coordinate of
>> that labelled vertex, am I simply using the x,y,z in brackets in the
>> panel? I attach a photo of what
>> I mean.
>>
>> Best wishes
>> Trisanna
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] Fwd: vertex MNI305

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

Still waiting for an answer to this!

Thanks!
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


-- Forwarded message --
From: Trisanna Sprung-Much 
Date: Thu, Jul 26, 2018 at 7:35 PM
Subject: vertex MNI305
To: Freesurfer support list 


Hi there

This might be a very silly question but I actually cannot find the answer
in the email archive:

Assuming I have loaded a label onto fsaverage in Freeview and want to get
the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z
in brackets in the panel? I attach a photo of what I mean.

Best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] vertex MNI305

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

This might be a very silly question but I actually cannot find the answer
in the email archive:

Assuming I have loaded a label onto fsaverage in Freeview and want to get
the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z
in brackets in the panel? I attach a photo of what I mean.

Best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi there

I uploaded these last week to the file drop and used Bruce's email as it
said it requires a  ".nmr.mgh.harvard.edu" email type.

Please let me know if you received icbm-202 and icbm-205 as tar.gz files.
As I mentioned, I was able to get surfaces for both of these but they
seemed to end at the labeling step.



best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jan 19, 2018 at 10:42 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu>
wrote:

> You can send it to either my email (ahoo...@mgh.harvard.edu) or Bruce’s
>
> best,
> Andrew
>
> On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>
>
> thanks Andrew. I had seen that and will give it a go - just wanted to make
> sure that my recipient email would be the FreeSurfer support list.
>
> Trisanna
>
> On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu>
> wrote:
>
>> Hi Trisanna,
>>
>> Okay - if your file is less than 2GiB, I suggest sending your data via
>> the Martinos file drop (directions at the bottom of this page:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
>>
>> best
>> Andrew
>>
>> On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>>
>> Hi Andrew
>>
>> Thank you for your response. I gave it a go and still no luck, unless I
>> am missing something completely obvious here
>>
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>> surfer.nmr.mgh.harvard.edu
>> Connected to surfer.nmr.mgh.harvard.edu.
>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>> site
>> 220-shows implicit consent to our Acceptable Use Policy outlined
>> at
>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>>
>> 220-
>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-
>> 220-   and nothing happens OR
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-500 Bad EPRT protocol.
>> 220-
>> 220-  try issuing the EPSV command prior to GET or PUT.
>> 220-
>> 220
>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>> 331 Please specify the password.
>> Password:
>> 230 Login successful.
>> Remote system type is UNIX.
>> Using binary mode to transfer files.
>> ftp> cd transfer/incoming
>> 250 Directory successfully changed.
>> ftp> quote PASV
>> 227 Entering Passive Mode (132,183,202,158,147,251).
>> ftp> put icbm-205.tar.gz
>> local: icbm-205.tar.gz remote: icbm-205.tar.gz
>> 200 PORT command successful. Consider using PASV.
>> 425 Failed to establish connection.
>>
>>
>>
>>
>>
>> On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu>
>> wrote:
>>
>>> Hi Trisanna,
>>>
>>> Try running 'quote PASV' in ftp before running 'put' - that should
>>> hopefully clear up this issue.
>>>
>>> best,
>>> Andrew
>>>
>>>
>>> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
>>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>>
>>> Sorry, Bruce. ignore my last email. Not sure what happened there.
>>>
>>> I now am trying to upload icbm-205.tar.gz (the subject that failed) but
>>> I get the following and it happens over and over. Any idea what the problem
>>> could be?
>>>
>>> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
>>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
>>> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
>>> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
>>> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
>>> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
>>> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
>>> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
>>> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
>>> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
>>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>>> surfer.nmr.mgh.harvard.edu
>>> Connected to surfer.nmr.mgh.harvard.edu.
>>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>>> site

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

thanks Andrew. I had seen that and will give it a go - just wanted to make
sure that my recipient email would be the FreeSurfer support list.

Trisanna

On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu>
wrote:

> Hi Trisanna,
>
> Okay - if your file is less than 2GiB, I suggest sending your data via the
> Martinos file drop (directions at the bottom of this page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
>
> best
> Andrew
>
> On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>
> Hi Andrew
>
> Thank you for your response. I gave it a go and still no luck, unless I am
> missing something completely obvious here
>
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> quote PASV
> 227 Entering Passive Mode (132,183,202,158,147,251).
> ftp> put icbm-205.tar.gz
> local: icbm-205.tar.gz remote: icbm-205.tar.gz
> 200 PORT command successful. Consider using PASV.
> 425 Failed to establish connection.
>
>
>
>
>
> On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu>
> wrote:
>
>> Hi Trisanna,
>>
>> Try running 'quote PASV' in ftp before running 'put' - that should
>> hopefully clear up this issue.
>>
>> best,
>> Andrew
>>
>>
>> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>> Sorry, Bruce. ignore my last email. Not sure what happened there.
>>
>> I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
>> get the following and it happens over and over. Any idea what the problem
>> could be?
>>
>> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
>> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
>> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
>> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
>> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
>> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
>> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
>> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
>> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>> surfer.nmr.mgh.harvard.edu
>> Connected to surfer.nmr.mgh.harvard.edu.
>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>> site
>> 220-shows implicit consent to our Acceptable Use Policy outlined
>> at
>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>>
>> 220-
>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-
>> 220-   and nothing happens OR
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-500 Bad EPRT protocol.
>> 220-
>> 220-  try issuing the EPSV command prior to GET or PUT.
>> 220-
>> 220
>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>> 331 Please specify the password.
>> Password:
>> 230 Login successful.
>> Remote system type is UNIX.
>> Using binary mode to transfer files.
>> ftp> cd transfer/incoming
>> 250 Directory successfully changed.
>> ftp> put icbm-205.tar.gz
>> local: icbm-205.tar.gz remote: icbm-205.tar.gz
>> 200 PORT command successful. Consider using PASV.
>> 425 Failed to establish connection.
>>
>>
>

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi Andrew

Thank you for your response. I gave it a go and still no luck, unless I am
missing something completely obvious here

trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> quote PASV
227 Entering Passive Mode (132,183,202,158,147,251).
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.





On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu>
wrote:

> Hi Trisanna,
>
> Try running 'quote PASV' in ftp before running 'put' - that should
> hopefully clear up this issue.
>
> best,
> Andrew
>
>
> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Sorry, Bruce. ignore my last email. Not sure what happened there.
>
> I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
> get the following and it happens over and over. Any idea what the problem
> could be?
>
> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> put icbm-205.tar.gz
> local: icbm-205.tar.gz remote: icbm-205.tar.gz
> 200 PORT command successful. Consider using PASV.
> 425 Failed to establish connection.
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>> Thanks Bruce. I have uploaded it but I would like to confirm that you
>> received the ICBM_305.tar. For some reason I was not able to compress it
>> any further.
>>
>> To clarify, subjects 205 and now subject 202 have both failed after
>> surface extraction.
>>
>> best
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu
>> > wrote:
>>
>>> you can put it on our ftp site:
>>>
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>>> On 

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
get the following and it happens over and over. Any idea what the problem
could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Thanks Bruce. I have uploaded it but I would like to confirm that you
> received the ICBM_305.tar. For some reason I was not able to compress it
> any further.
>
> To clarify, subjects 205 and now subject 202 have both failed after
> surface extraction.
>
> best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> you can put it on our ftp site:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>> On Tue, 16 Jan
>> 2018, Trisanna Sprung-Much
>> wrote:
>>
>> > Hi Bruce
>> > Thanks for the speedy reply. Should I attach it here or is there a
>> place I can upload it to?
>> >
>> > best
>> > Trisanna
>> >
>> > --
>> > Ph.D. CandidateMcGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   hmmm, I've never seen label2label core dump before. Can you tar,
>> gzip and
>> >   upload the entire subject dir?
>> >   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>> >   wrote:
>> >
>> >   > Hi there
>> >   >
>> >   > I ran Freesurfer 6.0 on a subject last night and it took about
>> 12 hours (seemed to get
>> >   to the very end) and then exited with
>> >   > errors. I can open my surfaces so I think it ended roughly with
>> the atlas labelling. I
>> >   attach the recon-all log file here.
>> >   >
>> >   > best wishes
>> >   >
>> >   > Trisanna
>> >   > --
>> >   > Ph.D. CandidateMcGill University
>> >   > Integrated Program in Neuroscience
>> >   > Psychology
>> >   >
>> >   >
>> >   >
>> >   >
>> >   ___
>> >   Freesurfer mailing list
>> >   Freesurfer@nmr.mgh.harvard.edu
>> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >   The information in this e-mail is intended only for the person to
>> whom it is
>> >   addressed. If you believe this e-mail was sent to you in 

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Thanks Bruce. I have uploaded it but I would like to confirm that you
received the ICBM_305.tar. For some reason I was not able to compress it
any further.

To clarify, subjects 205 and now subject 202 have both failed after surface
extraction.

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> you can put it on our ftp site:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> On Tue, 16 Jan
> 2018, Trisanna Sprung-Much
> wrote:
>
> > Hi Bruce
> > Thanks for the speedy reply. Should I attach it here or is there a place
> I can upload it to?
> >
> > best
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   hmmm, I've never seen label2label core dump before. Can you tar,
> gzip and
> >   upload the entire subject dir?
> >   On Tue, 16 Jan 2018, Trisanna Sprung-Much
> >   wrote:
> >
> >   > Hi there
> >   >
> >   > I ran Freesurfer 6.0 on a subject last night and it took about
> 12 hours (seemed to get
> >   to the very end) and then exited with
> >   > errors. I can open my surfaces so I think it ended roughly with
> the atlas labelling. I
> >   attach the recon-all log file here.
> >   >
> >   > best wishes
> >   >
> >   > Trisanna
> >   > --
> >   > Ph.D. CandidateMcGill University
> >   > Integrated Program in Neuroscience
> >   > Psychology
> >   >
> >   >
> >   >
> >   >
> >   ___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >   The information in this e-mail is intended only for the person to
> whom it is
> >   addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> >   contains patient information, please contact the Partners
> Compliance HelpLine at
> >   http://www.partners.org/complianceline . If the e-mail was sent
> to you in error
> >   but does not contain patient information, please contact the
> sender and properly
> >   dispose of the e-mail.
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi Bruce

Thanks for the speedy reply. Should I attach it here or is there a place I
can upload it to?

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> hmmm, I've never seen label2label core dump before. Can you tar, gzip and
> upload the entire subject dir?
> On Tue, 16 Jan 2018, Trisanna Sprung-Much
> wrote:
>
> > Hi there
> >
> > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours
> (seemed to get to the very end) and then exited with
> > errors. I can open my surfaces so I think it ended roughly with the
> atlas labelling. I attach the recon-all log file here.
> >
> > best wishes
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> ___
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Re: [Freesurfer] Brodmann areas - exvivo labels

[Trisanna Sprung-Much]

Thanks for the speedy reply, Matt and Bruce! In that case I'll go with the
.thresh for each Brodmann area.

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Oct 3, 2017 at 8:32 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> yes, I agree with Matt. You need different thresholds for different areas
> (e.g. V1 vs. BA44) and picking one that on average gives you the right
> sized label seems reasonable
>
> Bruce
> On Tue, 3 Oct 2017, Matt Glasser wrote:
>
> I would use the versions where the group size approximately matched the
>> individual size.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Trisanna
>> Sprung-Much
>> <trisanna.sprung-m...@mail.mcgill.ca>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Tuesday, October 3, 2017 at 7:36 PM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] Brodmann areas - exvivo labels
>>
>> Hi there
>>
>> If I wanted to compare some spatial probability maps of some sulci of
>> interest with the Juelich Data
>> provided by FreeSurfer, would it make more sense to use the unthresholded
>> Brodmann areas or the
>> .thresh ones? Based on my understanding of how the .thresh was created
>> (by creating a surface area
>> of the average BA label that best resembled the average surface area of
>> the label from each
>> individual hemisphere) in order to avoid including vertices that had a
>> probability of 10%, for
>> instance, I think using .thresh would be fine. However, I thought I would
>> verify. In input would be
>> greatly appreciated.
>>
>>
>> Best
>> Trisanna
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> ___ Freesurfer mailing list
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>> du/mailman/listinfo/freesurfer The
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[Freesurfer] Brodmann areas - exvivo labels

[Trisanna Sprung-Much]

Hi there

If I wanted to compare some spatial probability maps of some sulci of
interest with the Juelich Data provided by FreeSurfer, would it make more
sense to use the unthresholded Brodmann areas or the .thresh ones? Based on
my understanding of how the .thresh was created (by creating a surface area
of the average BA label that best resembled the average surface area of the
label from each individual hemisphere) in order to avoid including vertices
that had a probability of 10%, for instance, I think using .thresh would be
fine. However, I thought I would verify. In input would be greatly
appreciated.


Best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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[Freesurfer] Mid point on Freeview

[Trisanna Sprung-Much]

Hi there

I have a question concerning viewing a surface in Freeview (FS 6.0): *What
does the "mid point" variable refer to?* I can change it and it seems to
change the shading within the sulci when I am looking at a white matter
surface.

Many thanks

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] smoothing kernal

[Trisanna Sprung-Much]

Hi Doug

I'm doing just that - creating a statistical probability map to look at the
overlap across the 40 subjects for a given sulcus. When we do this
volumetrically it is traditional to smooth using FWHM of 3mm (about the
width of a sulcus). *I was told for surface data it needs to be more than
this, but I do not want to over-smooth.*
The command you gave me to do this back at the workshop in September was
mris_fwhm. I just wanted to know what an acceptable FWHM value would be.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, May 24, 2017 at 5:08 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> not sure what you are trying to do or why you would want to smooth the
> prob map
>
>
> On 05/24/2017 05:03 PM, Trisanna Sprung-Much wrote:
> > Hi there
> >
> > I labelled sulci in 40 T1 volumes and have created surface overlays
> > using mri_vol2surf and then registered these to fsaverage using
> > mri_surf2surf. I want to generate a statistical probability map using
> > mri_concat and then mris_fwhm for each sulcus. What is an acceptable
> > FWHM to use? It is the width of a sulcus on a pial surface of an
> > individual brain, i.e. about 2mm? Or on fsaverage, i.e. about 7mm?
> >
> > Thanks
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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[Freesurfer] smoothing kernal

[Trisanna Sprung-Much]

Hi there

I labelled sulci in 40 T1 volumes and have created surface overlays using
mri_vol2surf and then registered these to fsaverage using mri_surf2surf. I
want to generate a statistical probability map using mri_concat and then
mris_fwhm for each sulcus. What is an acceptable FWHM to use? It is the
width of a sulcus on a pial surface of an individual brain, i.e. about 2mm?
Or on fsaverage, i.e. about 7mm?

Thanks
Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] probability maps

[Trisanna Sprung-Much]

thanks Doug! I will give this a shot!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, May 15, 2017 at 9:56 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> you can do something like
>
> a = MRIread('map1.mgz');
>
> b = MRIread('map2.mgz');
>
> c = MRIread('map3.mgz');
>
> d = (a.vol > thresh + b.vol > thresh + d.vol> thresh)/3;
>
> [mm ii] = max(d);
>
> Then the vertex number will be ii-1 (need to convert from 1-based to
> 0-based)
>
>
>
>
> On 5/15/17 3:34 PM, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>
> The maps are .mgz format and are % overlap (across 40 subjects). They were
> generated using
>
> -labels turned into surface overlay using mri_vol2surf
> -then registered to fsaverage using mri_surf2surf
> -then averaged within fsaverage space using mri_concat and then mris_fwhm
> to smooth.
>
> Best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> what format is your map of p-values in?
>> On Mon, 15 May 2017, Trisanna
>> Sprung-Much wrote:
>>
>> > Hi Bruce
>> > I would not know where to start (not an avid matlab user) - what input
>> would
>> > be needed to be fed into matlab?
>> >
>> > Trisanna
>> >
>> > --
>> > Ph.D. CandidateMcGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> > wrote:
>> >   hmmm, should be pretty easy in matlab, no?
>> >   On Mon, 15 May 2017, Trisanna
>> >   Sprung-Much wrote:
>> >
>> >   > Hi there
>> >   > I have generated some anatomical probabilistic maps as
>> >   overlays on the
>> >   > fsaverage pial surface. Is there a way to automatically find
>> >   the vertex
>> >   > coordinates of the vertex with the highest probability of
>> >   overlap? Or does
>> >   > this have to be done manually in Freeview?
>> >   >
>> >   > Many thanks
>> >   >
>> >   > Trisanna
>> >   > --
>> >   > Ph.D. CandidateMcGill University
>> >   > Integrated Program in Neuroscience
>> >   > Psychology
>> >   >
>> >   >
>> >   >
>> >   >
>> >   ___
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>> >
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>> >   contains patient information, please contact the Partners
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Re: [Freesurfer] probability maps

[Trisanna Sprung-Much]

Hi Bruce

The maps are .mgz format and are % overlap (across 40 subjects). They were
generated using

-labels turned into surface overlay using mri_vol2surf
-then registered to fsaverage using mri_surf2surf
-then averaged within fsaverage space using mri_concat and then mris_fwhm
to smooth.

Best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> what format is your map of p-values in?
> On Mon, 15 May 2017, Trisanna
> Sprung-Much wrote:
>
> > Hi Bruce
> > I would not know where to start (not an avid matlab user) - what input
> would
> > be needed to be fed into matlab?
> >
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   hmmm, should be pretty easy in matlab, no?
> >   On Mon, 15 May 2017, Trisanna
> >   Sprung-Much wrote:
> >
> >   > Hi there
> >   > I have generated some anatomical probabilistic maps as
> >   overlays on the
> >   > fsaverage pial surface. Is there a way to automatically find
> >   the vertex
> >   > coordinates of the vertex with the highest probability of
> >   overlap? Or does
> >   > this have to be done manually in Freeview?
> >   >
> >   > Many thanks
> >   >
> >   > Trisanna
> >   > --
> >   > Ph.D. CandidateMcGill University
> >   > Integrated Program in Neuroscience
> >   > Psychology
> >   >
> >   >
> >   >
> >   >
> >   ___
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> >   contains patient information, please contact the Partners
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> >
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Re: [Freesurfer] probability maps

[Trisanna Sprung-Much]

Hi Bruce

I would not know where to start (not an avid matlab user) - what input
would be needed to be fed into matlab?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> hmmm, should be pretty easy in matlab, no?
> On Mon, 15 May 2017, Trisanna
> Sprung-Much wrote:
>
> > Hi there
> > I have generated some anatomical probabilistic maps as overlays on the
> > fsaverage pial surface. Is there a way to automatically find the vertex
> > coordinates of the vertex with the highest probability of overlap? Or
> does
> > this have to be done manually in Freeview?
> >
> > Many thanks
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> ___
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[Freesurfer] probability maps

[Trisanna Sprung-Much]

Hi there

I have generated some anatomical probabilistic maps as overlays on the
fsaverage pial surface. Is there a way to automatically find the vertex
coordinates of the vertex with the highest probability of overlap? Or does
this have to be done manually in Freeview?

Many thanks

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] smoothing kernel

[Trisanna Sprung-Much]

Hi Bruce

What I mean is - labeled sulci in volume space, overlaid onto surfaces and
then averaged across subjects.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Mar 30, 2017 at 12:56 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> what is a sulcal probability map?
> On Thu, 30 Mar 2017, Trisanna Sprung-Much
> wrote:
>
> > thanks, Bruce - that is what I am learning. And if it was to smooth data
> > from a sulcal probability map? A FWHM of 10 seems pretty high
> > best
> >
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Thu, Mar 30, 2017 at 12:17 PM, Trisanna Sprung-Much
> > <trisanna.sprung.m...@gmail.com> wrote:
> >   thanks, Bruce - that is what I am learning. And if it was to
> >   smooth data from a sulcal probability map? A FWHM of 10 seems
> >   pretty high
> > best
> >
> > Trisanna
> >
> > On Thu, Mar 30, 2017 at 9:45 AM, Bruce Fischl
> > <fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Trisanna
> >
> >   sorry, there is no easy answer to this question. It
> >   depends on what you
> >   are trying to do.
> >
> >   Bruce
> >   On Wed, 29 Mar 2017, Trisanna Sprung-Much wrote:
> >
> >   > Hi there
> >   > I am wondering whether there is an acceptable FWHM to
> >   use to smooth surface
> >   > data (for instance, a probability map)?
> >   >
> >   > Many thanks
> >   >
> >   > Trisanna
> >   > --
> >   > Ph.D. CandidateMcGill University
> >   > Integrated Program in Neuroscience
> >   > Psychology
> >   >
> >   >
> >   >
> >   >
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Re: [Freesurfer] smoothing kernel

[Trisanna Sprung-Much]

thanks, Bruce - that is what I am learning. And if it was to smooth data
from a sulcal probability map? A FWHM of 10 seems pretty high

best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Mar 30, 2017 at 12:17 PM, Trisanna Sprung-Much <
trisanna.sprung.m...@gmail.com> wrote:

> thanks, Bruce - that is what I am learning. And if it was to smooth data
> from a sulcal probability map? A FWHM of 10 seems pretty high
>
> best
>
> Trisanna
>
> On Thu, Mar 30, 2017 at 9:45 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Trisanna
>>
>> sorry, there is no easy answer to this question. It depends on what you
>> are trying to do.
>>
>> Bruce
>> On Wed, 29 Mar 2017, Trisanna Sprung-Much wrote:
>>
>> > Hi there
>> > I am wondering whether there is an acceptable FWHM to use to smooth
>> surface
>> > data (for instance, a probability map)?
>> >
>> > Many thanks
>> >
>> > Trisanna
>> > --
>> > Ph.D. CandidateMcGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> >
>> >
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[Freesurfer] smoothing kernel

[Trisanna Sprung-Much]

Hi there

I am wondering whether there is an acceptable FWHM to use to smooth surface
data (for instance, a probability map)?

Many thanks

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] recon-all error (6.0)

[Trisanna Sprung-Much]

Hi Bruce

I tried and still get the same error. Would this mean a space issue? I'm
not sure how this is possible as I'm working off a 2Tb drive

trisanna@kaplan:~$ mri_convert ./tmp.mri_nu_correct.mni.1798/nu1.mnc
orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.1798/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.1798/nu1.mnc...
mincRead(): can't find file ./tmp.mri_nu_correct.mni.1798/nu1.mnc


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Feb 24, 2017 at 9:45 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Trisanna
>
> are you  sure you aren't running out of disk space? If not, what happens
> when you run the mri_convert command directly on the command line?
>
> cheers
> Bruce
> On Thu, 23 Feb 2017,
> Trisanna Sprung-Much wrote:
>
> > Hi All
> >
> > I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and
> it stops when
> > trying to transform to the "conformed" space. I get the following error
> after about a
> > minute. I have not seen this error before.
> >
> > mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like
> orig.mgz
> > --conform
> > mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz
> --like orig.mgz
> > --conform
> > ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF
> file
> > miopen: MINC package entry point
> > Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc
> > mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.2860/
> nu1.mnc
> > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> > reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc...
> > Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC
> 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017
> >
> > To report a problem, see http://surfer.nmr.mgh.harvard.
> edu/fswiki/BugReporting
> >
> >
> > Any ideas?
> >
> > Best
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> >
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[Freesurfer] recon-all error (6.0)

[Trisanna Sprung-Much]

Hi All

I am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it
stops when trying to transform to the "conformed" space. I get the
following error after about a minute. I have not seen this error before.

mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like
orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc
mincRead(): error reading volume from file
./tmp.mri_nu_correct.mni.2860/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc...
Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Any ideas?

Best

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] license file not working

[Trisanna Sprung-Much]

The .license that it comes with is not the same as the license.txt that you
have to acquire. I was able to use an old license.txt from my Freesurfer
5.3 for 6.0.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:

> try to rename the file to license.txt?
>
> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>
>> Hello,
>>
>> I have been using Freesurfer for a number of years, and just installed
>> v6.0. I run into this problem:
>>
>> 
>> --
>> ERROR: Invalid FreeSurfer license key found in license file
>> /Applications/freesurfer/.license
>>If you are outside the NMR-Martinos Center,
>>go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>get a valid license file (it's free).
>>If you are inside the NMR-Martinos Center,
>>make sure to source the standard environment.
>> 
>> --
>>
>> I have a valid .license file, in the Freesurfer home directory
>>
>> Last login: Thu Feb  2 15:04:01 on ttys005
>>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /Applications/freesurfer
>> FSFAST_HOME   /Applications/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /Applications/freesurfer/subjects
>> MNI_DIR   /Applications/freesurfer/mni
>> [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>> [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>> -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>> [38c9862eb0b0:/Applications/freesurfer] adick%
>>
>> Any ideas?
>>
>> Thanks!
>>
>> Anthony
>>
>>
>> --
>> Anthony Steven Dick, Ph.D.
>> Associate Professor
>> Director, Cognitive Neuroscience Program and Graduate Certificate in
>> Cognitive Neuroscience
>> Department of Psychology
>> Florida International University Modesto A. Maidique Campus AHC4 454
>> 11200 S.W. 8th Street
>> Miami, FL 33199
>> Ph: 305-348-4202 <(305)%20348-4202>; Lab Ph: 305-348-9055
>> <(305)%20348-9055>; Fx: 305-348-3879 <(305)%20348-3879>
>> Email: ad...@fiu.edu
>> Webpage: http://myweb.fiu.edu/adick
>> Join the Society for the Study of Human Development:
>> http://www.sshdonline.org
>>
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>
>
> --
> 
> -
> Kong Xiangzhen
> State Key Laboratory of Cognitive Neuroscience and Learning,
> Beijing Normal University,
> Beijing, China, 100875.
>
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Re: [Freesurfer] How to check recon-all finished without any error

[Trisanna Sprung-Much]

Try checking your recon all.log in your scripts folder of the subject.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Feb 2, 2017 at 1:52 PM, shi yao wang 
wrote:

> Dear FS experts:
> How to check recon-all finished without any error?
> Sometime, there are showing no error message, however, when I running
> hippocampus subfield, it does not run.
>
> thanks
> Lawrence
> Emory
>
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Re: [Freesurfer] Freesurfer 6.0 and MNI template

[Trisanna Sprung-Much]

thanks Doug!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 25, 2017 at 6:27 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> Still in 305
>
>
> On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote:
> > Me again,
> >
> > Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in
> > MNI305 space or have they been updated to the MNI152 space?
> >
> > many thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] Freesurfer 6.0 and MNI template

[Trisanna Sprung-Much]

Me again,

Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305
space or have they been updated to the MNI152 space?

many thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Freeview in 6.0 - editing labels

[Trisanna Sprung-Much]

thanks! I will give this a shot.

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 25, 2017 at 12:41 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
wrote:

> Hi Trisanna,
>
> There is no straight-forward way to let you edit surface labels but you
> can try these steps:
>
> 1. Load a volume and a surface.
> 2. Load the label you want to edit as volume label (ROI).
> 3. Select the ROI in the layer list to bring up ROI property panel. Click
> on “Map to Surface” dropdown box and select the surface. You should see the
> label shown on the surface.
> 4. Switch to ROI Edit mode. You can start to edit the label on the
> surface. Click left mouse button to add vertex. Shift+Left button to remove
> vertex.
> 5. After edit, you might notice direct save button is still grayed out,
> which is a bug. But you can save it by “Save ROI as”. Sorry for the
> inconveneince.
>
> In future update we plan to simply label editing by combining surface and
> volume labels. Hopefully that will make label editing a lot easier.
>
> Best,
> Ruopeng
>
> On Jan 25, 2017, at 11:48 AM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>
> Hi there
>
> Does the 6.0 version of Freeview have a way to edit labels on surfaces
> similar to how tksurfer allowed us to do this?
>
> Thanks!
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
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[Freesurfer] Freeview in 6.0 - editing labels

[Trisanna Sprung-Much]

Hi there

Does the 6.0 version of Freeview have a way to edit labels on surfaces
similar to how tksurfer allowed us to do this?

Thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] Freesurfer 6.0 and ex-vivo T1

[Trisanna Sprung-Much]

thanks for the quick response Bruce!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 24, 2017 at 1:18 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Trisanna
>
> it is better about handling highres data, but the ex vivo recon stream is
> still a work in progress
>
> cheers
> Bruce
> On Tue, 24 Jan 2017, Trisanna Sprung-Much wrote:
>
> Hi there
>> I am wondering if the Freesurfer 6.0 version is more flexible with the
>> parameters used for ex-vivo scans other than what 5.3 required, as listed
>> here
>>  https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo.
>>
>> We acquired some ex-vivo scans at 0.4mm iso but not with those above
>> parameters.
>>
>> many thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
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> addressed. If you believe this e-mail was sent to you in error and the
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[Freesurfer] Freesurfer 6.0 and ex-vivo T1

[Trisanna Sprung-Much]

Hi there

I am wondering if the Freesurfer 6.0 version is more flexible with the
parameters used for ex-vivo scans other than what 5.3 required, as listed
here
 https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo.

We acquired some ex-vivo scans at 0.4mm iso but not with those above
parameters.

many thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Does anyone know who wrote the script for mri_concat? I would really like
to get this figured out.

thanks

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> thanks Bruce - I had indeed used this months ago but at the workshop this
> semester Doug had suggested mri_concat as it is a newer command and also
> doesn't blur the data. I am just having problems creating percentage values
> with mri_concat.
>
> *Would you know why mri_vol2surf is taking a binary minc file and creating
> values ranging from 0-255 that mri_concat then preserves?*
>
> best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Oct 21, 2016 at 9:29 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Trisanna
>>
>> not sure about mri_concat, but mri_average -noconform -p ... should do
>> the trick
>>
>> cheers
>> Bruce
>> On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
>>
>> Something weird is happening with mri_vol2surf - even though the data
>>> looks great, the values are odd
>>> which carries over when I try to average with mri_concat. I would just
>>> like to get percentage values
>>> with mri_concat.
>>> thanks!
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>>
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much <
>>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>>   Hi Doug
>>>
>>> Here is what I ran:
>>>
>>> trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/i
>>> cbm-113/label/label_aalf.mnc
>>> --o /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi
>>> lh --surf pial --regheader
>>> icbm-113
>>> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc
>>> srcreg unspecified
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = pial
>>> hemi = lh
>>> reshape = 0
>>> interp = nearest
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> INFO: changing type to float
>>> Done loading volume
>>> Computing registration from header.
>>>   Using /data-01/trisanna/freesurfer/icbm-113/mri/orig.mgz as target
>>> reference.
>>> Reading surface /data-01/trisanna/freesurfer/icbm-113/surf/lh.pial
>>> Done reading source surface
>>> Mapping Source Volume onto Source Subject Surface
>>>  1 0 0 0
>>> using old
>>> Done mapping volume to surface
>>> Number of source voxels hit = 53960
>>> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
>>> Dim: 159741 1 1
>>>
>>> When I open this in Freeview, the values are either 0 or 255 (see
>>> attached image). However, they
>>> were binary (0 or 1) in the label_aalf.mnc input file...
>>>
>>> Trisanna
>>>
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>>
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>   Hmmm, I don't know what could be going on. Can you send the
>>> command line
>>>   and all terminal output?
>>>
>>>
>>>   On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>>>   > Hi Doug
>>>   >
>>>   > So the pixel values are 0 and 1 *in the original .mnc*. It seems
>>> that
>>>   > after performing mri_vol2surf they become 0 and 255, and stay
>>> this way
>>>   > after mri_surf2surf as well. So, why would mri_vol2surf be
>>> changing
>>>   > the values?
>>>   >
>>>   > Trisanna
>>>   >
>>>   >
>>>   >
>>>   > --
>>>   > Ph.D. Candidate
>>>   > McGill University
>>>   > Integrated Program in Neuroscience
>>>   > Psychology
>>>   >
>>>   >
>>>   > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
>>>   > <gr...@nmr.m

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

thanks Bruce - I had indeed used this months ago but at the workshop this
semester Doug had suggested mri_concat as it is a newer command and also
doesn't blur the data. I am just having problems creating percentage values
with mri_concat.

*Would you know why mri_vol2surf is taking a binary minc file and creating
values ranging from 0-255 that mri_concat then preserves?*

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Oct 21, 2016 at 9:29 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Trisanna
>
> not sure about mri_concat, but mri_average -noconform -p ... should do the
> trick
>
> cheers
> Bruce
> On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
>
> Something weird is happening with mri_vol2surf - even though the data
>> looks great, the values are odd
>> which carries over when I try to average with mri_concat. I would just
>> like to get percentage values
>> with mri_concat.
>> thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>>
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>   Hi Doug
>>
>> Here is what I ran:
>>
>> trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/i
>> cbm-113/label/label_aalf.mnc
>> --o /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi
>> lh --surf pial --regheader
>> icbm-113
>> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = pial
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> Computing registration from header.
>>   Using /data-01/trisanna/freesurfer/icbm-113/mri/orig.mgz as target
>> reference.
>> Reading surface /data-01/trisanna/freesurfer/icbm-113/surf/lh.pial
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 0 0 0
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 53960
>> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
>> Dim: 159741 1 1
>>
>> When I open this in Freeview, the values are either 0 or 255 (see
>> attached image). However, they
>> were binary (0 or 1) in the label_aalf.mnc input file...
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. CandidateMcGill University
>>
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>   Hmmm, I don't know what could be going on. Can you send the command
>> line
>>   and all terminal output?
>>
>>
>>   On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>>   > Hi Doug
>>   >
>>   > So the pixel values are 0 and 1 *in the original .mnc*. It seems
>> that
>>   > after performing mri_vol2surf they become 0 and 255, and stay
>> this way
>>   > after mri_surf2surf as well. So, why would mri_vol2surf be
>> changing
>>   > the values?
>>   >
>>   > Trisanna
>>   >
>>   >
>>   >
>>   > --
>>   > Ph.D. Candidate
>>   > McGill University
>>   > Integrated Program in Neuroscience
>>   > Psychology
>>   >
>>   >
>>   > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
>>   > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
>> wrote:
>>   >
>>   > What are the pixel values in the mgz file? They should be
>> binary,
>>   > ie, 1=in a label, 0 = out of label
>>   >
>>   >
>>   > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>>   >> Overlays in .mgz format using mri_vol2surf
>>   >>
>>   >> --
>>   >> Ph.D. Candidate
>>   >> McGill University
>>   >> Integrated Program in Neuroscience
>>   >> Psychology
>>   >>
>>   >>
>>   >> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>>   >> <gr...@nmr.mgh.harvard.edu &l

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Something weird is happening with mri_vol2surf - even though the data looks
great, the values are odd which carries over when I try to average with
mri_concat. I would just like to get percentage values with mri_concat.

thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Hi Doug
>
> *Here is what I ran:*
>
> *trisanna@kaplan:~$ mri_vol2surf --mov
> /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc --o
> /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi lh
> --surf pial --regheader icbm-113*
> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Computing registration from header.
>   Using /data-01/trisanna/freesurfer/icbm-113/mri/orig.mgz as target
> reference.
> Reading surface /data-01/trisanna/freesurfer/icbm-113/surf/lh.pial
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 53960
> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> Dim: 159741 1 1
>
> When I open this in Freeview, the values are either 0 or 255 (see attached
> image). However, they were binary (0 or 1) in the label_aalf.mnc input
> file...
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hmmm, I don't know what could be going on. Can you send the command line
>> and all terminal output?
>>
>>
>> On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>> > Hi Doug
>> >
>> > So the pixel values are 0 and 1 *in the original .mnc*. It seems that
>> > after performing mri_vol2surf they become 0 and 255, and stay this way
>> > after mri_surf2surf as well. So, why would mri_vol2surf be changing
>> > the values?
>> >
>> > Trisanna
>> >
>> >
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > What are the pixel values in the mgz file? They should be binary,
>> > ie, 1=in a label, 0 = out of label
>> >
>> >
>> > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>> >> Overlays in .mgz format using mri_vol2surf
>> >>
>> >> --
>> >> Ph.D. Candidate
>> >> McGill University
>> >> Integrated Program in Neuroscience
>> >> Psychology
>> >>
>> >>
>> >> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>> >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
>> wrote:
>> >>
>> >> what is a labeled vertex? What file format? mgz? annot?
>> >>
>> >>
>> >> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>> >> > the source files are labelled vertices from 20 subjects:
>> >> >
>> >> > -T1s were labelled using an MNI software
>> >> > -Surfaces were created in FreeSurfer and surface overlays
>> >> of the
>> >> > labels were created using mri_vol2surf
>> >> > -Surface overlays were registered to fsaverage using
>> >> mri_surf2surf and
>> >> > then averaged to create a probability map, originally using
>> >> "mri_average"
>> >> >
>> >> > So, essentially the overlays are binary files of my labels
>> >>     I believe
>> >> > - I can send one over if you wish.
>> >> >
>> >> > Trisanna
>> >> >
>> >> >
>> >> > --
>> >> > Ph.D. Candidate
>> >> > McGill Unive

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Hi Doug

Any thoughts on this?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Oct 6, 2016 at 10:37 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Hi Doug
>
> So the pixel values are 0 and 1 *in the original .mnc*. It seems that
> after performing mri_vol2surf they become 0 and 255, and stay this way
> after mri_surf2surf as well. So, why would mri_vol2surf be changing the
> values?
>
> Trisanna
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>> What are the pixel values in the mgz file? They should be binary, ie,
>> 1=in a label, 0 = out of label
>>
>> On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>>
>> Overlays in .mgz format using mri_vol2surf
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> what is a labeled vertex? What file format? mgz? annot?
>>>
>>>
>>> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>>> > the source files are labelled vertices from 20 subjects:
>>> >
>>> > -T1s were labelled using an MNI software
>>> > -Surfaces were created in FreeSurfer and surface overlays of the
>>> > labels were created using mri_vol2surf
>>> > -Surface overlays were registered to fsaverage using mri_surf2surf and
>>> > then averaged to create a probability map, originally using
>>> "mri_average"
>>> >
>>> > So, essentially the overlays are binary files of my labels I believe
>>> > - I can send one over if you wish.
>>> >
>>> > Trisanna
>>> >
>>> >
>>> > --
>>> > Ph.D. Candidate
>>> > McGill University
>>> > Integrated Program in Neuroscience
>>> > Psychology
>>> >
>>> >
>>> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>> >
>>> > what are the source files ("all files"). What data type, value
>>> range,
>>> > where did they come from?
>>> >
>>> >
>>> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>>> > > Hi Doug
>>> > >
>>> > > So, of course now it works without --keep-filetype... :p it looks
>>> > > pretty much the same was when I use --keep-filetype.
>>> > >
>>> > > However, the values of Min and Max are still odd (out of 256) -
>>> see
>>> > > snapshot
>>> > >
>>> > > Trisanna
>>> > >
>>> > >
>>> >     >
>>> > >
>>> > >
>>> > > --
>>> > > Ph.D. Candidate
>>> > > McGill University
>>> > > Integrated Program in Neuroscience
>>> > > Psychology
>>> > >
>>> > >
>>> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
>>> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>> > <mailto:gr...@nmr.mgh.harvard.edu
>>> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>>> > >
>>> > > Depending upon the type of the data, the --keep-datatype may
>>> > mess
>>> > > things
>>> > > up quite a bit. What happens if you don't include that? It
>>> > will not
>>> > > create an annotation. maybe you mean some other file type?
>>> > >
>>> > >
>>> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>>> > > >
>>> > > > Hi Doug
>>> > > >
>>> > > > I spoke with you at the Freesurfer tutorial last week
>>> > about using
>>> > > > mri_average to average my sulcal labels and get a
>>> > probability map on
>>> > >

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Hi Doug

So the pixel values are 0 and 1 *in the original .mnc*. It seems that after
performing mri_vol2surf they become 0 and 255, and stay this way after
mri_surf2surf as well. So, why would mri_vol2surf be changing the values?

Trisanna



--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> What are the pixel values in the mgz file? They should be binary, ie, 1=in
> a label, 0 = out of label
>
> On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>
> Overlays in .mgz format using mri_vol2surf
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> > wrote:
>
>> what is a labeled vertex? What file format? mgz? annot?
>>
>>
>> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>> > the source files are labelled vertices from 20 subjects:
>> >
>> > -T1s were labelled using an MNI software
>> > -Surfaces were created in FreeSurfer and surface overlays of the
>> > labels were created using mri_vol2surf
>> > -Surface overlays were registered to fsaverage using mri_surf2surf and
>> > then averaged to create a probability map, originally using
>> "mri_average"
>> >
>> > So, essentially the overlays are binary files of my labels I believe
>> > - I can send one over if you wish.
>> >
>> > Trisanna
>> >
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > what are the source files ("all files"). What data type, value
>> range,
>> > where did they come from?
>> >
>> >
>> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>> > > Hi Doug
>> > >
>> > > So, of course now it works without --keep-filetype... :p it looks
>> > > pretty much the same was when I use --keep-filetype.
>> > >
>> > > However, the values of Min and Max are still odd (out of 256) -
>> see
>> > > snapshot
>> > >
>> > > Trisanna
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > --
>> > > Ph.D. Candidate
>> > > McGill University
>> > > Integrated Program in Neuroscience
>> >     > Psychology
>> > >
>> > >
>> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
>> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> > <mailto:gr...@nmr.mgh.harvard.edu
>> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>> > >
>> > > Depending upon the type of the data, the --keep-datatype may
>> > mess
>> > > things
>> > > up quite a bit. What happens if you don't include that? It
>> > will not
>> > > create an annotation. maybe you mean some other file type?
>> > >
>> > >
>> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>> > > >
>> > > > Hi Doug
>> > > >
>> > > > I spoke with you at the Freesurfer tutorial last week
>> > about using
>> > > > mri_average to average my sulcal labels and get a
>> > probability map on
>> > > > fsaverage. You had suggested using "mri_concat" instead,
>> > which is a
>> > > > newer command. So, I performed the following command:
>> > > >
>> > > > *mri_concat all files --o output.mgz --mean --keep-datatype*
>> > > >
>> > > > I had to put --keep-datatype or else it tried to create an
>> > annot
>> > > file.
>> > > >
>> > > > This worked just fine.
>> > > >
>> > > > My question then is concerning *the min and max values
>> > *when this
>> > > > aver

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

Overlays in .mgz format using mri_vol2surf

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> what is a labeled vertex? What file format? mgz? annot?
>
>
> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> > the source files are labelled vertices from 20 subjects:
> >
> > -T1s were labelled using an MNI software
> > -Surfaces were created in FreeSurfer and surface overlays of the
> > labels were created using mri_vol2surf
> > -Surface overlays were registered to fsaverage using mri_surf2surf and
> > then averaged to create a probability map, originally using "mri_average"
> >
> > So, essentially the overlays are binary files of my labels I believe
> > - I can send one over if you wish.
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > what are the source files ("all files"). What data type, value range,
> > where did they come from?
> >
> >
> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > > Hi Doug
> > >
> > > So, of course now it works without --keep-filetype... :p it looks
> > > pretty much the same was when I use --keep-filetype.
> > >
> > > However, the values of Min and Max are still odd (out of 256) - see
> > > snapshot
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > Depending upon the type of the data, the --keep-datatype may
> > mess
> > > things
> > > up quite a bit. What happens if you don't include that? It
> > will not
> > > create an annotation. maybe you mean some other file type?
> > >
> > >
> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > > >
> > > > Hi Doug
> > > >
> > > > I spoke with you at the Freesurfer tutorial last week
> > about using
> > > > mri_average to average my sulcal labels and get a
> > probability map on
> > > > fsaverage. You had suggested using "mri_concat" instead,
> > which is a
> > > > newer command. So, I performed the following command:
> > > >
> > > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > > >
> > > > I had to put --keep-datatype or else it tried to create an
> > annot
> > > file.
> > > >
> > > > This worked just fine.
> > > >
> > > > My question then is concerning *the min and max values
> > *when this
> > > > average is overlayed in Freeview. See the snapshot
> > attached. The
> > > > values seem to be based on 256 instead of percentage and
> > this is
> > > what
> > > > happens when I used "mri_average" without specifying the
> > "-p". Is
> > > > there a way to illustrate the values in percentage in a
> > similar way
> > > > with mri_concat?
> > > >
> > > > Many thanks!
> > > >
> > > > Trisanna
> > > >
> > > >
> > > > --
> > > > Ph.D. Candidate
> > > > McGill University
> > > > Integrated Program in Neuroscience
> > > > Psychology
> > > >
> > > >
> > > >
> > > > 

Re: [Freesurfer] mri_average vs mri_concat

[Trisanna Sprung-Much]

the source files are labelled vertices from 20 subjects:

-T1s were labelled using an MNI software
-Surfaces were created in FreeSurfer and surface overlays of the labels
were created using mri_vol2surf
-Surface overlays were registered to fsaverage using mri_surf2surf and then
averaged to create a probability map, originally using "mri_average"

So, essentially the overlays are binary files of my labels I believe  - I
can send one over if you wish.

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> what are the source files ("all files"). What data type, value range,
> where did they come from?
>
>
> On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So, of course now it works without --keep-filetype... :p it looks
> > pretty much the same was when I use --keep-filetype.
> >
> > However, the values of Min and Max are still odd (out of 256) - see
> > snapshot
> >
> > Trisanna
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Depending upon the type of the data, the --keep-datatype may mess
> >     things
> > up quite a bit. What happens if you don't include that? It will not
> > create an annotation. maybe you mean some other file type?
> >
> >
> > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi Doug
> > >
> > > I spoke with you at the Freesurfer tutorial last week about using
> > > mri_average to average my sulcal labels and get a probability map
> on
> > > fsaverage. You had suggested using "mri_concat" instead, which is a
> > > newer command. So, I performed the following command:
> > >
> > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > >
> > > I had to put --keep-datatype or else it tried to create an annot
> > file.
> > >
> > > This worked just fine.
> > >
> > > My question then is concerning *the min and max values *when this
> > > average is overlayed in Freeview. See the snapshot attached. The
> > > values seem to be based on 256 instead of percentage and this is
> > what
> > > happens when I used "mri_average" without specifying the "-p". Is
> > > there a way to illustrate the values in percentage in a similar way
> > > with mri_concat?
> > >
> > > Many thanks!
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.
> harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mai

Re: [Freesurfer] group analysis

[Trisanna Sprung-Much]

there is a tutorial with similar variables available here

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Oct 5, 2016 at 9:22 AM, charles laidi 
wrote:

> Dear FreeSurfers,
>
> I would like to study the interaction between age and cortical thickness
> in patients and controls.
> My hypothesis is that there is an interaction and that cortical thickness
> is decreasing faster with age in patients than in controls.
> I have both Male and Female included in 6 different centers.
> I would like to consider also Gender and Site (6 centers) as confounds.
>
> My understanding is that I should perform a surface based group analysis
> with freesurfer.
>
> I am not able to find an example for my problem in the documentation
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
>
> Would anyone had some tips to build the Fsgd file and the contrast file ?
>
> Thank you very much in advance.
>
> Best,
>
> Charles
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Warping an ROI from one subject to another

[Trisanna Sprung-Much]

I think it might have to do with the format of your output file - perhaps
try .mgz? This is what I used.

Then open the surface and use the "overlay" option to overlay your ROI as a
surface overlay.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Oct 3, 2016 at 3:14 PM, Joel Bruss 
wrote:

> Doug-
>
> I'm really sorry to keep pestering you about this but I just can't seem
> to get this to work.  See my replies below:
>
>
> On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> > First, bring up the ROI on the volume along with the surface in the
> > volume. You can do this with FreeView. Make sure that the ROI intersects
> > the surface.
> Yes, this looks fine
> >   Then run mri_vol2surf so sample the binary ROI volume onto
> > the surface.
> This is what I ran:
> mri_vol2surf  --src $SUBJECTS_DIR/subA/tmpdir/roi.mgz \
> --out $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \
> --regheader subA --hemi rh --surf pial
> >   You can view the ROI on the surface by loading it as an
> > overlay.
> This is a volume or a surface now?  Is it just a volume resampled to the
> surface space?  I can't get it to load in freeview as a surface (it just
> crashes), and it doesn't look like anything as an overlay.
> > Then run mri_cor2label using the surface-sampled ROI as input
> > and specifying --surf (see the --help) to make this a surface-based
> > label. You can also view this label in the surface in freeview. Finally,
> > run mri_label2label using the --regmethod surface
>
>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered by
> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is
> intended only for the use of the individual or entity to which it is
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>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

Ok so this is where my knowledge might be limited because you did a
slightly different thing than me by specifying the output type as "paint" -
that is what the .w format is. This is a label, I believe and needs to be
loaded as such.

What happens if you try to remove the "output_type" and try to load the
result as an overlay?

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org> wrote:

> Thank you! So good news, that worked and created wmparcSlh.w
>
> I'm not sure what the .w means. When I try to load it onto the surface, I
> get an error: "Failed to load Surface overlay."
>
> Thank you,
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 12:51 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> My apologies, I meant "--regheader subject"
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> Yeah, I get Error: Option unknown for --regmethod
>>
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 12:41 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> hmmm, yup not sure there. Did you try "--regmethod subject"
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> Just to make sure I am actually doing what you are suggesting my input
>>> and output is below.
>>>
>>> Thanks,
>>> Anna
>>>
>>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>>> --reg 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>>> --hemi lh --surf white --out_type paint
>>> INFO: output format is paint
>>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m
>>> ri/wmparc.mgz
>>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/s
>>> urf/lh.sphere.reg
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = white
>>> hemi = lh
>>> reshape = 0
>>> interp = nearest
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> INFO: changing type to float
>>> Done loading volume
>>> regio_read_register(): Success
>>> Error reading inplaneres from /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 12:08 PM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> Did you try --regmethod subjid? or --reg sphere.reg ?
>>>
>>> If that doesn't work then I'm not sure how to help - Bruce or Doug, any
>>> thoughts?
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org>
>>> wrote:
>>>
>>>> I am still having problems. If I do --reg subject I get an error back
>>>> that it is a directory. If I pick a specific file such as orig.mgz (default
>>>> according to help file), I get the same error as before.
>>>>
>>>> Thanks,
>>>> Anna
>>>> --
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>>> freesurfer-boun...@nmr.mgh.har

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

My apologies, I meant "--regheader subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org> wrote:

> Yeah, I get Error: Option unknown for --regmethod
>
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 12:41 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> hmmm, yup not sure there. Did you try "--regmethod subject"
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> Just to make sure I am actually doing what you are suggesting my input
>> and output is below.
>>
>> Thanks,
>> Anna
>>
>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>> --reg 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>> --hemi lh --surf white --out_type paint
>> INFO: output format is paint
>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> mri/wmparc.mgz
>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> surf/lh.sphere.reg
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> regio_read_register(): Success
>> Error reading inplaneres from /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 12:08 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> Did you try --regmethod subjid? or --reg sphere.reg ?
>>
>> If that doesn't work then I'm not sure how to help - Bruce or Doug, any
>> thoughts?
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> I am still having problems. If I do --reg subject I get an error back
>>> that it is a directory. If I pick a specific file such as orig.mgz (default
>>> according to help file), I get the same error as before.
>>>
>>> Thanks,
>>> Anna
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 11:04 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> Gotcha, so when I was trying to do something similar I used mri_vol2surf
>>> with --regmethod subjid since you don't actually want to perform a
>>> transformation.
>>>
>>> Maybe try that?
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org>
>>> wrote:
>>>
>>>> No problem. I'm not exactly sure, but I think I just want a surface
>>>> overlay so mri_vol2surf would be what I want. Right now, I am just trying
>>>> to get down the generic way of how to do it which is why I went with trying
>>>> to overlay the parcellation onto the inflated surface. Later, I will have
>>>> different modalities such as PET that I will want to overlay on the
>>>> inflated surface that will already be registered to the MRI. So I just
>>>> wanted to get the proper workflow of how to get a volume overlayed onto the
>>>> surface if that makes sense.
>>

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

hmmm, yup not sure there. Did you try "--regmethod subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org> wrote:

> Just to make sure I am actually doing what you are suggesting my input and
> output is below.
>
> Thanks,
> Anna
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
> --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
> --reg 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> --hemi lh --surf white --out_type paint
> INFO: output format is paint
> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/mri/wmparc.mgz
> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/surf/lh.sphere.reg
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): Success
> Error reading inplaneres from /mnt/netScratch/crawforda/
> BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 12:08 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> Did you try --regmethod subjid? or --reg sphere.reg ?
>
> If that doesn't work then I'm not sure how to help - Bruce or Doug, any
> thoughts?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> I am still having problems. If I do --reg subject I get an error back
>> that it is a directory. If I pick a specific file such as orig.mgz (default
>> according to help file), I get the same error as before.
>>
>> Thanks,
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 11:04 AM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> Gotcha, so when I was trying to do something similar I used mri_vol2surf
>> with --regmethod subjid since you don't actually want to perform a
>> transformation.
>>
>> Maybe try that?
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> No problem. I'm not exactly sure, but I think I just want a surface
>>> overlay so mri_vol2surf would be what I want. Right now, I am just trying
>>> to get down the generic way of how to do it which is why I went with trying
>>> to overlay the parcellation onto the inflated surface. Later, I will have
>>> different modalities such as PET that I will want to overlay on the
>>> inflated surface that will already be registered to the MRI. So I just
>>> wanted to get the proper workflow of how to get a volume overlayed onto the
>>> surface if that makes sense.
>>>
>>> Thank you,
>>> Anna
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 10:48 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> Sorry - always helps to read the whole question :D
>>>
>>> So, you are trying to create an inflated white surface? As far as I know
>>> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
>>> inflated surfaces that are the pial pushed outwards.
>>>
>>> Also, "mri_vol2surf" creates surface overlays on surfaces that already
>>> exist.
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
&

Re: [Freesurfer] Can I change the pial surface outline by the adding the control point?

[Trisanna Sprung-Much]

Hi there

To my understanding, if you want to edit the pial (push it outwards more)
then you need to edit the white matter, as the pial is made from the white
matter surface. You can do this by manually extending the white matter
surface and re-running your surfaces.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:07 PM, Seung Gul Kang 
wrote:

> Hi Freesurfer expert,
>
> I am doing visual editing.
> In some subjects, the pial surface border is somewhat narrow (within the
> border of graymatter in my view) although there is no skull stripping
> error.
> I heard that adding the control point might extend the border of
> graymatter as well as that of white matter from other researcher.
> Is it true?
> Or, is there other way to edit to extend the pial surface border?
>
> Thank you.
>
> Best,
> Seung-Gul
> ---
> *Seung Gul Kang, M.D., Ph.D. *
>
> *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil
> Medical Center, Gachon University, School of Medicine, 21, Namdong-daero
> 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
> *Research scholar*; Sleep Disorders Clinical Research Program, Department
> of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1
> Bowdoin Square, 9th floor, Boston, MA 02114, USA
> *Collaboration researcher*; Division of Sleep & Circadian Disorders,
> Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
> Boston MA 02115
> ᐧ
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

Did you try --regmethod subjid? or --reg sphere.reg ?

If that doesn't work then I'm not sure how to help - Bruce or Doug, any
thoughts?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org> wrote:

> I am still having problems. If I do --reg subject I get an error back that
> it is a directory. If I pick a specific file such as orig.mgz (default
> according to help file), I get the same error as before.
>
> Thanks,
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 11:04 AM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> Gotcha, so when I was trying to do something similar I used mri_vol2surf
> with --regmethod subjid since you don't actually want to perform a
> transformation.
>
> Maybe try that?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> No problem. I'm not exactly sure, but I think I just want a surface
>> overlay so mri_vol2surf would be what I want. Right now, I am just trying
>> to get down the generic way of how to do it which is why I went with trying
>> to overlay the parcellation onto the inflated surface. Later, I will have
>> different modalities such as PET that I will want to overlay on the
>> inflated surface that will already be registered to the MRI. So I just
>> wanted to get the proper workflow of how to get a volume overlayed onto the
>> surface if that makes sense.
>>
>> Thank you,
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 10:48 AM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> Sorry - always helps to read the whole question :D
>>
>> So, you are trying to create an inflated white surface? As far as I know
>> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
>> inflated surfaces that are the pial pushed outwards.
>>
>> Also, "mri_vol2surf" creates surface overlays on surfaces that already
>> exist.
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> I already ran recall-all. I am trying to create a different surface not
>>> created using recon-all.
>>>
>>> Anna
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 10:40 AM
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> You have to run recon-all to get the surfaces of a volume.
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to take nay volume that is registered and create an
>>>> inflated surface. I am trying to use mri_vol2surf. I am having problems
>>>> with the registration source. From the examples I could fine, it should be
>>>> --srcreg *.dat. The only *.dat file I have is segment.dat which does not
>>>> work. I also tried using the white matter volume which also didn't work. My
>>>> input and output is below. Could you offer some guidance on the
>>>> registration file?
>>>>
>>>> Thank you,
>>>> Anna
>>>>
>>>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>>>> /mnt/netScratch/crawforda/BrainStem

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

Gotcha, so when I was trying to do something similar I used mri_vol2surf
with --regmethod subjid since you don't actually want to perform a
transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org> wrote:

> No problem. I'm not exactly sure, but I think I just want a surface
> overlay so mri_vol2surf would be what I want. Right now, I am just trying
> to get down the generic way of how to do it which is why I went with trying
> to overlay the parcellation onto the inflated surface. Later, I will have
> different modalities such as PET that I will want to overlay on the
> inflated surface that will already be registered to the MRI. So I just
> wanted to get the proper workflow of how to get a volume overlayed onto the
> surface if that makes sense.
>
> Thank you,
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 10:48 AM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> Sorry - always helps to read the whole question :D
>
> So, you are trying to create an inflated white surface? As far as I know
> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
> inflated surfaces that are the pial pushed outwards.
>
> Also, "mri_vol2surf" creates surface overlays on surfaces that already
> exist.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> I already ran recall-all. I am trying to create a different surface not
>> created using recon-all.
>>
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 10:40 AM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> You have to run recon-all to get the surfaces of a volume.
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>>
>>> Hello,
>>>
>>> I am trying to take nay volume that is registered and create an inflated
>>> surface. I am trying to use mri_vol2surf. I am having problems with the
>>> registration source. From the examples I could fine, it should be --srcreg
>>> *.dat. The only *.dat file I have is segment.dat which does not work. I
>>> also tried using the white matter volume which also didn't work. My input
>>> and output is below. Could you offer some guidance on the registration file?
>>>
>>> Thank you,
>>> Anna
>>>
>>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>>> --srcreg 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>>> --hemi lh --surf white --out_type paint
>>> INFO: output format is paint
>>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m
>>> ri/wmparc.mgz
>>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m
>>> ri/segment.dat
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = white
>>> hemi = lh
>>> reshape = 0
>>> interp = nearest
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> INFO: changing type to float
>>> Done loading volume
>>> regio_read_register(): Success
>>> Error reading betplaneres from /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/mri/segment.dat
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>> Cleveland Clinic is ranked as one of the top hospitals in America by
>>> U.S.News & World Report (2015). Visit us online at
>>> http://www.clevelandclinic.org for a complete listing of our services,
>>> staff and locat

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know
this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
inflated surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already
exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:

> I already ran recall-all. I am trying to create a different surface not
> created using recon-all.
>
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 10:40 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> You have to run recon-all to get the surfaces of a volume.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> Hello,
>>
>> I am trying to take nay volume that is registered and create an inflated
>> surface. I am trying to use mri_vol2surf. I am having problems with the
>> registration source. From the examples I could fine, it should be --srcreg
>> *.dat. The only *.dat file I have is segment.dat which does not work. I
>> also tried using the white matter volume which also didn't work. My input
>> and output is below. Could you offer some guidance on the registration file?
>>
>> Thank you,
>> Anna
>>
>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>> --srcreg 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>> --hemi lh --surf white --out_type paint
>> INFO: output format is paint
>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> mri/wmparc.mgz
>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> mri/segment.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> regio_read_register(): Success
>> Error reading betplaneres from /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/mri/segment.dat
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>> Cleveland Clinic is ranked as one of the top hospitals in America by
>> U.S.News & World Report (2015). Visit us online at
>> http://www.clevelandclinic.org for a complete listing of our services,
>> staff and locations. Confidentiality Note: This message is intended for use
>> only by the individual or entity to which it is addressed and may contain
>> information that is privileged, confidential, and exempt from disclosure
>> under applicable law. If the reader of this message is not the intended
>> recipient or the employee or agent responsible for delivering the message
>> to the intended recipient, you are hereby notified that any dissemination,
>> distribution or copying of this communication is strictly prohibited. If
>> you have received this communication in error, please contact the sender
>> immediately and destroy the material in its entirety, whether electronic or
>> hard copy. Thank you.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
> ===
>
> Please consider the environment before printing this e-mail
> Cleveland Clinic is ranked as one of the top hospitals

Re: [Freesurfer] Volume to Surface

[Trisanna Sprung-Much]

You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna  wrote:

> Hello,
>
> I am trying to take nay volume that is registered and create an inflated
> surface. I am trying to use mri_vol2surf. I am having problems with the
> registration source. From the examples I could fine, it should be --srcreg
> *.dat. The only *.dat file I have is segment.dat which does not work. I
> also tried using the white matter volume which also didn't work. My input
> and output is below. Could you offer some guidance on the registration file?
>
> Thank you,
> Anna
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
> --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
> --srcreg 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
> --hemi lh --surf white --out_type paint
> INFO: output format is paint
> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/mri/wmparc.mgz
> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/mri/segment.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): Success
> Error reading betplaneres from /mnt/netScratch/crawforda/
> BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>
> ===
>
> Please consider the environment before printing this e-mail
> Cleveland Clinic is ranked as one of the top hospitals in America by
> U.S.News & World Report (2015). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
> hard copy. Thank you.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] license.txt?

[Trisanna Sprung-Much]

thank you!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 23, 2016 at 5:59 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote:

> freeview will work without the license file but most all freesurfer
> binaries will NOT work without the license file. Also, it seems the
> registration page is working:
>
>https://surfer.nmr.mgh.harvard.edu/registration.html
>
> On 09/23/2016 01:30 PM, Trisanna Sprung-Much wrote:
> > Hi there
> >
> > I am installing Freesurfer on a Mac for the workshop next week and I
> > cannot seem to get a license.txt because the page is no longer is
> > accessible. However, it seems to be running fine without this file.
> >
> > Thoughts?
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] license.txt?

[Trisanna Sprung-Much]

Hi there

I am installing Freesurfer on a Mac for the workshop next week and I cannot
seem to get a license.txt because the page is no longer is accessible.
However, it seems to be running fine without this file.

Thoughts?

Trisanna


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McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] colour scale

[Trisanna Sprung-Much]

how else would you suggest I generate a colour bar? tksurfer doesn't appear
to be working for me either.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Sep 12, 2016 at 7:53 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> thanks!
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Sep 12, 2016 at 7:24 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
> wrote:
>
>> It appears you are running version 5.3. The upcoming 6.0 should fix it.
>>
>> On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>> Hi there
>>
>> yup, so I had seen that. The issue is it looks like this and doesn't seem
>> to change no matter what changes I make in the GUI (heat vs colour map,
>> etc).
>>
>> Best
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu
>> > wrote:
>>
>>> There is a color bar button on the toolbar, or you can go to menu
>>> View->Show Color Scale.
>>>
>>> Ruopeng
>>>
>>>
>>> On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:
>>>
>>> Hi there
>>>
>>> is there a way to view a colour scale bar in Freeview rather than
>>> Tksurfer, for instance, for a probability map? I can alter the Min and Max
>>> by "Configure Overlay" but cannot seem to display the bar next to my
>>> surface.
>>>
>>> Many thanks
>>>
>>> Trisanna
>>>
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>>
>>>
>>> ___
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Re: [Freesurfer] colour scale

[Trisanna Sprung-Much]

thanks!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Sep 12, 2016 at 7:24 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
wrote:

> It appears you are running version 5.3. The upcoming 6.0 should fix it.
>
> On Sep 12, 2016, at 5:34 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Hi there
>
> yup, so I had seen that. The issue is it looks like this and doesn't seem
> to change no matter what changes I make in the GUI (heat vs colour map,
> etc).
>
> Best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Sep 12, 2016 at 5:05 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
> wrote:
>
>> There is a color bar button on the toolbar, or you can go to menu
>> View->Show Color Scale.
>>
>> Ruopeng
>>
>>
>> On 09/12/2016 03:50 PM, Trisanna Sprung-Much wrote:
>>
>> Hi there
>>
>> is there a way to view a colour scale bar in Freeview rather than
>> Tksurfer, for instance, for a probability map? I can alter the Min and Max
>> by "Configure Overlay" but cannot seem to display the bar next to my
>> surface.
>>
>> Many thanks
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
>> ___
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[Freesurfer] colour scale

[Trisanna Sprung-Much]

Hi there

is there a way to view a colour scale bar in Freeview rather than Tksurfer,
for instance, for a probability map? I can alter the Min and Max by
"Configure Overlay" but cannot seem to display the bar next to my surface.

Many thanks

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] ROIs defined in MNI space and vol2surf

[Trisanna Sprung-Much]

Hey there

I think you just need to use "--regmethod subject" instead of specifying a
registration .dat file. I had similar troubles a few months ago as my
labels were made on the volume and I simply wanted to overlay them onto
their surfaces in Freesurfer and didn't want any transformation to be made.

Best wishes

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jul 27, 2016 at 12:07 PM, Funk, Quentin 
wrote:

> All,
>
> I have a question regarding the required registration file in mri_vol2surf.
>
> I have some spherical ROI's in MNI space produced via 3dUndump--they're
> volume files that show up in the correct places when loaded in with an
> MNI standard subject such as fsaverage.
>
> I also have some patients scans. I'd really like to compute cortical
> thickness for these ROI's on my patient scans, so I attempt to follow
> the instructions at (
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ),
> but these instructions assume that the ROI is in the native space--which
> produces no problems until the step :
>
> cd $SUBJECTS_DIR/fsaverage/surf
> mri_vol2surf \
>--mov /path/to/ROI5.nii \
>--reg TT_avg152T1_to_fsaverage.dat \
>--projdist-max 0 1 0.1 \
>--interp nearest \
>--hemi lh \
>--out lh.fsaverage.ROI5.mgh \
>--reshape
>
> My question is then three parts:
>
> (1) Why does vol2surf require a registration file? Shouldn't it be
> possible to do it as a straight conversion of data types if I know that
> my surface is registered to the file that I want? Perhaps naive, my
> first intuition was to construct a TT.dat that was the identity matrix,
> but this fails, with the response listed in (2).
>
> (2) How can I do this without shifting my data? If I follow the
> instructions, when the surface is overlayed on fsaverage's lh.pial, the
> entire surface is included in the overlay.
>
> (3) What exactly do the numbers mean in the registration file TT.dat (as
> in the instructions on the website)? The 4x4 matrix is clear, and the
> first two numbers appear to have something to do with Voxel resolution,
> but I'm unable to find documentation that explains the notation in the
> output.
>
> Any help anyone can offer would be tremendously appreciated.
>
> -qf
>
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Re: [Freesurfer] Freesurfer 6.0?

[Trisanna Sprung-Much]

thanks, Doug!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jul 25, 2016 at 11:57 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> We are working pretty hard to get it out but we are still reluctant to set
> a hard date. I think we'll have a beta version in two weeks, but that's
> just a guess.
>
> doug
>
>
>
> On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:
>
>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create better surfaces using
> Freesurfer 6.0 and I am wondering if it really will improve surface
> extraction that much.
>
> Many thanks!
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
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[Freesurfer] Freesurfer 6.0?

[Trisanna Sprung-Much]

Hi there

Do we have a potential date for the Freesurfer 6.0 release? I was told I
would want to re-run all my subjects to create better surfaces using
Freesurfer 6.0 and I am wondering if it really will improve surface
extraction that much.

Many thanks!

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] registering subject pial to fsaverage

[Trisanna Sprung-Much]

Hi Doug

Is this what is meant by the example with --help? "Convert the surface
coordinates" to me sounds as if it would change the x,y,z of the
vertices... Additionally, when I watching the online tutorials surface
registration was explained as "aligning the anatomy" so I totally missed
that it doesn't change the x,y,z of the vertices.


3. Convert the surface coordinates of the lh.white of a subject to a
   (talairach) average (ie, a subject created by make_average_subject):

   mri_surf2surf --s yoursubject --hemi lh --sval-tal-xyz white
  --tval lh.white.yoursubject --tval-xyz --trgsubject youraveragesubject

   This will create youraveragesubject/surf/lh.white.yoursubject


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Jul 21, 2016 at 1:16 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> The only thing you are doing with this command is to change the number
> and identity of the vertices, the xyz will not change at all and so the
> appearance of the surface will not change (much).
>
> On 07/21/2016 01:11 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > not quite - I used mri_surf2surf *with the pial surfaces* and then
> > when I compared the original pial with the registered pial they look
> > pretty much the same. I followed an example from mri_surf2surf --help.
> >
> > See the command output and attached jpgs.
> >
> > If a surface is registered to a surface template, in my mind this
> > would mean that the cortical folding (i.e. the actual sulci) would
> > differ afterwards but I guess this is not the correct line of thinking?
> >
> > best
> >
> > Trisanna
> >
> >
> >
> > trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial
> > --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh
> > srcsubject = icbm-102
> > srcval = (null)
> > srctype=
> > trgsubject = fsaverage
> > trgval = lh.pial.icbm102
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= lh
> > trghemi= lh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg
> > Loading source data
> > Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
> > Reading target surface reg
> > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > Done
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (163842)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (169941)
> > Reverse Loop had 44416 hits
> > Surf2Surf: Dividing by number of hits (163842)
> > INFO: nSrcLost = 0
> > nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057
> > nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits
> > = 2.28035
> > Saving target data
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Thu, Jul 21, 2016 at 11:41 AM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > So if I understand, you used mri_surf2surf to map the curv from your
> > subject to fsaverage. You then viewed the original curv on the
> > original
> > subject and then you viewed the fsaveage-mapped curv on faverage
> > and you
> > find that they are very similar. Is that right? This would not
> > surprise
> > me much. If you still have questions, pictures would help alot
> >
> >
> > On 07/21/2016 10:50 AM, Trisanna Sprung-Much wrote:
> > > Hi Doug
> > >
> > > What I mean to say is that the pial surface created by recon-all
> and
> > > the pial surface that has been nonlinearly registered to fsaverage
> > > look pretty much identical in sulcal patterns, but I do not
> > understand
> > > how this can be the case if one surface has been registered to a
> > > surface template based on cortical folding.
> > > Shouldn't the cortical folding for this registered surface
> > change even
> > > a little bit?
> > >
> > > best
> > > Trisanna
> > >
> >

Re: [Freesurfer] registering subject pial to fsaverage

[Trisanna Sprung-Much]

Hi Doug

What I mean to say is that the pial surface created by recon-all and the
pial surface that has been nonlinearly registered to fsaverage look pretty
much identical in sulcal patterns, but I do not understand how this can be
the case if one surface has been registered to a surface template based on
cortical folding.
Shouldn't the cortical folding for this registered surface change even a
little bit?

best
Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jul 19, 2016 at 10:29 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> I don't understand what you did or what the problem is. Can you elaborate?
>
> On 7/19/16 5:23 PM, Trisanna Sprung-Much wrote:
>
> Hi there
>
> I tested registering a subject's pial surface to fsaverage and compared
> the original pial (from recon-all) with this registered pial surface. It
> turns out that they are almost identical in nature, and I am wondering how
> this is possible if recon-all does not alter the input data.
>
> Below is the command that I ran. Is there something I am missing here?
>
> many thanks
>
> Trisanna
>
>
> trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial
> --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh
> srcsubject = icbm-102
> srcval = (null)
> srctype=
> trgsubject = fsaverage
> trgval = lh.pial.icbm102
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= lh
> trghemi= lh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg
> /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg
> Loading source data
> Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
> Reading target surface reg
> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> Done
> Mapping Source Volume onto Source Subject Surface
> surf2surf_nnfr: building source hash (res=16).
> Surf2Surf: Forward Loop (163842)
>
> surf2surf_nnfr: building target hash (res=16).
> Surf2Surf: Reverse Loop (169941)
> Reverse Loop had 44416 hits
> Surf2Surf: Dividing by number of hits (163842)
> INFO: nSrcLost = 0
> nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057
> nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits =
> 2.28035
> Saving target data
>
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
>
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