Re: [Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

[Douglas N. Greve]

Mostly these:

https://pubmed.ncbi.nlm.nih.gov/15501102/

https://doi.org/10.1016/S0896-6273(02)00569-X

For a separate fornix seg, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic


On 5/22/2024 1:34 PM, Ahsan Ali wrote:


External Email - Use Caution

Hello everyone,

Could anyone please help me to know which Atlas is used in the 
segmentation of corpus callosum, hippocampus, and fornix using 
freeSurfer from Brian MR images. I have gone through the literature 
but couldn't find it.


With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

-- Forwarded message -
From: *Fischl, Bruce R.,PHD* 
Date: Wed, May 22, 2024, 10:52 PM
Subject: RE: Atlas Used in FreeSurfer for Segmentation of Fornix, 
Corpus Callosum, Hippocampus

To: Ahsan Ali 


Can you please post to the list so that others can answer?

*From:*Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 1:04 PM
*To:* Fischl, Bruce R.,PHD 
*Subject:* Re: Atlas Used in FreeSurfer for Segmentation of Fornix, 
Corpus Callosum, Hippocampus


*External Email - Use Caution *

Dear sir,

It is not clear from these papers to me.

With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

On Wed, May 22, 2024, 8:19 PM Fischl, Bruce R.,PHD 
 wrote:


Mostly these:

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://pubmed.ncbi.nlm.nih.gov/15501102/



*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://doi.org/10.1016/S0896-6273(02)00569-X



cheers

Bruce

*From:*Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 4:31 AM
*To:* Freesurfer support list ;
Huang, Yujing ; Fischl, Bruce R.,PHD

*Subject:* Atlas Used in FreeSurfer for Segmentation of Fornix,
Corpus Callosum, Hippocampus

*External Email - Use Caution *

Dear FreeSurfer Team,

After reviewing the literature, I have a question: which atlases
are used in the segmentation of the fornix, corpus callosum, and
hippocampus from magnetic resonance images using FreeSurfer? This
is a significant question for me, and I would appreciate a clear
and concise answer. Please provide some relevant references.


With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

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
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https://www.massgeneralbrigham.org/complianceline


.

The information in this e-mail is intended only for the person to whom 
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[Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

[Ahsan Ali]

External Email - Use Caution

Hello everyone,

Could anyone please help me to know which Atlas is used in the segmentation
of corpus callosum, hippocampus, and fornix using freeSurfer from Brian MR
images. I have gone through the literature but couldn't find it.

With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

-- Forwarded message -
From: Fischl, Bruce R.,PHD 
Date: Wed, May 22, 2024, 10:52 PM
Subject: RE: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus
Callosum, Hippocampus
To: Ahsan Ali 


Can you please post to the list so that others can answer?



*From:* Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 1:04 PM
*To:* Fischl, Bruce R.,PHD 
*Subject:* Re: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus
Callosum, Hippocampus



*External Email - Use Caution*

Dear sir,



It is not clear from these papers to me.



With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics (Biomedical Engineering Group)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552



On Wed, May 22, 2024, 8:19 PM Fischl, Bruce R.,PHD 
wrote:

Mostly these:



https://secure-web.cisco.com/1DKaAagv5wrZcn_HucsSWH8TG1zknHKvHLkGgJhoy1pwq5h5Gy44-n3iYuTFbU_IjGt0vWiNR5NG5XUSF6Q86czJMoJRU0GQjjHxn1JLn23qbq8MvFW4_ghw2XFXMtfI-eVfZKljxj-ITwDft1q3zamXDRxoqvtVjobVOc38fJ8jiQ-rMfBSME1Fd6s-JihLgk5Ce-PUNTmh2x8QhuXpIFDOZ7Ob6S_nzRnFJEli7zUouGvihFDaMjgZgwemDtvJYDkt2VtJ4teOYPxp0K8wVYeMBKWgaGggZAgMAepMQgJT_HVq57ig8bJF9mafB3-AVbgHynMDW-WfxgRdqSAL1-A/https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F15501102%2F


https://secure-web.cisco.com/1XuxKv5CEuHRfXAdPzciFLM-HiNv8hX8h1hN2vYlGz0J9uz79NMgzaagVvButgJoxFDkR-H-CJv1KSQY8x3C_ddrl7Cq7SjoKAFNvx9gRCIbcYwGpsjlOwC_s6rSgvtGUQlXc42701tL_kY8uM6THlNnJ6A2xmfWKOxL6Dwhjk8PW-A7jHqpunbBkm--S533jTawiFOd_XS6mZYORq7q3eOaUjx57irYEbluTAkAUwi_KucSWnQK4bwZrUyvv-SvCMO-ONY2flGkql0hkSP32ZPpfSO53UHIOU5r8-xd5XkHGYVOoMhAPT9mle8XCEoWTVveyaWSxhSMmA6sKq9MXMw/https%3A%2F%2Fdoi.org%2F10.1016%2FS0896-6273%2802%2900569-X




cheers

Bruce

*From:* Ahsan Ali 
*Sent:* Wednesday, May 22, 2024 4:31 AM
*To:* Freesurfer support list ; Huang,
Yujing ; Fischl, Bruce R.,PHD <
bfis...@mgh.harvard.edu>
*Subject:* Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus
Callosum, Hippocampus



*External Email - Use Caution*

Dear FreeSurfer Team,

After reviewing the literature, I have a question: which atlases are used
in the segmentation of the fornix, corpus callosum, and hippocampus from
magnetic resonance images using FreeSurfer? This is a significant question
for me, and I would appreciate a clear and concise answer. Please provide
some relevant references.




With Regards
Ahsan
-
Ahsan Ali
Ph.D Scholar
Department of Applied Mechanics and Biomedical Engineering (AMBE)
Indian Institute of Technology Madras
Chennai-600036, Tamil Nadu, INDIA
Mob.:- +91-8899605552

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 Mass General
Brigham Compliance HelpLine at
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Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Douglas N. Greve]

Can you be even more specific? Operationally, what does it entail? Are 
you just trying to correlate, say, cognitive deficits to, say, thickenss?


On 2/25/2024 9:12 PM, Martin Juneja wrote:


External Email - Use Caution

Hi Doug,

Sorry for not elaborating in my previous email.

Voxel lesion symptom mapping (VLSM) is a method to calculate symptom 
localization by estimating statistical relationships between damage to 
specific brain regions (it could be stroke lesion, tumor lesion or TBI 
lesion etc.) and resulting deficits (e.g., *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724038/ 
 
and *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://academic.oup.com/brain/article/137/9/2532/2848278 
). 
This method can guide the development of targeted interventions and 
rehabilitation strategies aimed at improving symptoms by targeting 
specific brain regions (or networks, if we use network lesion symptom 
mapping: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9724189/ 
).


On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve 
 wrote:


Sorry, don't know what VLSM is. Can you elaborate?

On 2/6/2024 3:19 PM, Martin Juneja wrote:


External Email - Use Caution

Dear FreeSurfer community and experts,

I would greatly appreciate any help/response with the following.

Thanks.

-- Forwarded message -
From: *Martin Juneja* 
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom mapping
To: Freesurfer support list 


Greetings FreeSurfer community,

I was just wondering if it's possible to perform vertex/voxel
lesion symptom mapping (VLSM) using FreeSurfer? In other words, I
would like to assess the impact of lesion topography (of course,
heterogenous locations across patients) on
neurocognitive function in brain tumor patients.

I would greatly appreciate any help/response.

Thanks!

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



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The 

Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Martin Juneja]

External Email - Use Caution

Hi Doug,

Sorry for not elaborating in my previous email.

Voxel lesion symptom mapping (VLSM) is a method to calculate symptom
localization by estimating statistical relationships between damage to
specific brain regions (it could be stroke lesion, tumor lesion or TBI
lesion etc.) and resulting deficits (e.g.,
https://secure-web.cisco.com/1UiWVbssc136ehHR7fbKC3mJg7kJQVmdWhaRoU7E29vpu5yNgNVpd0lZiq4aR019jbUXsgd9ifhWAi0IlkNaX6x9xio5om5mkSpOTNvua1cW-cEEjvzxDi3L2sB29VZVsnhEZ8Tb3UH9P0xee7U6UR5dzGEOh8QJNPNhtL65F1jvipA-Phq6I6tlLdM_es5V3bNy-Uc2GG6yXw2BY9-tSYOxCFzZ8xvUgiqlPE8H6y5TPAXxx9g0S5ELQ2MYBhZc4scdk6uSlw8_4_qsmFzE3pHqfDGZ0Q_Jv3szY1k1AqHkxkI9t7LPh8R6dSgTpNeL4WUyRopXxirT8r-0IxK7nYA/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4724038%2F
 and
https://secure-web.cisco.com/1Sv3DQt7ECt7yYskA3qSYiurVnqwYgQMrW8bVWoluBQmsM_yLtTYU5rsNedrt7kfxvXWRFNBdsUI4A1g3RXw72SMBIG6ZQrrv9cyiZQGDsnk8bidCzCK_lFen7x0alY7ZhJs5O1HBwG06GFvTNxoPfkbR1hD87w8QzlmPBxoAV_migSoy78DKyb73PilyF7D9vRCcWNAx4UOdo0SSrO_Shf1_py0ygzhtUB2FOJo-0Z-5e1wnn3cKO0-MJMcDUhRdVzUXTYWyey2rVOBEqbKBye_yDzoaxLIKzESNFAVFJGY8t8AlAjZS0kE9aqzZKXXtHqmihL1X2aNJDuA_eQsRZA/https%3A%2F%2Facademic.oup.com%2Fbrain%2Farticle%2F137%2F9%2F2532%2F2848278).
 This method can
guide the development of targeted interventions and rehabilitation
strategies aimed at improving symptoms by targeting specific brain regions
(or networks, if we use network lesion symptom mapping:
https://secure-web.cisco.com/10LgUitf4Y4lehNjHOInoyAOPPrjXpKyw8QudhBNFrI-HEs531siCcOCZApchqgDvWDYKy7cM6QODz-i1dQPhiBuCX-00bXDcm2EF8XZrhB_Rknetjx1FVS8u1BBOZ16mMYnGswaNPzNgbt15-7OR0ZajBrz3jJMaAXx2tGeFbJuIT_cwpTPX2u7uVcKu40byzK3CksUD9sBXUODMzo1dWFYJ7dqv9jzjPyhXiM51d49k7iGamx_SlWvcrdjka0R328JXdXbqwiXqt2FEwAVsz1ioBdFbSPNdth73sqgmm1hDt5vQsBMMp8Txr8bGJeZxE6q-ZHf8yqwxiFsXOOVtBw/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC9724189%2F).

On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve 
wrote:

> Sorry, don't know what VLSM is. Can you elaborate?
>
> On 2/6/2024 3:19 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear FreeSurfer community and experts,
>
> I would greatly appreciate any help/response with the following.
>
> Thanks.
>
> -- Forwarded message -
> From: Martin Juneja 
> Date: Wed, Jan 31, 2024 at 7:51 PM
> Subject: Vertex / voxel lesion symptom mapping
> To: Freesurfer support list 
>
>
> Greetings FreeSurfer community,
>
> I was just wondering if it's possible to perform vertex/voxel lesion
> symptom mapping (VLSM) using FreeSurfer? In other words, I would like to
> assess the impact of lesion topography (of course, heterogenous locations
> across patients) on neurocognitive function in brain tumor patients.
>
> I would greatly appreciate any help/response.
>
> Thanks!
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1alsgzukF08chGbO4w3NpaC-q1jyAoVRBYCmqJ8DQ9uwjuWe5DnmfMEG7N1wKmnXrsrj_0xQbF_ascWzT5d5GBYDzSIX7gQ8Pw4g3wlr-CW6PMOYkG67sygGJZHQVwVOqew3dKsQC0AEERTonULgd3WhPp6WSa8bB89yU5ImcoUgdec9qghXdvLvk0dSFUVuw2D--xnnsvtAewoxDa1oA6UQ6GyOeh7WpoK9aVvgeHx0MJ7aiJyplUL99rC4to4QdoSm9vumFVCuTNilhJQhu4BPN2Lt5WmwSOwh4HufaNeLaM9ms8NP-1taLlbygGgLr-kd2dXZNWUWdHLwrNAtWeQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 Mass General
> Brigham Compliance HelpLine at
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>  <
> https://secure-web.cisco.com/1Fe3pAdF_zpv0bjDlDdYJbIAdjcnJMPg6flNKGZB9YifGOW2TBwUeH6unIqwddgtUwSADCDS71ArGnzjpmT64-ocKgDwhrvduxQ-iDE7BIvH20RfkIBovwla2F3odLaOUTeNozsFj5S6_ZDSqcEkp_HyOXlUxeiVXkU7kfo-4C2R4xt0CNC0wqWsDZaxA3P_phUlR9McUiaHCCGOjwzYvMwOCI2QLQdj57EPP7pdl9aimUxjsQYzMlHg_y3_r8fkOn5JF5SEgpOwkeEu_j7WZwTiXNxIViC1h87j4QNEJb67AAKQVqRe8kXB8gc1Ehg5T9bOFnBMORfB03RsN7_VCVw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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>
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Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Douglas N. Greve]

Sorry, don't know what VLSM is. Can you elaborate?

On 2/6/2024 3:19 PM, Martin Juneja wrote:


External Email - Use Caution

Dear FreeSurfer community and experts,

I would greatly appreciate any help/response with the following.

Thanks.

-- Forwarded message -
From: *Martin Juneja* 
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom mapping
To: Freesurfer support list 


Greetings FreeSurfer community,

I was just wondering if it's possible to perform vertex/voxel lesion 
symptom mapping (VLSM) using FreeSurfer? In other words, I would like 
to assess the impact of lesion topography (of course, heterogenous 
locations across patients) on neurocognitive function in brain tumor 
patients.


I would greatly appreciate any help/response.

Thanks!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

[Martin Juneja]

External Email - Use Caution

Dear FreeSurfer community and experts,

I would greatly appreciate any help/response with the following.

Thanks.

-- Forwarded message -
From: Martin Juneja 
Date: Wed, Jan 31, 2024 at 7:51 PM
Subject: Vertex / voxel lesion symptom mapping
To: Freesurfer support list 


Greetings FreeSurfer community,

I was just wondering if it's possible to perform vertex/voxel lesion
symptom mapping (VLSM) using FreeSurfer? In other words, I would like to
assess the impact of lesion topography (of course, heterogenous locations
across patients) on neurocognitive function in brain tumor patients.

I would greatly appreciate any help/response.

Thanks!
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Fwd: Case-controls study !

[Martin Juneja]

External Email - Use Caution

Hi FS experts,

I was wondering if someone could help me get the following issue resolved.

Thanks.

-- Forwarded message -
From: Martin Juneja 
Date: Fri, Dec 8, 2023 at 11:03 AM
Subject: Case-controls study !
To: Freesurfer support list 


Hello FreeSurfer experts,

In my case-control study, I have a dataset of 5 healthy controls (HCs) and
one patient (PAT). I was wondering if there is any way to perform GLM for
PAT > HCs on brain morphometry data.

When I tried to follow instructions from here:
https://secure-web.cisco.com/1aK-KNfU8HH_e-fpaIAGAkK_0d2hcDIl4JpjyDUomASQEQQJehjuhA0YYNd1-yCMyLrNtRVInHC0sL4ZGQSm_hx-e7WqN75sm22gAExeDyUksUiv3NFy2UeyAzhzh7cNHQd3Uf5EAsh0E1za-xLWZQArzwTi3Bn_5I9N1UoxsMjYkGv5oZxPiqEXVD5BEsxQiOPkQtZJuTIDOtckipDfTK-LEDpsCXFCAShvieYfbxxg0ec00jOhHeoAyF4ZLaU_-CqhBmbOtWCJUC56qpOxRmizvYekBnUs8Nlzv3M50Fu7V8kklIdu8eSaJSTnIRHLld9QqWlnqRDFQoChfS_1bcQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis,
 the
mri_glm fit command gives me the following error:

Class Size and Means of each Continuous Variable

1 HC  5  24.2000   0.6000

2 Tumor  1  50.   1.

ERROR: Class Tumor has 1 members. With 2 variables and using DODS, you need
at least 3 members


It seems at-least three subjects are required in the Tumor category -
because I have age and sex covariates in my fsgd file.


I was wondering if there is any way to still perform the above GLM analysis
or any other alternatives available to compare HCs vs one PAT.


Thanks!
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Re: [Freesurfer] Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label

[Huang, Yujing]

Freesurfer distributes ‘fsaverage’ under $FREESURFER_HOME/subjects directory. 
recon-all should create symbolic link to $FREESURFER_HOME/subjects/fsaverage 
under $SUBJECTS_DIR.

This is from your recon-all.log
“
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/Freesurfer
“

You are setting SUBJECTS_DIR to your Freesurfer install directory. It is a good 
idea to set SUBJECTS_DIR to some other directory that you have write permission.

Your recon-all failed because of “Too many levels of symbolic links”. Can you 
check what you have under $FREESURFER_HOME/subjects?
>ls -l $FREESURFER_HOME/subjects

You should have these in the directory:
drwxrwsr-x. 2 zkaufman fsbuild4096 Mar 13  2012 cvs_avg35
drwxrwsr-x. 2 zkaufman fsbuild4096 Apr 14  2015 cvs_avg35_inMNI152
dr-xr-sr-x. 2 ah221fsbuild4096 Mar  8  2023 fsaverage
drwxrwsr-x. 2 zkaufman fsbuild4096 Sep 22  2009 fsaverage3
drwxrwsr-x. 2 zkaufman fsbuild4096 Sep 22  2009 fsaverage4
drwxrwsr-x. 2 zkaufman fsbuild4096 May 31  2011 fsaverage5
drwxrwsr-x. 2 zkaufman fsbuild4096 Sep 22  2009 fsaverage6
drwxrwsr-x. 2 zkaufman fsbuild4096 Apr 12  2018 fsaverage_sym
drwxrwsr-x. 2 zkaufman fsbuild4096 Mar 30  2010 lh.EC_average
-rw-rw-r--. 1 zkaufman fsbuild1512 Dec 29  2016 README
drwxrwsr-x. 2 zkaufman fsbuild4096 Mar 30  2010 rh.EC_average
-rw-rw-r--. 1 zkaufman fsbuild 6280209 Dec 29  2016 sample-001.mgz
-rw-rw-r--. 1 zkaufman fsbuild 6269785 Dec 29  2016 sample-002.mgz
drwxrwsr-x. 2 zkaufman fsbuild4096 Nov 11  2008 V1_average

Your recon-all should have created this link ‘fsaverage -> 
/usr/local/freesurfer/subjects/fsaverage’ in the directory as well. Remove 
link. Set SUBJECTS_DIR to some other directory and restart recon-all.

Best,

Yujing








From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Suman Saha
Sent: Monday, November 27, 2023 11:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: ERROR reading 
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label


External Email - Use Caution

Hello FreeSurfer Developers,



I'm attempting to run recon-all command, but  I get the following error when I 
run the "recon-all -i sub.mgz -s sub1 -all" command:



ERROR:

ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label
Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov  2 
18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023

Does anyone have any thoughts on how to trouble-shoot this one? I've attached 
the recon-all.log.



1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu 22.04.1

3) recon-all.log: see attached

4) recon-all.error : see attached


-- Forwarded message -
From: Suman Saha mailto:ecesuma...@gmail.com>>
Date: Sat, Nov 25, 2023 at 8:17 AM
Subject: ERROR reading 
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label
To: mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello FreeSurfer Developers,



I'm attempting to run recon-all command, but  I get the following error when I 
run the "recon-all -i sub.mgz -s sub1 -all" command:



ERROR:

ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label
Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov  2 
18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023

Does anyone have any thoughts on how to trouble-shoot this one? I've attached 
the recon-all.log.



1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu 22.04.1

3) recon-all.log: see attached

4) recon-all.error : see attached
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Re: [Freesurfer] Fwd: Errors in LGI command

[Douglas N. Greve]

Copy the attached matlab file into $FREESURFER/matlab/freesurfer_read_surf.m

On 11/24/2023 12:53 PM, 笹林大樹 wrote:


External Email - Use Caution

Dear Freesurfer experts,

I’m sorry, I would like to add some missing information about the 
following question.


OS: CentOS Linux 7
FS ver: fs7.1.0
Matlab ver: R2017a or R2022a

I would be grateful for your answer when you have time.

Best,

Daiki Sasabayashi


転送されたメッセージ:

*差出人: *笹林大樹 
*件名: **[Freesurfer] Errors in LGI command*
*日付: *2023年11月22日 15:19:36 GMT-5
*宛先: *Freesurfer support list 
*返信先: *Freesurfer support list 

External Email - Use Caution


Dear Freesurfer experts,

I have run the following command:
*recon-all -s sub-1001 -localGI -no-isrunning*

However, I got the error message as below.

>> Warning: Input argument must be a character vector.
> In ver (line 41) In freesurfer_read_surf (line 70) In 
find_corresponding_center_FSformat (line 26)

Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>>
ERROR: find_corresponding_center_FSformat did not complete 
successfully! Linux dn003 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 
7 15:41:52 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s sub-1001 exited with ERRORS at Wed Nov 22 14:59:33 EST 2023

How can I resolve the problem?
Thank you for your consideration.

Best,

Daiki Sasabayashi
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function [vertices, faces] = freesurfer_read_surf(fname)

% freesurfer_read_surf - FreeSurfer I/O function to read a surface file
% 
% [vertices, faces] = freesurfer_read_surf(fname)
% 
% Reads the vertex coordinates (mm) and face lists from a surface file.
% 
% Surface files are stored as either triangulations or quadrangulations.
% That is, for a triangulation, each face is defined by 3 vertices.  For a
% quadrangulation, each face is defined by 4 vertices.  The rows of 'faces'
% contain indices into the rows of 'vertices', the latter holds the XYZ
% coordinates of each vertex.
%
% The freesurfer faces index the vertices in counter-clockwise order (when
% viewed from the outside of the surface).  This is consistent with a
% right-hand rule.  If we have vertices
%
% C   B
%
%
%   A
%
% Then we can calculate an edge vector from A to B (ie, AB = B - A) and
% another edge vector from A to C (ie, AC = C - A).  If you form a "gun"
% with your thumb and forefinger of the right hand, then align your thumb
% with the AB vector and your forefinger with the AC vector, your palm is
% facing out of the screen and extending your middle finger in the
% orthogonal direction to the plane of the screen will give the outward
% surface normal of the triangle ABC.  (If you lookup "triangle" on
% Wolfram's mathworld, you can see that AB is referred to as c and AC is
% referred to as b.)
%
% However, if this surface is read into matlab, it will give INWARD surface
% normals in the matlab patch command.  For some reason, matlab is not
% following the right hand rule.  To get OUTWARD normals with the matlab
% patch command, use faces(:,[1 3 2]) (see below).
%
% The vertex coordinates are in mm.  The FreeSurfer coordinate
% system for surfaces is quite simple, but relating to their MRI
% cor-??? files is too confusing to explain here; see the FreeSurfer
% homepage or google the documentation by Graham Wideman.  For the
% surfaces, at least, the origin is somewhere in the center of the
% head, and the vertex XYZ coordinates are oriented such that +X is
% right, +Y is anterior and +Z is superior (this is the
% FreeSurfer RAS coordinate system).
%
% Note that reading the faces of a quad file can take a long
% time due to their compact storage format.  In this case, the return of
% vertices can be faster if the face output variable is not specified; in
% this case, the faces are not read.
% 
% Try this to visualize the surface:
% Hp = patch('vertices',vertices,'faces',faces(:,[1 3 2]),...
%   'facecolor',[.5 .5 .5],'edgecolor','none')
% camlight('headlight','infinite')
% vertnormals = get(Hp,'vertexnormals');
%
% See also freesurfer_write_surf, freesurfer_read_curv,
%  freesurfer_read_wfile
%

[Freesurfer] Fwd: Errors in LGI command

[笹林大樹]

External Email - Use Caution

Dear Freesurfer experts,

I’m sorry, I would like to add some missing information about the following 
question.

OS: CentOS Linux 7
FS ver: fs7.1.0
Matlab ver: R2017a or R2022a

I would be grateful for your answer when you have time.

Best,

Daiki Sasabayashi

> 転送されたメッセージ:
> 
> 差出人: 笹林大樹 
> 件名: [Freesurfer] Errors in LGI command
> 日付: 2023年11月22日 15:19:36 GMT-5
> 宛先: Freesurfer support list 
> 返信先: Freesurfer support list 
> 
> External Email - Use Caution
> 
> 
> Dear Freesurfer experts,
> 
> I have run the following command:
> recon-all -s sub-1001 -localGI -no-isrunning
> 
> However, I got the error message as below.
> 
> >> Warning: Input argument must be a character vector.  
> > In ver (line 41) In freesurfer_read_surf (line 70) In 
> > find_corresponding_center_FSformat (line 26)  
> Error using fprintf 
> Function is not defined for 'struct' inputs.  
> 
> Error in freesurfer_read_surf (line 70) 
> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));  
> 
> Error in find_corresponding_center_FSformat (line 26) 
> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);  
> 
> >>  
> ERROR: find_corresponding_center_FSformat did not complete successfully! 
> Linux dn003 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 15:41:52 UTC 2023 
> x86_64 x86_64 x86_64 GNU/Linux  
> 
> recon-all -s sub-1001 exited with ERRORS at Wed Nov 22 14:59:33 EST 2023
> 
> How can I resolve the problem?
> Thank you for your consideration.
> 
> Best,
> 
> Daiki Sasabayashi
> ___
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> Please note that this e-mail is not secure (encrypted).  If you do not wish 
> to continue communication over unencrypted e-mail, please notify the sender 
> of this message immediately.  Continuing to send or respond to e-mail after 
> receiving this message means you understand and accept this risk and wish to 
> continue to communicate over unencrypted e-mail. 

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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Fwd: About Mean LGI value

[Douglas N. Greve]

If the difference is only between 3.0761 and 3.0327, then that is 
acceptably small to disregard.


On 11/21/2023 10:40 AM, 笹林大樹 wrote:


External Email - Use Caution

Dear Dr. Greve,

I trust this message finds you well. I wanted to follow up on the 
inquiry I posted to the FreeSurfer mailing list a while back regarding 
"About Mean LGI value" as below.
I understand you are busy, and I appreciate your dedication to the 
community. If possible, could you revisit my query when time permits?

Thank you for your time, and I look forward to hearing from you.

Best,
Daiki Sasabayashi

転送されたメッセージ:

*差出人: *笹林大樹 
*件名: **Re: [Freesurfer] About Mean LGI value*
*日付: *2023年11月9日 10:37:38 GMT-5
*宛先: *Freesurfer support list 
*返信先: *Freesurfer support list 

External Email - Use Caution


Dear. Dr. Greve,

Thank you for your response.
I attached both “*h.aparc.pial_lgi.stats” and 
“*h.aparc.mean_pial_lgi.stats” files.
For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, 
Seg0001, is it correct as mean LGI value?), while the average of the 
LGI values is about 3.0327 (the sum of the LGI values of the 34 DK 
atlas ROIs divided by 34: value calculated here).

Are these values acceptable?

Daiki Sasabayashi



2023/11/09 9:33、Douglas N. Greve のメール:

How different are the values? Those two stats files are created with 
different programs, so there could be some small differences. But if 
you're seeing large differences, then that is something else. If the 
latter, then send both stats files.


On 11/3/2023 9:14 AM, 笹林大樹 wrote:


External Email - Use Caution

Dear Freesurfer experts,

I have calculated the mean LGI value for each hemisphere by 
referring to previous archives below.
However, this mean LGI value differs from the average of the LGI 
values listed in *h/aparc.pial_lgi.stats (i.e., the sum of the LGI 
values of the 34 DK atlas ROIs divided by 34).

Are these values originally subject to discrepancy?

Best,

Daiki Sasabayashi


  Re: [Freesurfer] Mean Gyrification index
  


Dougla s N. Greve 
 
Wed, 09 Sep 2020 08:26:32 -0700 



It is giving you values for two segmentations: inside the label and 
outside the label. Use --id 1 to get only values inside the cortex 
label

On 9/9/2020 11:27 AM, vittal korann wrote:

 External Email - Use Caution

Dear FreeSurfer experts

I am working on the gyrification index of schizophrenia
patients. I had collated global brain values such as thickness,
GM, and WM volumes. In addition, I wanted to tabulate
gyrification values. Using the below link I was able to extract
the hemispheric mean gyrification values.

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html  


But it is giving me 2 rows of output that are adding more
ambiguity to the existing problem. Below is the command which I
used to get mean gyrification for the left hemisphere and also
the corresponding output.

[Freesurfer] Fwd: About Mean LGI value

[笹林大樹]

External Email - Use CautionDear Dr. Greve,I trust this message finds you well. I wanted to follow up on the inquiry I posted to the FreeSurfer mailing list a while back regarding "About Mean LGI value" as below.I understand you are busy, and I appreciate your dedication to the community. If possible, could you revisit my query when time permits?Thank you for your time, and I look forward to hearing from you.

Best,Daiki Sasabayashi転送されたメッセージ:差出人: 笹林大樹 件名: Re: [Freesurfer] About Mean LGI value日付: 2023年11月9日 10:37:38 GMT-5宛先: Freesurfer support list 返信先: Freesurfer support list External Email - Use CautionDear. Dr. Greve,Thank you for your response.I attached both “*h.aparc.pial_lgi.stats” and “*h.aparc.mean_pial_lgi.stats” files.For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, Seg0001, is it correct as mean LGI value?), while the average of the LGI values is about 3.0327 (the sum of the LGI values of the 34 DK atlas ROIs divided by 34: value calculated here).Are these values acceptable?Daiki Sasabayashi

lh.aparc.pial_lgi.stats
Description: Binary data


lh.aparc.mean_pial_lgi.stats
Description: Binary data


rh.aparc.pial_lgi.stats
Description: Binary data


rh.aparc.mean_pial_lgi.stats
Description: Binary data
2023/11/09 9:33、Douglas N. Greve のメール:

  
  
How different are the values? Those two stats files are created with
different programs, so there could be some small differences. But if
you're seeing large differences, then that is something else. If the
latter, then send both stats files.

On 11/3/2023 9:14 AM, 笹林大樹 wrote:

External
  Email - Use Caution
  
Dear Freesurfer experts,


I have calculated the mean LGI value for each
  hemisphere by referring to previous archives below. 
However, this mean LGI value differs from the
  average of the LGI values listed in *h/aparc.pial_lgi.stats
  (i.e., the sum of the LGI values of the 34 DK atlas ROIs
  divided by 34). 
Are these values originally subject to
  discrepancy?


Best,
  
  
  
  Daiki Sasabayashi
  
  
  

  

  Re: [Freesurfer] Mean
Gyrification indexDougla
 s N.
Greve Wed, 09 Sep 2020 08:26:32
-0700

It is giving you values for two segmentations:
inside the label and outside the label. Use --id 1 to get only
values inside the cortex label
  On 9/9/2020 11:27 AM, vittal korann wrote:

  
External Email - Use Caution

Dear FreeSurfer experts


I am working on the gyrification index of
  schizophrenia patients. I had collated global brain values such as
  thickness, GM, and WM volumes. In addition, I wanted to tabulate
  gyrification values. Using the below link I was able to extract the
  hemispheric mean gyrification values.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html


But it is giving me 2 rows of output that are
  adding more ambiguity to the existing problem. Below is the command which I used to get mean
  gyrification for the left hemisphere and also the corresponding
  output.
*Command Line: *

mri_segstats --slabel CSRI104 lh
/usr/local/freesurfer//subjects/CSRI104/label/lh.cortex --i
/usr/local/freesurfer//subjects/CSRI104/surf/lh.pial_lgi --sum

lh.aparc.pial_lgi.stats 
*Output: *

# NRows 2
# NTableCols 10
# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
StdDev Min Max Range
  1   0      6879     4687.8  Seg     2.4509     0.2838  
1.8067     2.8873     1.0806
  2   1    128054    84259.7  Seg0001     3.0148     0.6366  

1.9369     4.7611     2.8242 My confusion is that which row I should take
  it as a mean gyrification value for the left hemisphere (seg or
  seg0001)?Please guide me if there is a way to combine
  two hemispheric values and make it as mean gyrification alike mean
  thickness.
With regards
Korann



On Wed, Sep 9, 2020 at 4:51 PM vittal korann
  MailScanner
has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
gmail.com 

[Freesurfer] Fwd: recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.

[fsbuild]

External Email - Use Caution

If you have not already done so, I would try installing and using the newest 
version of theMatlab runtime environment that the 7.4.1 release was 
tested with, i.e. R2019b. Once you have set $FREESURFER_HOME, then run 
the fs_install_mcr script included with the freesurfer distribution 
$ export FREESURFER_HOME=your install path
$ cd $FREESURFER_HOME/bin
$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
… answer y to any installer questions ...
Then I think it should work to find the Matlab libraries by at least start off 
with setting,
$ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64
Please make sure you have otherwise removed from your environment and 
references to the previous Matlab R2022b setup.
- R.

Begin forwarded message:From:Benjamin Cole Sherman 
bshe...@stanford.edu
Subject:[Freesurfer] recon-all error: matlab gives: Unrecognized function 
or variable 'make_outer_surface'.
Date:August 30, 2023 at 12:02:09 EDT
To:"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Reply-To:Freesurfer support list freesurfer@nmr.mgh.harvard.edu

External Email - Use 
CautionHi FreeSurfer Team,I'm 
trying to run recon-all on an MRI nii.gz file and I believe most of the command 
runs as the error doesn't happen until several hours in, however once matlab is 
initiated I consistently get the following output:MATLAB is selecting SOFTWARE 
OPENGL rendering. 
  M A T L A B (R)   
   Copyright 1984-2022 The 
MathWorks, Inc. 
R2022b (9.13.0.2049777) 64-bit (glnxa64) 
  August 
24, 2022Warning: Function iscolumn has the same name as a MATLAB builtin. We 
suggestyou rename the function to avoid a potential name conflict.Warning: 
Function ismatrix has the same name as a MATLAB builtin. We suggestyou rename 
the function to avoid a potential name conflict.Warning: Function isrow has the 
same name as a MATLAB builtin. We suggest yourename the function to avoid a 
potential name conflict.Warning: Function narginchk has the same name as a 
MATLAB builtin. We suggestyou rename the function to avoid a potential name 
conflict.Warning: Function isequaln has the same name as a MATLAB builtin. We 
suggestyou rename the function to avoid a potential name conflict.Warning: 
Function istable has the same name as a MATLAB builtin. We suggest yourename 
the function to avoid a potential name conflict.Warning: Function isfile has 
the same name as a MATLAB builtin. We suggest yourename the function to avoid a 
potential name conflict.Warning: Function isfolder has the same name as a 
MATLAB builtin. We suggestyou rename the function to avoid a potential name 
conflict..Warning: Function isstring has the same name as a MATLAB builtin. We 
suggestyou rename the function to avoid a potential name conflict.For 
online documentation, 
seehttps://secure-web.cisco.com/1A7cHJG7OTQToCpTNsg3ycqt5UEObzYbnyuy3_pfg1wlC1F4jIcVd5Pf6qNpHle7gAqT6177JQQHGrD_FY6ddsPj56KJNkyqORfZ-yq1A_uco2Hs4cdMVZQlYtvfMd8x_lRoSbGgA6HkBbAlHw3Q-AOuQ__pYiP83887FgmXZJoCFrKjnw3CsPha7iaVbaHPnfA7ZxSpDnyTRx8SR9Lf1azZHdNBwnNBsOPaZ1tDgP3AdDr-vLWNWNGjJa4MSRiWI_dpdoFbTBvkXze5zrUv2R0w8MgXoHQdv0b1UtwSdrSJMTpEhgSqbsVxDqMJhG-S3EN862Yz_ti_Gc66ckcWp4w/https%3A%2F%2Fwww.mathworks.com%2FsupportFor
 product information, 
visithttp://secure-web.cisco.com/1PkNE_zNSBM0yzYMjwH_cGeVC4O7UdJdfnliIOnqoaBcy5GHeqYRm_4T9_WR9vGAfol8V0_h_BBmmgtxSeq1hM7DAzUz2W8u9riITxG6WdjCZo6evmQDs2w70OLY4bBtE9v14Mw-xplN4Bax9dYaGZJinqA1-khI72MQgDmD-GNqYeGUSK4_PoYikluiayoPmvJ3sDu83lphtc86T2XqofDnHgRz4xHVDKv4x4IzRF_k90VuY4qtwhiWQcGFroyQqUnRlwBy8MxzppbNN1vt2O5sFg60fZM18Ksgvk1xxX8wXaurrhAhfCK-lB5rJZX3QwumhPOjvG3htgVFHOsYbJA/http%3A%2F%2Fwww.mathworks.com.%26nbsp;;
 Unrecognized function or variable 
'make_outer_surface'.ERROR: make_outer_surface did not 
create output file 
'/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!Command
 exited with non-zero status 1I haven't been able to find anything in the 
support archives so I was hoping you could help us out.1)Freesurfer version: 
freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb84602)Platform: Ubuntu 
20.04.6 LTS3)recon-all.log: see attachedThanks for any help you can 
provide!___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Fwd: error in recon all

[Douglas N. Greve]

   External Email - Use Caution

Have you looked at this page 
https://secure-web.cisco.com/1BV2hYoaSBjdqCI3ji_zfSci2RFzSKvskUEpLSzz9KZZmJ3W692xmbGJZYtcILbXwSeNGChMfif4QJenV0WIKvqU9-y6rwrLkf3PY6_kwKAA0UMsTELNqJZjOgJBdeZO_ohao1RiTq7M-MGJ54JDw6BQyJbBIkgZZ28P8CWJqFlnQxggUkQBtLaA1W-aXp2lULZOsopkFEwYhd83mmd256M6879E7uCvLGO3pK-iksNanE7ZRwomYQJsIvF4Dmfq8oRuuaMf7z2nELCOz0Nb0vg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach_freeview ?


On 6/22/2023 2:38 AM, alanood alsaleh wrote:


External Email - Use Caution





Hello Freesurfer developer

I tried to run a recon all commands for 36 subjects, and 30 finished 
without any issues. However, 6 of them were terminated with the ERROR 
(Talairach failed!). Can you please help me to sort this problem out?


Please find the attachments (I attached the recon all script I used 
and the log file that I got for the subject with an error ).


Regards
Alanood

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[Freesurfer] Fwd: The results of your email commands

[Rob Kudyba]

External Email - Use Caution

does this message mean my email was rejected?

Also the link to subscrobe on
https://secure-web.cisco.com/1C8Ww8WKzb-WR8JygU7XB0JN4vWN1-1IzwWYF8eJpyXmp6qQYv5hiX72bRS68pEcQzs0ePzH5sPk5qwX49YI54Ura4xV3zvLKduPj4hb0wxH2P6CKUXW4IUotdslBOmWOFndcnTcMiE5Tb7PKczX7P5dw7QLFAqcH-DjYRFlG-wbfjqIxdZyoxYqIY-Bu45XtGlV2LD5eMPrHxGiT003x09Hih_eBigeOunOvZxOA7KwNSwFQ-qrDcTqcvKIQUsvjuT9NregApoIJNO9yhvt797KF8MjzlDStuONYGqIuxxPeh9CUJ4sktTWMKpttR8777wg0jChEf2GYovhuW7kqlw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurferSupport
 are broken as
they should point to the https version, e.g., the link to subscribe
http://secure-web.cisco.com/1Rs_mL5ODuvETF1LGNBWxqNLByNtjtuyy843X-XuQN3-JxnU_BTZgFBfB0IdOmQ3n9qPVyMmpppO_FPQQdr2ORsEzZnptuYgXWTLAYNxwaAdyg35QLK-d8inv_akfFLBVwOARKA594SnWYy6K1m_gB-_ea1YacCKy8DWVstHIAUo97ZatT0SDOtlTTfvDi_DKMF3M_9KCGyDFX8CRmyZvERKNy0s1rU1hBkRiSrcDLghI7TW1PCr7UCw3AqyjkC-h8AY9-hgXQy_UPNeCSTni2OjRPIjDDmq7vk_cx0buaPRhnQFNb2o1vJWeNohpHsflpdEf_jPDuzdfGbPUM4mcfQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

-- Forwarded message -
From: 
Date: Fri, May 26, 2023 at 11:25 AM
Subject: The results of your email commands
To: 


The results of your email command are provided below. Attached is your
original message.

- Results:
Ignoring non-text/plain MIME parts

- Unprocessed:

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- Done.

The information in this e-mail is intended only for the person to whom it
is addressed.  If you 

[Freesurfer] Fwd: questions about mri_normalize

[Fischl, Bruce R.,PHD]

External Email - Use Caution

Hi John


  1.  We empirically set it at 2, but that was a long time ago, but the optimal 
number is dependent on a lot of things, mostly image CNR. If the gray/white 
contrast is good enough you can run it for more, but you have to make sure that 
the normalization doesn’t start creeping into the gray matter. It is 
essentially a coarse segmentation that tries to find the bulk of the wm, then 
normalize it to 110. In regions of low gray/white CNR it would sometimes start 
normalizing the deeper layers to 110 at which point the thickness and surface 
placements will of course be wrong.
  2.  Yes, if the wm is not around 110 then something went wrong. You can also 
just put a single control point in the body of the wm, but I don’t think I’ve 
seen it not center most of the wm on 110, so maybe something else is going on?

Cheers
Bruce



External Email - Use Caution

Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the intensity of 
FLAIR images , and I've observed that increasing the sigma parameter up to 25 
is effective in improving the quality of the normalized images for noisy 
datasets.
mri_normalize -sigma 25 -g 1 FLAIR_skullstripped.nii 
FLAIR_skullstripped_norm.mgz

However, I have questions about the n argument, which is set to 2 by default. 
For noisy images, white matter intensity after normalization is around 140-150. 
When using n=10, I noticed that the white matter intensity decreased from 
140-150 to around 110-120, resulting in better quality normalized images.
1) I'm wondering if there is a cut-off value for the number of iterations, or 
if a higher number of iterations always yields better results.
2) Also, if the intensity of the white matter after normalization is not around 
110, but instead around 140 or 150, does that indicate that the normalization 
was not effective and that we need to increase the number of iterations?

Thank you for your assistance.
John
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Fwd: questions about mri_normalize

[John Anderson]

External Email - Use Caution

Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy datasets.
mri_normalize -sigma 25 -g 1 FLAIR_skullstripped.nii
FLAIR_skullstripped_norm.mgz

However, I have questions about the n argument, which is set to 2 by
default. For noisy images, white matter intensity after normalization is
around 140-150. When using n=10, I noticed that the white matter intensity
decreased from 140-150 to around 110-120, resulting in better quality
normalized images.
1) I'm wondering if there is a cut-off value for the number of iterations,
or if a higher number of iterations always yields better results.
2) Also, if the intensity of the white matter after normalization is not
around 110, but instead around 140 or 150, does that indicate that the
normalization was not effective and that we need to increase the number of
iterations?

Thank you for your assistance.
John
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Fwd: Password to VirtualMachine request

[Gromki Hados]

External Email - Use Caution

Hi,

I would like to kindly ask you for the password for FreeSurfer 7.2.0
Virtual Machine.

I tried using old password (brain.map), but that doesn't work anymore.

Also, is there a possiblity of getting sudo password? It was quite annoying
to work on previous version without it.

Thank you in advance!

Best regards,
Jakub Wojciechowski
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Fwd: Turku PET Centre Brain Imaging Course / September 19th-21st 2022

[Douglas N. Greve]

   External Email - Use Caution


 Forwarded Message 
Subject: 	Re: Turku PET Centre Brain Imaging Course / September 
19th-21st 2022

Date:   Mon, 17 Apr 2023 06:34:32 +
From:   Lauri Nummenmaa 
To: petpub...@tyks.fi 



External Email - Use Caution

Dear friends and colleagues,

we are delighted to announce that the fourth edition of the *Turku PET 
Centre Neuroimaging Course* will be held in September 11th-15th 2023.


The course will give a hands-on overview on processing, modelling, and 
statistical analysis of brain-PET data, but we also cover principles of 
analyzing structural and functional MR images. The course is aimed at 
PhD students, post-docs, and scientists working on medical, cognitive, 
and computational neuroimaging. The course will be held on site, but all 
the lectures will be also streamed live on Echo360  and stored 
permanently for viewing.


The *course is free of charge* but registration is mandatory as we have 
limited seats on site (yet unlimited capacity for participating online). 
Please see the course webpage for schedule, registration and further 
information:


http://secure-web.cisco.com/1I_1yioEhKGCtw0sMY5h8PNj8csB-rEYYtEnf7iVnPHNsBNwN9aZ7y5L__fMkORRbx8WXKvSQ3oOuEDzF8eosfwAeGIaMq_15gd59s06GMeVUWGZXNmzMoRflkIzNPg6oc-cjBvvpfEmFHlxHzdN7Tj6c-99SmzBR0tT4WOV2NI13W89r9Zm4symHstu6FAe40zXzF0AHZfl57Sd18JRgwYVfYJP6hf9fbc1fyu0BoPvD6BzqxcwmdLgnMRIro7qZrbnfTFvhbuaAt8giD63_Mw/http%3A%2F%2Femotion.utu.fi%2Fneurocourse

Please pass this information to your students and colleagues, we hope to 
see you in Turku in September!


All the best

Lauri

P.S. The lectures, slides and other materials from last year’s course 
are also available for viewing here: 
https://secure-web.cisco.com/1sXxvtRBEukIO3TS0NLxM536AwMBVlWxgjYn8OK-nThBFj4T3GfIKivceqr3RJ75kDbPMwcW6_NdxWRXl99w-ob4d2OKRHHUA00qmco3khofs1C842q9uXRXjvPbgiYl89muIaYDVZ0mp7VUmKjKXsunafnRmiD07-H1AhMLxEZIjcUHEEN3uBN0gAjpfTJsVYcqJYOFSRFO948-Mu-sYPvVVuqNPC8FxwGyM9q7wCa-TSdNmKk9MB4nBFmMTZWxbvQJtbqbT5FKyMNT8m4zFWg/https%3A%2F%2Femotion.utu.fi%2Fneurocourse-2022%2F 



-
Dr Lauri Nummenmaa
Professor, Turku PET Centre
University of Turku
FI-20014, Turku, Finland

tel +358 50 574 7933
www http://secure-web.cisco.com/1lX4q7XtRnK8MPnSKpWbdQ3khprqntVBga2D-EFxjd1GStE25aHOQ3CbwseYDomDEHYLv_gt1XiBQn6RR-lxaNZLTB23jzpDW3jCAnbv3UHCVdgIsmvyPLZRhDlI8zFRaVTIyj45SXLsW7H-r6sUm2MK6s6l7cmYZuGBn3Ax0tgcME0_K39sh7rTJJt6mrpmaewdHiYomN99l8_cxX19CDTDr8DqhH6Uo363zaHYh4ubu4Gl1zjnTHxq5Xm3pJF-FKQZgfi4XpDIj7yE70RH7FA/http%3A%2F%2Femotion.utu.fi 







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[Freesurfer] Fwd: FS VM zip password

[Kiarash Danesh]

External Email - Use Caution

-- Forwarded message -
From: Kiarash Danesh 
Date: Fri, Apr 14, 2023 at 9:43 PM
Subject: FS VM zip password
To: 


Dear developers,


I am attempting to set up virtual box with the Ubuntu image provided in the
installation guide. I would like to request the password to unzip
'FS_7_2_0_ubuntu_18_04_06.ova.7z'.

Thank you in advance!

- Kiarash Danesh
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[Freesurfer] Fwd: Research scientist positions at OSUMC!

[Douglas N. Greve]

Forwarding on an interesting job working Jessica Turner!


 Forwarded Message 
Subject:Research scientist positions at OSUMC!
Date:   Fri, 7 Apr 2023 13:42:55 +
From:   Turner, Jessica 
To: Douglas N. Greve 



External Email - Use Caution

https://osu.wd1.myworkdayjobs.com/OSUCareers/job/Medical-Center-Campus/Senior-Researcher_R74255-1 



_Job Description_

The Senior Researcher designs and conducts independent complex 
experimental research in a foundational (basic) biological/health 
science research laboratory with a psychiatric neuroimaging and genetics 
research program, in the Department of Psychiatry and Behavioral Health. 
 Expected responsibilities include developing and investigating 
neuroimaging models of symptoms and response to various treatments 
across diagnostic groups; applying current analysis techniques to the 
analysis of behavioral, neurophysiological, and genetic data in 
combinations; interpreting and evaluating research data; working with 
collaborative multi-site teams in the analysis of large-scale data 
collections; preparing manuscripts, articles, reports and abstracts for 
publication in peer-reviewed journals; attending and presenting results 
at national and international scientific conferences, seminars, and 
workshops; collaboratively developing and contributing to grant 
proposals to obtain extramural funding to support research; developing 
and implementing new research projects; directing and training other 
research staff, participating in laboratory meetings and project 
meetings.  Some mentoring of other research personnel may be available.


_Minimum Education Required _

Doctorate (Academic) in psychology, biology, engineering, computer 
science, or a relevant field.


_Required Qualifications _

The candidate will be analyzing data as part of their research work and 
must be capable of independently using some neuroimaging analysis 
pipelines (for example, fmriprep, SPM, FSL), ideally for structural, 
resting state, task-based analyses (the more imaging modalities the 
candidate has worked with, the better).  The ability to work in a Linux 
environment is a must. Experience with multivariate analyses of 
functional MRI data or combined analysis of imaging and other datatypes 
such as EEG, EMA, PET, genetics is a strength. An interest in the 
integration of genetic data with neuroimaging and behavioral data within 
clinical populations is ideal.  Clinical experience is not required but 
would be a strength. The candidate will also be writing in support of 
the research program, and must be capable of developing first author 
papers on neuroimaging results (as demonstrated by previous publications).


Many thanks!

Jess

Jessica A. Turner, Ph.D.

/Professor, Department of Psychiatry and Behavioral Health/

/Wexner Medical Center/

/The Ohio State University/

/jessica.tur...@osumc.edu/

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Re: [Freesurfer] Fwd: Segmentation fault (core dumped)

[Huang, Yujing]

Hi Tracy,

I looked at your recon-all.log.

There are total of 19 runs.  The first 4 runs from 2015 and 2016 finished 
without errors. They were all run on hippocampus.umd.edu. The later failed ones 
with segmentation fault were run a different machine - seahorse.umd.edu. Since 
you are using Freesurfer 5.1 built for centos4, I’m wondering if there are some 
compatibility issues.

Can you try running it on hippocampus.umd.edu?

I did notice that you tried 6.0.0 and 7.1.1 but those runs reported a different 
error.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tracy Riggins
Sent: Thursday, March 9, 2023 6:26 PM
To: freesurfer@nmr.mgh.harvard.edu; Allard, Tamara Lynn 

Subject: [Freesurfer] Fwd: Segmentation fault (core dumped)


External Email - Use Caution
Yujing
Any insight on this?
Thanks,
Tracy
-- Forwarded message -
From: Tracy Riggins mailto:rigg...@umd.edu>>
Date: Mon, Mar 6, 2023, 10:44 PM
Subject: Re: Segmentation fault (core dumped)
To: mailto:freesurfer@nmr.mgh.harvard.edu>>

Yujing
Yes, we have run this successfully with other participants (although it was a 
while ago).
Attached is the recon-all.log
thanks for your help!
Tracy

On Sun, Mar 5, 2023 at 1:21 PM Tracy Riggins 
mailto:rigg...@umd.edu>> wrote:
Greetings FS experts:

We are trying to run recon-all -s -qcache on a handful of brains processed in 
freesurfer v5.1.0.   (it's an old dataset...5.1 makes the most sense for our 
purpose.)

The error is below:

[cid:image001.png@01D952C1.6B05D390]

--
#@# 1/1 HMN080 Fri Mar  3 12:14:44 EST 2023 --
---
mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.51930/HMN080.1.mgh --sval 
/export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv 
--noreshape --no-cortex
Segmentation fault (core dumped)
Linux 
seahorse.umd.edu<http://secure-web.cisco.com/1241La8UANSF3aFvnvgmz2aBZoq4NP_I-Xg2zP9nsXxcY4aONgoneZ5-sAXRFXwbt-ifz1SW2xFxyQkOfaqEnD-XV7M2XwnlfIzVp0MhUkSnB2AQRIoZXQ4KJ-jWL_c-_iWGGNDOchXYLDrVxNx3Hqe91pj9dTuBogQhAQopasVfYqjA_Q4oObo1Q8CZEgd-NFs6FbUbgoCRsx6nBY9B_Y-Z674xtNPMoAm83W1IbtnTEbGHj1mt_2YRFnwmLPGfmmyOFDjm8iFw2cayKrkI_wO5sMnHDvBW0r3844_4kJaSMm92Lgp61N3oH9ogfOdSE/http%3A%2F%2Fseahorse.umd.edu>
 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 
x86_64 GNU/Linux

recon-all -s HMN080 exited with ERRORS at Fri Mar  3 12:14:48 EST 2023

Can you assist?  OR perhaps tell us where to find the core dump file, which may 
have more information?

--
Tracy Riggins, Ph.D.
Pronouns<https://secure-web.cisco.com/15wAiYp1A8Jpo8jBJZdshwdMzWaNyB4fxtd5_lhEG04EuWCWsUMrHcr0ouzCJ9NN_jHOiVKV23omSiR_8ZPREj0EKe1GuhZN-vdOPoIbE3INrW3cSDpVCklwRRSHL37D_2fDnf7m_8PUzVat9HBLTR27uHEvqpFZ550I-jwVu7CINJEWISD516Eahdcrq4ufh3dRPzD-xmGzWwyLWAM8p8XiodRzyjrC2DxErje1nQvl7zLHpNvDaHLUE1IlZtX25XMzsNZDa-yaq9rsJP5a1OtnlkuZqkE3A7ROR0-dqsqXmiQwORluEG2oHjEX_Ydag/https%3A%2F%2Fwww.mypronouns.org%2F>:
 she/her/hers
Associate Professor of Psychology
4094 Campus Drive, Biology/Psychology Building 2147J
University of Maryland, College Park, MD 20742
Zoom Meeting ID: 
6751666548<https://secure-web.cisco.com/1nA801X9aPl34ExfhmIqsB8n7JAuhOs7P8RPlnbm6yVwEYH-i4oHqla7YtOqLgaAy_3vuL8zeG68aClILxvNE6l6We60ihVyRUreALH85NmamMOOwLlvcLcKV0388XfXr27c-BcXR9vFcu7h3uZ-Uuz-oEGWvBrIdKl1zM6-enE3-YCSIDK8AfdAzOAGVvLv_4PG3fv74ByDbDxaGxWk-oQeAs4j2kDJhZhypRHe8OtfRLm58_2iuPd493XekBs2pKOu6bktOn_FV1Em5a6RLACzZ7ZWrN2Bb247W41dJR3sp5HtdJHyHHtssj0tlUFlY/https%3A%2F%2Fumd.zoom.us%2Fj%2F6751666548>
*
Research info:  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://ncdl.umd.edu<http://secure-web.cisco.com/1OXZSKXV26nbLZxbbXNJOYZ9E0NifXMMN8ZtEqQg7ZusmSd4C57VfgVQ6h-1bx7AiGUw7rl0FgzRDDt822JJ1K9_YW5khaB0VgytuGm-20mK0INNWTz9VWeS7jItXxMR2ClPBoEZ5lMtXbN9mCc2a3jHlfzIomK3AcHDPoLnEoelJH19jpFZGQEOpgsO0x-CUSkgjsezSGDhtjbz4mYuDCkgMjvSCe983UWCMMqjpxAuHi11gY_xGC5oIGb5PT-MYsPI7g0CkvEAUBMiDy7hd1Cpr3T3vJhe8oS3mcFb1O9-lvWOYLeQgXd-uTGFpYB5k/http%3A%2F%2Fncdl.umd.edu>
 and MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.facebook.com/NCDLumd<https://secure-web.cisco.com/1RElR-oGmLBKk11mKGpbdVhFTPRV5OJO3NlW5cRrF-0AsxVeVKjwFsuoXhRSszGgDmoqnnqTHzwSjl2NsonYit8h3YlpRsP0MWYNRbWQepkuHfL_CEsvMPYgH4UdyB0sNTJXWKCTTzKiM3LuxQBwWP0smiLXJI7wNMZOr1LlaO11ULTWGEeqn0IA5plvkF1OpFGwhVhfe2gAI_au8hQxkTi2HpB52BtCQlnuesecCm2-HzjpWm1n1oF0cuWWcwtMRxAt7uoNemT7MwOvDHK6cPstPEoVGZ80A3h2vcRu9MHpynAQLrPMq9Zm46x71faCk/https%3A%2F%2Fwww.facebook.com%2FNCDLumd>
Black lives matter in 
academia<https://secure-web.cisco.com/1YlrNk6v-bahHVhsFijSj8glfi1Lwz2W71dAfzAgC0wpWQUKRDURQFiZ1nOU_Ef2eGdXdDwgebktIha6gp-DbAysTsdY

[Freesurfer] Fwd: infant Freesurfer - subcortical/white matter segmentation

[Inga Harting]

External Email - Use Caution

Gesendet: Mittwoch, 8. März 2023 16:17
An: 'Zollei, Lilla,Ph.D.' ; 
freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] infant Freesurfer - subcortical/white matter 
segmentation

 

Hi Lilla,

 I got infant_recon_all to run through, but the segmentation did not produce 
the subcortical results I was hoping for. Looking stepwise at results it seemed 
as if the registration process “bloated” the central structures  = basal 
ganglia, internal capsules (email and your answer below).

I’d be happy if you have any suggestions looking at the label fusion step.

 

Best regards, Inga

 

Von: Zollei, Lilla,Ph.D.  
Gesendet: Montag, 6. März 2023 17:18
An: freesurfer@nmr.mgh.harvard.edu
Cc: Harting, Inga 
Betreff: Re: [Freesurfer] infant Freesurfer - subcortical/white matter 
segmentation

 

Hi Inga,

 

Sorry, I missed this message on the mailing list. 

 

This is a new issue to me, so I will take a look at the label fusion step.

 

And yes, we are working on including T2w images in the pipeline as at the 
newborn stage it would help with the GM/WM segmentation accuracy.

 

Best, Lilla

 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Inga Harting 

Sent: Monday, October 31, 2022 3:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Inga_klinik 
Subject: [Freesurfer] infant Freesurfer - subcortical/white matter segmentation

 

External Email - Use Caution

Hello experts,

I've begun using infantFS for neonates and I'am interested in the
subcortical segmentation.

I noticed that the internal capsule is delineated in the
manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's
having gmwm or not), but that ist lost after mri_label_fusion when the
thalamus has suddenly increased, swallowing PLIC and corona radiata, the
basal ganglia have also expanded and the corpus of the caudate nucleus
is large and pushed upwards.

Is there a way to preserve the subcortical anatomy?

Would labelling e.g. capsula interna help? Is there a way to include 2D
T2axial to help with gmwm contrast?

Best regards, Inga.


--
Dr.med. Inga Harting

Dpt. Neuroradiology
Heidelberg University Medical Center
INF 400
69120 Heidelberg
inga.hart...@med.uni-heidelberg.de

Mühltalstr. 124b
69121 Heidelberg
inga.hart...@gmx.de


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[Freesurfer] Fwd: VirtualBox pass code

[Jennifer Kilmer]

External Email - Use Caution

Hello,

I am following up on this request. Is there any way to receive the passcode to 
unlock VirtualBox FS_7_2_0_ubuntu_18_04_06.ova.7z ?

Thanks in advance,
Jennifer 

> Begin forwarded message:
> 
> From: Jennifer Kilmer 
> Subject: VirtualBox pass code
> Date: February 28, 2023 at 19:56:50 GMT+1
> To: freesurfer@nmr.mgh.harvard.edu, 
> 
> Hello,
> 
> Is it possible to have the virtual box passcode sent to me?
> 
> Thank you in advance!
> Jennifer

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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Fwd: Pass code to open FS_7_2_0_Ubuntu_18_04_06.ova.7z

[Idaiane Batista de Assunção Leme]

External Email - Use Caution

Dear,

Please, request to pass code to open the file
FS_7_2_0_Ubuntu_18_04_06.ova.7z


Kind regards,


-- 
Idaiane Batista de Assunção Leme
Biomédica, PhD
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[Freesurfer] Fwd: Freeview 'quit unexpectedly' before opening

[Rankin McGugin]

External Email - Use Caution

Here is my error log:

Last login: Wed Feb  8 12:03:23 on ttys000

Rankins-MacBook-Pro:~ rankinmcgugin$ export
FREESURFER_HOME=/Applications/freesurfer/7.3.2

Rankins-MacBook-Pro:~ rankinmcgugin$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-darwin-macOS-7.3.2-20220804-6354275 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer/7.3.2

FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects

MNI_DIR   /Applications/freesurfer/7.3.2/mni

Rankins-MacBook-Pro:~ rankinmcgugin$

Rankins-MacBook-Pro:~ rankinmcgugin$ which freeview

/Applications/freesurfer/7.3.2/bin/freeview

Rankins-MacBook-Pro:~ rankinmcgugin$ freeview

/Applications/freesurfer/7.3.2/bin/freeview: line 2:  1592 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"

Rankins-MacBook-Pro:~ rankinmcgugin$





*Rankin W. McGugin, PhD *Research Assistant Professor

Department of Psychology

Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu

work phone: (615) 322-4644


-- Forwarded message -
From: Rankin McGugin 
Date: Wed, Feb 8, 2023 at 12:47 PM
Subject: Freeview 'quit unexpectedly' before opening
To: 


Hello,

I am a longtime FS user. I have read threads on this topic but no
suggestions work in my case.  I have the license file in place. I removed
my previous version of FS and have updated to 7.3.2.  However, now when I
try to start Freeview, I get this problem report before the app even opens:
[image: image.png]
I have tried downloading the standalone Freeview, but get the same error.
I have restarted the computer, completely removed everything and
redownloaded it, but still the same issue persists.
I am using macOS Mojave, 10.16.6
Are you able to guide me how to fix this and open Freeview?

Thank you!


*Rankin W. McGugin, PhD *Research Assistant Professor

Department of Psychology

Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu

work phone: (615) 322-4644
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Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

[Andrew Beaudin]

   External Email - Use Caution


Hi Yujing,
 No problem at all.  I really appreciate yours, and now Martin's, help with this issue.  If you would like to 
start with dicoms, please let me know.


Again, thank you both for your help.

Andrew


*Andrew Beaudin, PhD* | Research Associate
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273


--
*From:* Huang, Yujing [mailto:yhuan...@mgh.harvard.edu]
*Sent:* Wednesday, December 7, 2022 at 10:27
*To:* Andrew Beaudin , Freesurfer support list 

*Cc:* Reuter, Martin,Ph.D. 
*Subject:* [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


[△EXTERNAL]



Hi Andrew,

Sorry for the late response. I’m able to reproduce your error.

I have included Martin to the communication. He is the author of the program. He is going to take a look at 
your data.


Best,

Yujing

*From:*Andrew Beaudin 
*Sent:* Friday, November 25, 2022 3:25 PM
*To:* Huang, Yujing ; Freesurfer support list 

*Subject:* RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

*External Email - Use Caution *

Hi Huang,

  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires on Dec. 2).  I have also 
included a brief word document at the link that includes some details of the nifti images.


https://secure-web.cisco.com/1u-XjnB7jp5aUY3P1eL9t3mjpEr4XAP3TY2U7XxL4Sk87YBdOSl_IQZ5JxeKcPMFrkH1D-DL51W3gJTpja96AmSeeT6NQ-dEWQRnDoseAfuoXPdol4fUEj456GfCfg6j6TtlrWRZoceOKpLjcxVFnsacYsf16cLSN-f6q0Sbbc0InWMXztU4Wy6y0t1g_7ySgm0Nc6-uXHG8pXVATn179wXImzhZu1it0pGrkoYjI0g6eUpUKXmb5AwPI0oaQZUaiMUxvvZMEIDGHEmGBTYBoZBfCSn_YRcLlNDAPu9m1IlJo22qTgCbu8sgHPQszXhUWwLqcZSrhBQP4hmRgdIJumtNtYVbbc8YuFjLZXax3WT0/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ 
<https://secure-web.cisco.com/1hstJ7MT7lbWknwArluI7lsJDpCaPEnPjFOntWZC705TN7hf2zZ6yi6kYZOC0uvnzY4lhzK3ZM6JenT-iUCVRXmGQD3uftAD8OYL8nRsUntQSgd62pdkysnwz7Ei0MpfFScbOiKSm0zYOh7orQWmOfvRZJYI8GvWgu9XtDcLuLHMfgMkdllTtYJdE5Ht3Rh2a17I1tqEXZCjpKzzl_Hdx6NaDHJPqGxeKLX0pSSO_LGk3WyZ7S3YL04EgD6GiMRV2KCYSn4mx2cLl7I06xdwOr9DxyUFAXoLsVoBpaUDi-KcISE065Vag1H-7HyUhCIAgQFmsEVYjvotyAmUOYZvUQw/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ>


The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 
2001B2template.lta --average 1 --template 2001_template.nii.gz --satit


  However, while troubleshooting I have also tried the following with no 
success:


1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)

2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error

5) running mri_robust_template call on Catalina and Big Sur systems with FS v6.0 - same 
MyMatrix::RotationMean Error.


Again, thank you for the help….and please let me know if your need any additional information or anything 
clarified.


Andrew


*Andrew Beaudin, PhD* | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273

*From:*Huang, Yujing 
*Sent:* November 22, 2022 7:32 AM
*To:* Freesurfer support list 
*Cc:* Andrew Beaudin 
*Subject:* RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

[△EXTERNAL]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command line that you are having trouble 
with.


Thanks.

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu  *On Behalf Of *Andrew 
Beaudin

*Sent:* Wednesday, June 29, 2022 10:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

*External Email - Use Caution *

Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) outside of the Freesurfer 
longitudinal pipeline to generate within-participant T1 templates from 2 time points.  Unfortunately, I am 
coming up against a 'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our GE 3T 
Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  I have pasted the output from the 
--debug flag below (and attached as text file - line 188 is the MyMatrix message).   If helpful, images can 
be download from the following link: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.co

Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

[Huang, Yujing]

Hi Andrew,

Sorry for the late response. I’m able to reproduce your error.

I have included Martin to the communication. He is the author of the program. 
He is going to take a look at your data.

Best,

Yujing



From: Andrew Beaudin 
Sent: Friday, November 25, 2022 3:25 PM
To: Huang, Yujing ; Freesurfer support list 

Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error


External Email - Use Caution
Hi Huang,
  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires 
on Dec. 2).  I have also included a brief word document at the link that 
includes some details of the nifti images.

https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ<https://secure-web.cisco.com/1hstJ7MT7lbWknwArluI7lsJDpCaPEnPjFOntWZC705TN7hf2zZ6yi6kYZOC0uvnzY4lhzK3ZM6JenT-iUCVRXmGQD3uftAD8OYL8nRsUntQSgd62pdkysnwz7Ei0MpfFScbOiKSm0zYOh7orQWmOfvRZJYI8GvWgu9XtDcLuLHMfgMkdllTtYJdE5Ht3Rh2a17I1tqEXZCjpKzzl_Hdx6NaDHJPqGxeKLX0pSSO_LGk3WyZ7S3YL04EgD6GiMRV2KCYSn4mx2cLl7I06xdwOr9DxyUFAXoLsVoBpaUDi-KcISE065Vag1H-7HyUhCIAgQFmsEVYjvotyAmUOYZvUQw/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ>


The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 
2001A2template.lta 2001B2template.lta --average 1 --template 
2001_template.nii.gz --satit

  However, while troubleshooting I have also tried the following with no 
success:

1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error
5) running mri_robust_template call on Catalina and Big Sur systems with FS 
v6.0 - same MyMatrix::RotationMean Error.


Again, thank you for the help….and please let me know if your need any 
additional information or anything clarified.

Andrew

Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273

From: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
Sent: November 22, 2022 7:32 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Andrew Beaudin mailto:abeau...@ucalgary.ca>>
Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

[△EXTERNAL]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command 
line that you are having trouble with.

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Beaudin
Sent: Wednesday, June 29, 2022 10:45 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) 
outside of the Freesurfer longitudinal pipeline to generate within-participant 
T1 templates from 2 time points.  Unfortunately, I am coming up against a 
'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our 
GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  
I have pasted the output from the --debug flag below (and attached as text file 
- line 188 is the MyMatrix message).   If helpful, images can be download from 
the following link: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ?e=lcovfR<https://secure-web.cisco.com/1FGQFgBoMNs00DgWtLCrKSIIdug6juLkb2Nu2KrASFJPZBjdCx_joSq08q6GYn899WbiMHITtkL3x-o5AHvRXbH-2JHAu0_Gw5aFmg9rIhsPy0Zu8zpryZYHjsE4umwwEylBRyd0TGNV3m-d5k9_IsQhRu2SYc6vj4WIaJ8F_q9uIcsgpX_QVuppEMG4lRVPp3RvveMfZRpMkehNDZJ_pJT9pje_N5viL2Zb7XZPRfaNnCKK7hTcevtyaKDqtmy85Rm2GqvtUB9vFnPFssxAMeZH7UBH2-8RQCzhCokbVocDQ7-m0q6rQ-kCKxQSNMpVdE3gMPmdjbjJ6vIqZ0RuPLkj9Labe95_FuZXUxmFfL8Y/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR>

Briefly:
   - the images are skull-stripped niftis and I am running Freesurfer 6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 
18.04 installation.
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 
--template 2001

Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

[Andrew Beaudin]

External Email - Use Caution

Hi Huang,
  Thank you very much for your help with this.  Apologies for the delay.

  You should be able to retrieve sample images from the following link (expires 
on Dec. 2).  I have also included a brief word document at the link that 
includes some details of the nifti images.

https://secure-web.cisco.com/1Ey_DY3jZ8b1bW8m_xwPzSRElxfKGmEgDwV0bkOmCuHK0Kmxdv7PKs6Jf0G7VgjddMANZwnWTUhEkpcXnNc-96yDxI3bWzeA0Shj-XSErS9IAKrfDc7rNvVFPk1gthZEdOQwpsO2ftHEeDdRcRMhPtE95Sbr66ryahiNvWcOGsE6LnyqWNwEsbH-NScaHhp7-dhJJBNI9XYicWZirFUE05sqtmsy6i7TC_38L5ZnmXAHJ2lL-aYYsZN8LW07dvy4pvWHQn2yvnif3YyGhux-QTUVMa9dF5CbSsGe4tMj0cuCKDHH1sLW_P7kXdQLhcN-H2DAwyCRCvjoxORFabjtSKXHEXY65fDl6SnKXtM_emps/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ


The command call I am using is:

mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 
2001A2template.lta 2001B2template.lta --average 1 --template 
2001_template.nii.gz --satit


  However, while troubleshooting I have also tried the following with no 
success:

1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for 
log)
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error
5) running mri_robust_template call on Catalina and Big Sur systems with FS 
v6.0 - same MyMatrix::RotationMean Error.


Again, thank you for the help….and please let me know if your need any 
additional information or anything clarified.

Andrew

Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273

From: Huang, Yujing 
Sent: November 22, 2022 7:32 AM
To: Freesurfer support list 
Cc: Andrew Beaudin 
Subject: RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean 
Error

[△EXTERNAL]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command 
line that you are having trouble with.

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Andrew Beaudin
Sent: Wednesday, June 29, 2022 10:45 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) 
outside of the Freesurfer longitudinal pipeline to generate within-participant 
T1 templates from 2 time points.  Unfortunately, I am coming up against a 
'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our 
GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  
I have pasted the output from the --debug flag below (and attached as text file 
- line 188 is the MyMatrix message).   If helpful, images can be download from 
the following link: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/15jKivBPGuiIgzDk9U3fdenEjYAzvpM8z1gjSuYI9TbA6LHUwfOwbvVm65-DjSCqWjMCkWyJFTNIaQ7LKC6u2eC4c4ar3SpKKFcVGTLDzQBqTuxstngHtYy-l0nj6S-UaciytceRn2u4NQfqsV0qU20belkAGT3hGf15PoQzH1qyct_xi_jrBcbkfqjIDrm2NwIbP-ECAml2nRs7dlw7oUJ1oBwNOSZWhBU1HJtR2rOQ-OXAILkt_fJbCZa4BfObRaj2EHelZLhWgkFcgOMQ9SrQZyQ-H0LZ4hoYekPlm8M9iOp76dVNNfEzEx-VTQbED-b4TvGMuavH6dOPqtfkdE5ygdml7xIpFC5vQKVawu9E/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR<https://secure-web.cisco.com/1FGQFgBoMNs00DgWtLCrKSIIdug6juLkb2Nu2KrASFJPZBjdCx_joSq08q6GYn899WbiMHITtkL3x-o5AHvRXbH-2JHAu0_Gw5aFmg9rIhsPy0Zu8zpryZYHjsE4umwwEylBRyd0TGNV3m-d5k9_IsQhRu2SYc6vj4WIaJ8F_q9uIcsgpX_QVuppEMG4lRVPp3RvveMfZRpMkehNDZJ_pJT9pje_N5viL2Zb7XZPRfaNnCKK7hTcevtyaKDqtmy85Rm2GqvtUB9vFnPFssxAMeZH7UBH2-8RQCzhCokbVocDQ7-m0q6rQ-kCKxQSNMpVdE3gMPmdjbjJ6vIqZ0RuPLkj9Labe95_FuZXUxmFfL8Y/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR>

Briefly:
   - the images are skull-stripped niftis and I am running Freesurfer 6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 
18.04 installation.
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 
--template 2001_template.nii.gz --satit

   -  I have tried the following with no success:
1) using the --iscale flag - same result as shown below.
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --averag

Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

[Huang, Yujing]

Hi Andrew,

Can you send us some data to debug? The link has expired. Also, the command 
line that you are having trouble with.

Thanks.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Andrew Beaudin
Sent: Wednesday, June 29, 2022 10:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error


External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF registration) 
outside of the Freesurfer longitudinal pipeline to generate within-participant 
T1 templates from 2 time points.  Unfortunately, I am coming up against a 
'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our 
GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images.  
I have pasted the output from the --debug flag below (and attached as text file 
- line 188 is the MyMatrix message).   If helpful, images can be download from 
the following link: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ?e=lcovfR<https://secure-web.cisco.com/1FGQFgBoMNs00DgWtLCrKSIIdug6juLkb2Nu2KrASFJPZBjdCx_joSq08q6GYn899WbiMHITtkL3x-o5AHvRXbH-2JHAu0_Gw5aFmg9rIhsPy0Zu8zpryZYHjsE4umwwEylBRyd0TGNV3m-d5k9_IsQhRu2SYc6vj4WIaJ8F_q9uIcsgpX_QVuppEMG4lRVPp3RvveMfZRpMkehNDZJ_pJT9pje_N5viL2Zb7XZPRfaNnCKK7hTcevtyaKDqtmy85Rm2GqvtUB9vFnPFssxAMeZH7UBH2-8RQCzhCokbVocDQ7-m0q6rQ-kCKxQSNMpVdE3gMPmdjbjJ6vIqZ0RuPLkj9Labe95_FuZXUxmFfL8Y/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR>

Briefly:
   - the images are skull-stripped niftis and I am running Freesurfer 6.0 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 
18.04 installation.
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 
--template 2001_template.nii.gz --satit

   -  I have tried the following with no success:
1) using the --iscale flag - same result as shown below.
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same result as shown below
4) using Freesurfer v7.2 - same result as below
5) running mri_robust_template call on Catalina and Big Sur systems with FS 
v6.0 - same result as below.

  Currently, the only way to get mri_robust_template to work with our GE images 
is to run it with the --affine flag.  I would prefer to use the rigid body 
registration but am at a loss for why these images are failing using the rigid 
body registration is failing. Any help/insights/recommendations are greatly 
appreciated.

Thank you very much.

Andrew


Andrew Beaudin, PhD | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273


DEBUG REPORT:

$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

--mov: Using 2001A_T1o_brain.nii.gz as movable/source volume.
--mov: Using 2001B_T1o_brain.nii.gz as movable/source volume.
Total: 2 input volumes
--lta: Will output LTA transforms
--average: Using method 1 for template computation.
--template: Using 2001_template.nii.gz as template output volume.
--satit: Will estimate SAT iteratively!
--debug: Will output debug info and files!
reading source '2001A_T1o_brain.nii.gz'...
converting source '2001A_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
reading source '2001B_T1o_brain.nii.gz'...
converting source '2001B_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
Will use TP 2 as random initial target (seed 108242 ).

MultiRegistration::initializing Xforms (init 2 , maxres 0 , iterate 5 , epsit 
0.01 ) :

 MultiRegistration Parameters

 Outdir:./
 TransOnly: false
 Rigid: true
 Robust:true
 Satit: true
 Iscale:false
 IscaleOnly:false
 NoMulti:   false
 SubsampleSize: -1
 HighIt:-1
 FixVoxel:  false
 KeepType:  true
 Average:   1
 DoublePrec:false
 BackupWeights: false
 SampleType:5
 CRASCenter:false
 Debug: 1


[init] = TP 1 to TP 2 ==
 Register TP 1 ( 2001A_T1o_brain.nii.gz )
  to  TP 2 ( 2001B_T1o_brain.nii.gz )

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
   Type Source : 3  Type Target : 3  keeping type
   Mov: (1, 1, 1)mm  and dim (176, 256, 256)
   Dst: (1, 1, 1)mm  and dim (176, 256, 256)
   Asserting both images: 1mm isotropic
- no Mov reslice necessary
- no Dst reslice necessary


 Registration::findSaturation
   - computing centroids
   - computing initial transform
 -- using translation info
   - Get 

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

[Huang, Yujing]

Hi Julie,

Sorry for the late response. You will need to pass -bv (big ventricles) flag to 
cross, base, and long processes.

Best,

Yujing

From: Julie Ottoy 
Sent: Tuesday, November 15, 2022 11:56 AM
To: Huang, Yujing 
Cc: Freesurfer support list ; fsbuild 

Subject: Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts 
at -Sphere for all participants


External Email - Use Caution
Hi,

I just wanted to check in with my questions below? Thanks!
Julie

On Thu, 10 Nov 2022 at 17:03, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:
Hi,

Yes you are right! Taking out the -parallel solved the issue! Does this mean v7 
longitudinal recon-all does not support this flag?
I have one other question, any help would be appreciated. I ran the baseline 
recon-all with the -bv (big ventricles) flag. Should I add this flag for 
longitudinal processing as well, or will it not matter?

Thanks again for your support,
Best wishes
Julie


On Wed, 9 Nov 2022 at 15:36, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Julie,

I noticed that you were running recon-all with ‘-parallel’ flag. It is causing 
the error.

The process should work if you remove ‘-parallel’ from recon-all command.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julie Ottoy
Sent: Tuesday, November 8, 2022 9:27 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>; 
fsbuild mailto:fsbu...@contbay.com>>
Subject: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at 
-Sphere for all participants


External Email - Use Caution
Hi FS team,

Just wanted to follow up with my question below. Thanks!
Julie
-- Forwarded message -
From: Julie Ottoy mailto:julie.jj.ot...@gmail.com>>
Date: Fri, 4 Nov 2022 at 00:11
Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at 
-Sphere for all participants
To: fsbuild mailto:fsbu...@contbay.com>>

Hi Fsbuild team,

Thank you for your reply. Sorry for the confusion, my system was actually 
Linux, not Windows. It did not run on top of Windows (sorry again for the 
confusion).
In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 
consistently on Linux. I also used two different machines (our institute server 
as well as ComputeCanada, hence I do not believe it's a memory issue). Each run 
got stuck at the -Sphere x.long.x step as indicated in my previous email. 
Interestingly, I tried today with the longitudinal FS v6.0.0 (kept all the rest 
the same) and it ran fine! Could there be any bug in the v7 series for 
longitudinal processing that was not present in the v6 series? I tried on two 
different types of input T1w data acquired from different centers and they 
point to the same issue => -Sphere error in x.long.x for v7 , while it runs 
fine for v6. Please see attached log files and screenshots for both.

I am also thinking if it would be ok to run the longitudinal with v6 since we 
ran the baseline data with v7.2. Could you please advise on this?

Last, I was wondering if there is a way to receive more detailed log/error 
files? As indicated from my previous email and screenshots, the code just 
exited at Sphere but did not indicate why it went wrong there.

Thank you for your help!
Best regards
Julie

On Wed, 2 Nov 2022 at 17:02, fsbuild 
mailto:fsbu...@contbay.com>> wrote:
One way we’ve seen recon-all eventually fail running on Linux hosted on Windows 
is whatever is virtualizing Linux to run on top of the Windows OS - simply runs 
out of memory at some point in the processing pipeline.  That can result in a 
message in the recon-all.log like a file was not found, i.e., a computation 
fails and the results are not saved in a file that later on is expected to be 
found, opened and read.  I don’t see messages like that in your log.

It might be helpful to know more about how you are running Linux on windows, 
e.g., if you are using the built-in Windows Subsystem for Linux (WSL) or using 
a VM running on something like VirtualBox.

You could also send along the output in the linux terminal from:
$ cat /etc/os-release
$ cat $FREESURFER_HOME/build-stamp.txt

- R.

On Nov 2, 2022, at 15:03, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/13ufA-ekuK2MZpRFhFHNqISeb4EuYyQ6sVhw26U_Nhmx-KbcJYM1e0blL_qiwT_zLrSdsOk4YvkR2WPs1eE2tbs2zaTAbbswVHnGYbKEASxre9Nqv7cnPKyMHI8OJaMZd651QL14BKfpOwZRez4mPesl0qO7vcQsgEqq9XMvEKDOzo0RubyxkwVaf9sV2noRGUohzpkMwKODn_UAzTKmBrrWzypLKNA4_ywUQWNom5f2-sA_aCuQmrvZ7lXoYfQQvW0AhpjgtdnYmNnvidc8OhxNcmegXxu90KY8fCLXxTa61Y9mZUrgFIjGfGF-MCKw

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

[Julie Ottoy]

External Email - Use Caution

Hi,

I just wanted to check in with my questions below? Thanks!
Julie

On Thu, 10 Nov 2022 at 17:03, Julie Ottoy  wrote:

> Hi,
>
> Yes you are right! Taking out the -parallel solved the issue! Does this
> mean v7 longitudinal recon-all does not support this flag?
> I have one other question, any help would be appreciated. I ran the
> baseline recon-all with the -bv (big ventricles) flag. Should I add this
> flag for longitudinal processing as well, or will it not matter?
>
> Thanks again for your support,
> Best wishes
> Julie
>
>
> On Wed, 9 Nov 2022 at 15:36, Huang, Yujing 
> wrote:
>
>> Hi Julie,
>>
>>
>>
>> I noticed that you were running recon-all with ‘-parallel’ flag. It is
>> causing the error.
>>
>>
>>
>> The process should work if you remove ‘-parallel’ from recon-all command.
>>
>>
>>
>> Best,
>>
>>
>>
>> Yujing
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
>> *Sent:* Tuesday, November 8, 2022 9:27 AM
>> *To:* Freesurfer support list ; fsbuild <
>> fsbu...@contbay.com>
>> *Subject:* [Freesurfer] Fwd: Longitudinal FS pipeline consistently
>> interrupts at -Sphere for all participants
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi FS team,
>>
>>
>>
>> Just wanted to follow up with my question below. Thanks!
>>
>> Julie
>>
>> -- Forwarded message -
>> From: *Julie Ottoy* 
>> Date: Fri, 4 Nov 2022 at 00:11
>> Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently
>> interrupts at -Sphere for all participants
>> To: fsbuild 
>>
>>
>>
>> Hi Fsbuild team,
>>
>>
>>
>> Thank you for your reply. Sorry for the confusion, my system was actually
>> Linux, not Windows. It did *not* run on top of Windows (sorry again for
>> the confusion).
>>
>> In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2
>> consistently on Linux. I also used two different machines (our institute
>> server as well as ComputeCanada, hence I do not believe it's a memory
>> issue). Each run got stuck at the -Sphere x.long.x step as indicated in my
>> previous email. Interestingly, I tried today with the longitudinal FS
>> v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug
>> in the v7 series for longitudinal processing that was not present in the v6
>> series? I tried on two different types of input T1w data acquired from
>> different centers and they point to the same issue => -Sphere error in
>> x.long.x for v7 , while it runs fine for v6. Please see attached log files
>> and screenshots for both.
>>
>>
>>
>> I am also thinking if it would be ok to run the longitudinal with v6
>> since we ran the baseline data with v7.2. Could you please advise on this?
>>
>>
>>
>> Last, I was wondering if there is a way to receive more detailed
>> log/error files? As indicated from my previous email and screenshots, the
>> code just exited at Sphere but did not indicate why it went wrong there.
>>
>>
>>
>> Thank you for your help!
>>
>> Best regards
>>
>> Julie
>>
>>
>>
>> On Wed, 2 Nov 2022 at 17:02, fsbuild  wrote:
>>
>> One way we’ve seen recon-all eventually fail running on Linux hosted on
>> Windows is whatever is virtualizing Linux to run on top of the Windows OS -
>> simply runs out of memory at some point in the processing pipeline.  That
>> can result in a message in the recon-all.log like a file was not found,
>> i.e., a computation fails and the results are not saved in a file that
>> later on is expected to be found, opened and read.  I don’t see messages
>> like that in your log.
>>
>>
>>
>> It might be helpful to know more about how you are running Linux on
>> windows, e.g., if you are using the built-in Windows Subsystem for Linux
>> (WSL) or using a VM running on something like VirtualBox.
>>
>>
>>
>> You could also send along the output in the linux terminal from:
>>
>> $ cat /etc/os-release
>>
>> $ cat $FREESURFER_HOME/build-stamp.txt
>>
>>
>>
>> - R.
>>
>>
>>
>> On Nov 2, 2022, at 15:03, Julie Ottoy  wrote:
>>
>>
>>
>> 
>>
>>
>>
>> ___

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

[Julie Ottoy]

External Email - Use Caution

Hi,

Yes you are right! Taking out the -parallel solved the issue! Does this
mean v7 longitudinal recon-all does not support this flag?
I have one other question, any help would be appreciated. I ran the
baseline recon-all with the -bv (big ventricles) flag. Should I add this
flag for longitudinal processing as well, or will it not matter?

Thanks again for your support,
Best wishes
Julie


On Wed, 9 Nov 2022 at 15:36, Huang, Yujing  wrote:

> Hi Julie,
>
>
>
> I noticed that you were running recon-all with ‘-parallel’ flag. It is
> causing the error.
>
>
>
> The process should work if you remove ‘-parallel’ from recon-all command.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy
> *Sent:* Tuesday, November 8, 2022 9:27 AM
> *To:* Freesurfer support list ; fsbuild <
> fsbu...@contbay.com>
> *Subject:* [Freesurfer] Fwd: Longitudinal FS pipeline consistently
> interrupts at -Sphere for all participants
>
>
>
> *External Email - Use Caution*
>
> Hi FS team,
>
>
>
> Just wanted to follow up with my question below. Thanks!
>
> Julie
>
> -- Forwarded message -
> From: *Julie Ottoy* 
> Date: Fri, 4 Nov 2022 at 00:11
> Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts
> at -Sphere for all participants
> To: fsbuild 
>
>
>
> Hi Fsbuild team,
>
>
>
> Thank you for your reply. Sorry for the confusion, my system was actually
> Linux, not Windows. It did *not* run on top of Windows (sorry again for
> the confusion).
>
> In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2
> consistently on Linux. I also used two different machines (our institute
> server as well as ComputeCanada, hence I do not believe it's a memory
> issue). Each run got stuck at the -Sphere x.long.x step as indicated in my
> previous email. Interestingly, I tried today with the longitudinal FS
> v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug
> in the v7 series for longitudinal processing that was not present in the v6
> series? I tried on two different types of input T1w data acquired from
> different centers and they point to the same issue => -Sphere error in
> x.long.x for v7 , while it runs fine for v6. Please see attached log files
> and screenshots for both.
>
>
>
> I am also thinking if it would be ok to run the longitudinal with v6 since
> we ran the baseline data with v7.2. Could you please advise on this?
>
>
>
> Last, I was wondering if there is a way to receive more detailed log/error
> files? As indicated from my previous email and screenshots, the code just
> exited at Sphere but did not indicate why it went wrong there.
>
>
>
> Thank you for your help!
>
> Best regards
>
> Julie
>
>
>
> On Wed, 2 Nov 2022 at 17:02, fsbuild  wrote:
>
> One way we’ve seen recon-all eventually fail running on Linux hosted on
> Windows is whatever is virtualizing Linux to run on top of the Windows OS -
> simply runs out of memory at some point in the processing pipeline.  That
> can result in a message in the recon-all.log like a file was not found,
> i.e., a computation fails and the results are not saved in a file that
> later on is expected to be found, opened and read.  I don’t see messages
> like that in your log.
>
>
>
> It might be helpful to know more about how you are running Linux on
> windows, e.g., if you are using the built-in Windows Subsystem for Linux
> (WSL) or using a VM running on something like VirtualBox.
>
>
>
> You could also send along the output in the linux terminal from:
>
> $ cat /etc/os-release
>
> $ cat $FREESURFER_HOME/build-stamp.txt
>
>
>
> - R.
>
>
>
> On Nov 2, 2022, at 15:03, Julie Ottoy  wrote:
>
>
>
> 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/135XF05YrgXN9hdbbM4w7HVq0tQXXsoAh1ELrzudg_qqq4RH4p8yJnSLbNCbSbEcz93BkEoPEFd6jZIaujpNPD-hH0uyaDp18RKPIcwL_Vr1bBraTZbqIp2sHFOz-kHdG_pUVOkJZ6QWtXqnEjlrDP5pEz7w_0H5cfJ9NmCzPcZQckz168TeDH-oU4G0URqWm3veHmY2MC0jvREO7Hfigvk5FnYQNHbuJGl3nCVoQ2iLb5pg32-KwN7sY7rwB-vVEL9JOMM1OQxF1Ere5x_iah1wXaA1ZUxTqvasx5Ygbw-b5C7oLtrVW8tltE6-9pD08/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

[Huang, Yujing]

Hi Julie,

I noticed that you were running recon-all with ‘-parallel’ flag. It is causing 
the error.

The process should work if you remove ‘-parallel’ from recon-all command.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julie Ottoy
Sent: Tuesday, November 8, 2022 9:27 AM
To: Freesurfer support list ; fsbuild 

Subject: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at 
-Sphere for all participants


External Email - Use Caution
Hi FS team,

Just wanted to follow up with my question below. Thanks!
Julie
-- Forwarded message -
From: Julie Ottoy mailto:julie.jj.ot...@gmail.com>>
Date: Fri, 4 Nov 2022 at 00:11
Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at 
-Sphere for all participants
To: fsbuild mailto:fsbu...@contbay.com>>

Hi Fsbuild team,

Thank you for your reply. Sorry for the confusion, my system was actually 
Linux, not Windows. It did not run on top of Windows (sorry again for the 
confusion).
In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 
consistently on Linux. I also used two different machines (our institute server 
as well as ComputeCanada, hence I do not believe it's a memory issue). Each run 
got stuck at the -Sphere x.long.x step as indicated in my previous email. 
Interestingly, I tried today with the longitudinal FS v6.0.0 (kept all the rest 
the same) and it ran fine! Could there be any bug in the v7 series for 
longitudinal processing that was not present in the v6 series? I tried on two 
different types of input T1w data acquired from different centers and they 
point to the same issue => -Sphere error in x.long.x for v7 , while it runs 
fine for v6. Please see attached log files and screenshots for both.

I am also thinking if it would be ok to run the longitudinal with v6 since we 
ran the baseline data with v7.2. Could you please advise on this?

Last, I was wondering if there is a way to receive more detailed log/error 
files? As indicated from my previous email and screenshots, the code just 
exited at Sphere but did not indicate why it went wrong there.

Thank you for your help!
Best regards
Julie

On Wed, 2 Nov 2022 at 17:02, fsbuild 
mailto:fsbu...@contbay.com>> wrote:
One way we’ve seen recon-all eventually fail running on Linux hosted on Windows 
is whatever is virtualizing Linux to run on top of the Windows OS - simply runs 
out of memory at some point in the processing pipeline.  That can result in a 
message in the recon-all.log like a file was not found, i.e., a computation 
fails and the results are not saved in a file that later on is expected to be 
found, opened and read.  I don’t see messages like that in your log.

It might be helpful to know more about how you are running Linux on windows, 
e.g., if you are using the built-in Windows Subsystem for Linux (WSL) or using 
a VM running on something like VirtualBox.

You could also send along the output in the linux terminal from:
$ cat /etc/os-release
$ cat $FREESURFER_HOME/build-stamp.txt

- R.


On Nov 2, 2022, at 15:03, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:



___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Fwd: average lobar cortical thickness

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

Dear James and FreeSurfer experts,
for lobes average cortical thickness we use this solution
https://secure-web.cisco.com/12kn5RGwkDP8VJQa9PtCWSWT_3GfJlJYy06k6EpiyBm3DNksk5cBO1m_9Le5zbQFSumsT0NoxwNy2VNIh9LcoRkXkj5UlRW4ZVXK_mdgK-47PUJnpHKrnofShRBd4hn04wUndNIeo9qSFfwRuTCFZskpYzu_dEmSTfNuVH1YD9HszB8ZT58BL0-Oeu3k-_DzqTnsZDIIXHLZvQCrbQ7piw80BQs5FRBpW6WPRUf_ESj7p9BCvwjmzbrdNpfar1S9GUTa01DctAIO9o7810uXB9HXlros3aZXIKNPSevhYnE6HxGRs49xo3zx4Onil9efsTKtHy2JNy2TAmbw8Ze37eg/https%3A%2F%2Fgithub.com%2Fcnnp-lab%2FCorticalFoldingAnalysisTools,
 hope it helps!

Best,
Fernanda

Fernanda Hansen P. de Moraes
fernandahmor...@gmail.com
Doutora em Ciências Médicas |  metaBIO (IF-UFRJ) e Instituto D'Or de
Pesquisa e Ensino

On Wed, Nov 9, 2022 at 11:35 AM Douglas N. Greve 
wrote:

> I would weight by the number of vertices in each ROI
>
> On 11/8/2022 12:20 PM, James Brown wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
> I would like to know if this procedure is correct.
> I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
> (i.e. output of recon-all). I need average cortical thickness in frontal,
> parietal, temporal, cingulate and occipital lobes. Is it correct to average
> thickness measurement of every sub lobe roi (e.g. average thickness in
> frontal lobe = average of:
>
>- Superior Frontal
>- Rostral and Caudal Middle Frontal
>- Pars Opercularis, Pars Triangularis, and Pars Orbitalis
>- Lateral and Medial Orbitofrontal
>- Precentral
>- Paracentral
>- Frontal Pole
>
> and so on for other lobes...
>
> Do we need to correct for the number of vertices in every region when we
> measure the lobar average thickness?
>
> Alternatively, do I need to run these commands to generate lobes then
> measure thickness in every lobe?
>
> # mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
> # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
> # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
> #   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
> #   --annot lobes --base-offset 200 [--base-offset must be last arg]
>
>
> Thank you
> James
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1g09wOx4W856aItHj4QzY4FFQdJKxAoTlFtbuLROvtDTsCnjHRmED3ZYPU19GooWKZkBrSmOBIKlZb5WZNIJz4a4VsFIaZ0ngYO2507YB0vLM1ZeiLCVYPE7bt8WbEaBnaE4a_dAbCqohtKS0AT-0FUBF9n5ven3CKjyGmT56NT0ZLU7u9pS_rxHYSXiQYY7QclZi-wF-HWcjZo3XoUZweaTW5NIXp6Uum33gJBJid3odO59BUHGqr_bji5h6puctE2j4Xd8fbtHPZVCumT-2i6tq3WX4kFyjJqY7t91El3sNyELVkl8mp859GXbMT7-W70pTZAkVINi0ZeZRFhVzaA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1kdEANE9nCVMm7GA3EzCDzKmUqLLckMOCL-0IYtIcuzPWSPhDxOkpxHBQlQWk597JU6MFs9nOjC8a1IvWHRRs-Wk1AJmNy1mnfBBXgAx_sNp8BLNY-QySLu5r-V09q8H3qDbB0RMdwiHMPMPZ4U_m2CWMe0l5qi53_KRhvM-22FkXbd8_asUzRBt3Q2g-tsawfNpSKx0IsC25vZg0VD6A2MtxGbiFLnSdjvU4K2oS-SX70vJhu5hfL9JIiILRnktAk91Qn-4uAv31IxhJqG-okW7557puyANF1TR2KwC7_WT7WxtQly2O-nzBGNVliucjTiv5fW6hYZDzHzm9nlpKEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1kdEANE9nCVMm7GA3EzCDzKmUqLLckMOCL-0IYtIcuzPWSPhDxOkpxHBQlQWk597JU6MFs9nOjC8a1IvWHRRs-Wk1AJmNy1mnfBBXgAx_sNp8BLNY-QySLu5r-V09q8H3qDbB0RMdwiHMPMPZ4U_m2CWMe0l5qi53_KRhvM-22FkXbd8_asUzRBt3Q2g-tsawfNpSKx0IsC25vZg0VD6A2MtxGbiFLnSdjvU4K2oS-SX70vJhu5hfL9JIiILRnktAk91Qn-4uAv31IxhJqG-okW7557puyANF1TR2KwC7_WT7WxtQly2O-nzBGNVliucjTiv5fW6hYZDzHzm9nlpKEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


-- 
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino e metaBIO
(IF-UFRJ)
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 

Re: [Freesurfer] Fwd: average lobar cortical thickness

[Douglas N. Greve]

I would weight by the number of vertices in each ROI

On 11/8/2022 12:20 PM, James Brown wrote:


External Email - Use Caution


Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK 
atlas (i.e. output of recon-all). I need average cortical thickness in 
frontal, parietal, temporal, cingulate and occipital lobes. Is it 
correct to average thickness measurement of every sub lobe roi (e.g. 
average thickness in frontal lobe = average of:


  * Superior Frontal
  * Rostral and Caudal Middle Frontal
  * Pars Opercularis, Pars Triangularis, and Pars Orbitalis
  * Lateral and Medial Orbitofrontal
  * Precentral
  * Paracentral
  * Frontal Pole

and so on for other lobes...

Do we need to correct for the number of vertices in every region when 
we measure the lobar average thickness?


Alternatively, do I need to run these commands to generate lobes then 
measure thickness in every lobe?

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]

Thank you
James

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Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

[Huang, Yujing]

Hi Julie,

Thank you for using Freesurfer and bought the problem to our attention.

We are looking into the issue.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julie Ottoy
Sent: Tuesday, November 8, 2022 9:27 AM
To: Freesurfer support list ; fsbuild 

Subject: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at 
-Sphere for all participants


External Email - Use Caution
Hi FS team,

Just wanted to follow up with my question below. Thanks!
Julie
-- Forwarded message -
From: Julie Ottoy mailto:julie.jj.ot...@gmail.com>>
Date: Fri, 4 Nov 2022 at 00:11
Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at 
-Sphere for all participants
To: fsbuild mailto:fsbu...@contbay.com>>

Hi Fsbuild team,

Thank you for your reply. Sorry for the confusion, my system was actually 
Linux, not Windows. It did not run on top of Windows (sorry again for the 
confusion).
In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 
consistently on Linux. I also used two different machines (our institute server 
as well as ComputeCanada, hence I do not believe it's a memory issue). Each run 
got stuck at the -Sphere x.long.x step as indicated in my previous email. 
Interestingly, I tried today with the longitudinal FS v6.0.0 (kept all the rest 
the same) and it ran fine! Could there be any bug in the v7 series for 
longitudinal processing that was not present in the v6 series? I tried on two 
different types of input T1w data acquired from different centers and they 
point to the same issue => -Sphere error in x.long.x for v7 , while it runs 
fine for v6. Please see attached log files and screenshots for both.

I am also thinking if it would be ok to run the longitudinal with v6 since we 
ran the baseline data with v7.2. Could you please advise on this?

Last, I was wondering if there is a way to receive more detailed log/error 
files? As indicated from my previous email and screenshots, the code just 
exited at Sphere but did not indicate why it went wrong there.

Thank you for your help!
Best regards
Julie

On Wed, 2 Nov 2022 at 17:02, fsbuild 
mailto:fsbu...@contbay.com>> wrote:
One way we’ve seen recon-all eventually fail running on Linux hosted on Windows 
is whatever is virtualizing Linux to run on top of the Windows OS - simply runs 
out of memory at some point in the processing pipeline.  That can result in a 
message in the recon-all.log like a file was not found, i.e., a computation 
fails and the results are not saved in a file that later on is expected to be 
found, opened and read.  I don’t see messages like that in your log.

It might be helpful to know more about how you are running Linux on windows, 
e.g., if you are using the built-in Windows Subsystem for Linux (WSL) or using 
a VM running on something like VirtualBox.

You could also send along the output in the linux terminal from:
$ cat /etc/os-release
$ cat $FREESURFER_HOME/build-stamp.txt

- R.


On Nov 2, 2022, at 15:03, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:



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[Freesurfer] Fwd: average lobar cortical thickness

[James Brown]

External Email - Use Caution

Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
(i.e. output of recon-all). I need average cortical thickness in frontal,
parietal, temporal, cingulate and occipital lobes. Is it correct to average
thickness measurement of every sub lobe roi (e.g. average thickness in
frontal lobe = average of:

   - Superior Frontal
   - Rostral and Caudal Middle Frontal
   - Pars Opercularis, Pars Triangularis, and Pars Orbitalis
   - Lateral and Medial Orbitofrontal
   - Precentral
   - Paracentral
   - Frontal Pole

and so on for other lobes...

Do we need to correct for the number of vertices in every region when we
measure the lobar average thickness?

Alternatively, do I need to run these commands to generate lobes then
measure thickness in every lobe?

# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes
# mri_annotation2label --subject subject --hemi rh --lobesStrict lobes
# mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \
#   --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \
#   --annot lobes --base-offset 200 [--base-offset must be last arg]


Thank you
James
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[Freesurfer] Fwd: FreeSurfer Mac crash

[Parya Rahimi]

External Email - Use Caution

> Hello, I recently downloaded freesurfer and when I try to load a volume, the 
> application just crashes and shows me the error I copied below. Please let me 
> know how to fix this. Thank you
> 
> Regards,
> Parya Rahimi
> 
> 
> 
> -
> Translated Report (Full Report Below)
> -
> 
> Process:   freeview [1362]
> Path:  
> /Applications/freesurfer/*/Freeview.app/Contents/MacOS/freeview
> Identifier:com.freesurfer.freeview
> Version:   ???
> Code Type: X86-64 (Native)
> Parent Process:launchd [1]
> User ID:   501
> 
> Date/Time: 2022-10-23 18:24:46.7621 +0200
> OS Version:macOS 12.6 (21G115)
> Report Version:12
> Anonymous UUID:5E923B12-E9EF-424E-26EE-BF6B598D9ADF
> 
> Sleep/Wake UUID:   063BF1C1-8539-488A-966D-05B67E6523CB
> 
> Time Awake Since Boot: 2600 seconds
> Time Since Wake:   1376 seconds
> 
> System Integrity Protection: enabled
> 
> Crashed Thread:0  Dispatch queue: com.apple.main-thread
> 
> Exception Type:EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes:   KERN_INVALID_ADDRESS at 0x433febf5db70
> Exception Codes:   0x0001, 0x433febf5db70
> Exception Note:EXC_CORPSE_NOTIFY
> 
> Termination Reason:Namespace SIGNAL, Code 11 Segmentation fault: 11
> Terminating Process:   exc handler [1362]
> 
> VM Region Info: 0x433febf5db70 is not in any region.  Bytes after previous 
> region: 73936327797617  Bytes before following region: 31611295507600
>  REGION TYPESTART - END [ VSIZE] PRT/MAX 
> SHRMOD  REGION DETAIL
>  CoreUI image data   147668000-14767f000[   92K] r--/r-- 
> SM=PRV  
> --->  GAP OF 0x5ffeb8981000 BYTES
>  MALLOC_NANO  6000-6800 [128.0M] rw-/rwx 
> SM=PRV  
> 
> Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
> 0   QtGui0x11c67272d 
> QPen::QPen(Qt::PenStyle) + 205
> 1   QtGui0x11c60edd5 
> QPaintEngineExPrivate::QPaintEngineExPrivate() + 181
> 2   QtGui0x11c6172f5 
> QRasterPaintEngine::QRasterPaintEngine(QPaintDevice*) + 37
> 3   QtGui0x11c4194c2 
> QImage::paintEngine() const + 98
> 4   QtWidgets0x11b816b7c 
> QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, 
> QFlags, QPainter*, QWidgetRepaintManager*) + 
> 1628
> 5   QtWidgets0x11b7f8f86 0x11b7db000 + 122758
> 6   QtWidgets0x11b7f7455 0x11b7db000 + 115797
> 7   QtWidgets0x11b846a54 0x11b7db000 + 440916
> 8   QtWidgets0x11b843a46 0x11b7db000 + 428614
> 9   QtWidgets0x11b7eb9ea 
> QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
> 10  QtWidgets0x11b7ece11 
> QApplication::notify(QObject*, QEvent*) + 497
> 11  QtCore   0x11d1b3a34 
> QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
> 12  QtGui0x11c3c17f2 
> QGuiApplicationPrivate::processExposeEvent(QWindowSystemInterfacePrivate::ExposeEvent*)
>  + 306
> 13  QtGui0x11c39d8f3 bool 
> QWindowSystemInterfacePrivate::handleWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*)
>  + 115
> 14  QtGui0x11c3a4f92 void 
> QWindowSystemInterface::handleExposeEvent(QWindow*,
>  QRegion const&) + 178
> 15  libqcocoa.dylib  0x11b50820c 0x11b4e6000 + 139788
> 16  libqcocoa.dylib  0x11b510afb 0x11b4e6000 + 174843
> 17  AppKit0x7ff80ffbee05 -[_NSBackingLayer 
> display] + 462
> 18  AppKit0x7ff80ff343ad 
> -[_NSViewBackingLayer display] + 554
> 19  QuartzCore0x7ff8144faa07 
> CA::Layer::display_if_needed(CA::Transaction*) + 873
> 20  QuartzCore0x7ff8146522aa 
> CA::Context::commit_transaction(CA::Transaction*, double, double*) + 640
> 21  QuartzCore0x7ff8144dbe6d 
> CA::Transaction::commit() + 777
> 22  AppKit0x7ff80ffd01d1 
> __62+[CATransaction(NSCATransaction) 
> NS_setFlushesWithDisplayLink]_block_invoke + 285
> 23  AppKit0x7ff810717f5c 
> ___NSRunLoopObserverCreateWithHandler_block_invoke + 41
> 24  CoreFoundation0x7ff80d42b520 
> __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23
> 25  CoreFoundation0x7ff80d42b3b2 
> __CFRunLoopDoObservers + 

Re: [Freesurfer] Fwd: Error

[Douglas N. Greve]

not sure what is going on. It received a kill signal (the 9 mentioned at 
the end). This often means that it was killed externally. Does this 
happen repeatedly? Does this happen on other subjects? How much memory 
did you allocate to your virtual box?


On 9/23/2022 1:04 AM, Ahmad Khan wrote:


External Email - Use Caution


Dear Free Surfer Development Team.

I am using the recon -all command to compute the volume of different 
regions of the brain. I am running the free surfer version 
freesurfer-linux-centos7_x86_64-7.1.1-20200723 on Ubuntu 20.4 
installed on a virtual box. I am getting the following errors and the 
log file is also attached with this email.

*ERROR: mri_ca_register with non-zero status 137*
Your timely response would be highly appreciated.

Best Regards
 Dr. Ahmad Raza Khan
(Ramalingaswami Fellow)
Center of Bio-Medical Research (CBMR)
SGPGI Campus, Raibareli Road
Lucknow-226014, UP, INDIA

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Re: [Freesurfer] Fwd: eTIV

[Bouchra Guelib]

External Email - Use Caution

I want to use eTIV to normalize also the  normDev, normMean of subcortical
regions as well as the morphological variables of cortical regions such as
gray matter volume, rectified mean curvature.
Should I devide them on eTIV ?

Le jeu. 28 juil. 2022 à 18:24, Douglas N. Greve  a
écrit :

> I usually just divide the volume by the eTIV (you can do this in
> asegstats2table with the --etiv flag). Some people will use it as a
> nuisance regressor in the GLM
>
> On 7/27/2022 3:11 PM, Bouchra Guelib wrote:
>
> External Email - Use Caution
>
> -- Forwarded message -
> De : Bouchra Guelib 
> Date: mer. 27 juil. 2022 à 19:28
> Subject: eTIV
> To: 
>
>
> I hope you can help me with this  point
> I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and
> 'rh.aparc.stats'. Now I want to use these measures as input data for my
> model. However, I read that we need to normalize this data using eTIV. Can
> you tell me how?
>
> --
> *GUELIB Bouchra: *Ph.D. student
> *Lire *Laboratory
> University: Constantine 2-Abdelhamid Mehri- *Algeria *
> Alternative email: guelibbouc...@gmail.com
>
>
>
>
>
> ___
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>  .
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> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
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Re: [Freesurfer] Fwd: eTIV

[Douglas N. Greve]

I usually just divide the volume by the eTIV (you can do this in 
asegstats2table with the --etiv flag). Some people will use it as a 
nuisance regressor in the GLM


On 7/27/2022 3:11 PM, Bouchra Guelib wrote:


External Email - Use Caution


-- Forwarded message -
De : *Bouchra Guelib* 
Date: mer. 27 juil. 2022 à 19:28
Subject: eTIV
To: 


I hope you can help me with this  point
I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and 
'rh.aparc.stats'. Now I want to use these measures as input data for 
my model. However, I read that we need to normalize this data using 
eTIV. Can you tell me how?


--
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com**





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[Freesurfer] Fwd: eTIV

[Bouchra Guelib]

External Email - Use Caution

-- Forwarded message -
De : Bouchra Guelib 
Date: mer. 27 juil. 2022 à 19:28
Subject: eTIV
To: 


I hope you can help me with this  point
I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and
'rh.aparc.stats'. Now I want to use these measures as input data for my
model. However, I read that we need to normalize this data using eTIV. Can
you tell me how?

-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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[Freesurfer] Fwd: Passcode for the VM

[MANUEL RUOCCO]

External Email - Use Caution

Hello,

I would like to ask for the passcode for the VM file containing
FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you for your assistance.
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[Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error

[Andrew Beaudin]

  External Email - Use Caution
Hello Freesurfer Community,
  I am trying to use mri_robust_template (with its default 6 DOF
registration) outside of the Freesurfer longitudinal pipeline to
generate within-participant T1 templates from 2 time points. 
Unfortunately, I am coming up against a 'MyMatrix::RotationMean
input(s) not rotation' error on images acquired on our GE 3T
Discovery 750 system, but not our colleagues' Seimens 3T Prisma
images.  I have pasted the output from the --debug flag below (and
attached as text file - line 188 is the MyMatrix message).   If
helpful, images can be download from the following link:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://uofc-my.sharepoint.com/:f:/g/personal/abeaudin_ucalgary_ca/EmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ?e=lcovfR

Briefly: 
   - the images are skull-stripped niftis and I am running
Freesurfer 6.0
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a
WSL2 Ubuntu 18.04 installation. 
   - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz
2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta
--average 1 --template 2001_template.nii.gz --satit

   -  I have tried the following with no success:
1) using the --iscale flag - same result as shown below.
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same result as shown below
4) using Freesurfer v7.2 - same result as below
5) running mri_robust_template call on Catalina and Big Sur systems
with FS v6.0 - same result as below.

  Currently, the only way to get mri_robust_template to work with
our GE images is to run it with the --affine flag.  I would prefer
to use the rigid body registration but am at a loss for why these
images are failing using the rigid body registration is failing. Any
help/insights/recommendations are greatly appreciated.

Thank you very much.

Andrew


  Andrew Beaudin, PhD | Postdoctoral
Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273  
  

DEBUG REPORT:

$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter
Exp $

--mov: Using 2001A_T1o_brain.nii.gz as movable/source volume.
--mov: Using 2001B_T1o_brain.nii.gz as movable/source volume.
    Total: 2 input volumes
--lta: Will output LTA transforms
--average: Using method 1 for template computation.
--template: Using 2001_template.nii.gz as template output
volume.
--satit: Will estimate SAT iteratively!
--debug: Will output debug info and files!
reading source '2001A_T1o_brain.nii.gz'...
converting source '2001A_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
reading source '2001B_T1o_brain.nii.gz'...
converting source '2001B_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
Will use TP 2 as random initial target (seed 108242 ).

MultiRegistration::initializing Xforms (init 2 , maxres 0 ,
iterate 5 , epsit 0.01 ) : 

 MultiRegistration Parameters 

 Outdir:    ./
 TransOnly: false
 Rigid: true
 Robust:    true
 Satit: true
 Iscale:    false
 IscaleOnly:    false
 NoMulti:   false
 SubsampleSize: -1
 HighIt:    -1
 FixVoxel:  false
 KeepType:  true
 Average:   1
 DoublePrec:    false
 BackupWeights: false
 SampleType:    5
 CRASCenter:    false
 Debug: 1


[init] = TP 1 to TP 2
==
 Register TP 1 ( 2001A_T1o_brain.nii.gz )
  to  TP 2 ( 2001B_T1o_brain.nii.gz )

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
   Type Source : 3  Type Target : 3  keeping type 
   Mov: (1, 1, 1)mm  and dim (176, 256, 256)
   Dst: (1, 1, 1)mm  and dim (176, 256, 256)
   Asserting both images: 1mm isotropic 
    - no Mov reslice necessary
    - no Dst reslice necessary


 Registration::findSaturation 
   - computing centroids 
   - computing initial transform
 -- using translation info
   - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) 
   - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 3 )

   - Build Gaussian Pyramid ( Limits min 

[Freesurfer] Fwd: Pass code to expand archive for VirtualBox

[Cody Slater]

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Hello,

I am following the instructions to install the VirtualBox for Freesurfer
7.2.0 and would like access to the code for expanding the archive.

Regards,

Cody Slater
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[Freesurfer] Fwd: Pass code request for 7z

[Lesly Manresa]

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Hi,

I am writing to request the pass code to unzip the
FS_7_2_0_Ubuntu_18_04_06.ova.7z file.

Thanks,

Lesly
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[Freesurfer] Fwd: PET postdoc at NIH

[Douglas N. Greve]

 Forwarded Message 
Subject:PET postdoc at NIH
Date:   Wed, 8 Jun 2022 19:44:38 +
From:   Innis, Robert (NIH/NIMH) [E] 
To: Innis, Robert (NIH/NIMH) [E] 



External Email - Use Caution

A postdoctoral position will be available in my lab starting in late 
2022 or early 2023. Please forward the attached advertisement to anyone 
who may be interested.


Although immodest of me to say, the lab’s research projects are at a 
very exciting and productive stage. The two major goals are 
translational studies of neuroinflammation (i.e., COX-1, COX-2, and 
TSPO) and indirect markers of cAMP signaling (via PDE4B and PDE4D). The 
studies extend from transgenic mice to monkeys and to patients, 
including those with depression or dementia.


Stay safe and many thanks,

Bob Innis


Robert B. Innis, MD, PhD

Chief, Molecular Imaging Branch

National Institute of Mental Health

10 Center Drive, MSC-1026

Bldg. 10, Rm. B1D43

Bethesda, MD 20892-1026

Tel: 301-594-1368

Fax: 301-480-3610

Email: robert.in...@nih.gov 

Branch Administrative Manager:  Elizabeth Alzona

Tel:  301-594-1089

Email: alzo...@irp.nimh.nih.gov 

Molecular Imaging Branch 
website





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reply email and destroy all copies of the original message.


PET Imaging Postdoc Innis @ NIH start 2022 or 2023.docx
Description: MS-Word 2007 document
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[Freesurfer] Fwd: Passcode for FreeSurfer VM

[Aleksandra Petrovskaia]

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Dear all,

I hope you are doing well. I am an intern at the University of Gothenburg,
Sweden,  could you please provide me with a passcode for FreeSurfer VM
image? I would like to use this version:
https://secure-web.cisco.com/127-d9kyXBAbuHxZ2r3WcK3IY6FDnW58dIK_iXlD5z24YayxRsYB8XQvLW3w1GheaRoo21nU10_WclgHGfOgCJFY2EZs0_6wG7AJRabyA-4LWtRWGqn9A1SMLUF8r6jdmUqKARhuKfgdZRQmlOQ71HLUtJB8CyUzbJfHdI6DtIswdUzAmxmqq2FU_YP6UljmkV8JbkoN7MEWsEiBhkVJ30J3Gu7tO9ndunYW5DL1cuUKH_otzq4YDPogDgFrKAq80YLhwAGACaIVgydePpyy8RPVoM6kaWNkBZBo0glrLf9MvLd3krmvIjRfdXZ3Xmy4jyAf6kGulb7F5V1gms_ZAYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2FFS_7_2_0_ubuntu_18_04_06.ova.7z

Best wishes,
Alexandra
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[Freesurfer] Fwd: Gcut error: gcutted brain is much smaller than the mask.

[Begüm Cerrahoğlu]

External Email - Use Caution

Dear developers,


I am trying to clean up the extra dura left after skullstripping.
Watershed parameter does not prove to be much helpful and when I try
gcut I get the error below.
In the archives I came across this exact problem before,
https://secure-web.cisco.com/1JREA1RCtgfPRaolYsneD7S5EwcqlaqoCEQHN3rqgzcSwxBEjdNtgTr8t7ZOeDaAha0Kki9Kl1S34m3C6Y-Usou9I7zEqKMNDzHvMZUU9CWxfExUg2V9QXFmu7wru-gvNU9p_0-qFl574-z2_H2ltRBeIvPjgyfbdzlu-2nXXHbuwdJpOk3ZBgEfFIvqqlBRY5h9p1sT0tmkC0oP31-iURa7FriWfXrva0Ss4sLl-kYlXj76qX4w6wyvUzQNIGTEcHfXzX6izhG_r80Jd0VWRoRZPI27jFpnY8T_B3gYQ-pXDnJ_aGdI_hPWLPGxB5SIdSQjHYrr-cOw5EMpi31TwKw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18797.html

However, there was not an end solution available in the archived email
exchange. I am not interested in cerebellum and am okay with cutting
the cerebellum out of
the brain mask as long as it does not interfere with being able to
distinctly separate cortex from cerebellum in the following steps.
From skullstripping tutorials,
I have read that one should not start erasing cerebellum from the
brainmask directly and was wondering if you could let me know why?

In sum, are there important reasons to keep the cerebellum despite
only being interested in analyzing the cortex?


If not, could you please let me know what could be the reason for
gcut's failure and if there is anyway to disable failure detection so
I can see if the gcutted
brain is usable?

>> " rm -f brainmask.gcuts.mgz
>> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz
>> brainmask.gcuts.mgz
>>
>> INFO: Care must be taken to thoroughly inspect your data
>>  when using mri_gcut. In particular, inspect the edges of
>>  gm and cerebellum for over-aggressive cutting.
>>  Add -segmentation brainmask.gcuts.mgz to the tkmedit
>>  command string to view the voxels which gcut has removed.
>>
>> reading mask...
>> white mean: 107.529232
>> threshold set to: 107.529232*0.40=43.011693
>> calculating weights...
>> doing mincut...
>> now doing maxflow, be patient...
>> g-cut done!
>> post-processing...
>> post-processing done!
>> masking...
>> ** Gcutted brain is much smaller than the mask!
>> ** Using the mask as the output instead!
>>
>> cp brainmask.auto.mgz brainmask.mgz "


1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.
2) Platform: Linux Mint 20.2

Thank you greatly for your time and efforts.

Kindest regards,

Begum Cerrahoglu
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[Freesurfer] Fwd: VM password

[REEM ABU BAKR BAHATHIQ]

External Email - Use Caution

Dear Freesurfer mailing list,

I have just downloaded the virtual machine + ubuntu package, as outlined on the
website when running a VM in windows. However, ubuntu is asking for a developer
password to open within the VM. I see on the help page (on the website) that
the log in ID could be in the README doc, but I can't actually get the VM open
to get there.

Does anyone know the password so I can set up the VM and get started with
freesurfer?

Thanks so much in advance!
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[Freesurfer] Fwd: INS Meeting

[Rosalia Dacosta Aguayo]

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FYI!!
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[Freesurfer] Fwd: OpenNeuroPET hackathon at MGH -- Dec 6th and 7th

[Douglas N. Greve]

For those interested in PET and BIDS, this should be pretty useful.


 Forwarded Message 
Subject:OpenNeuroPET hackathon at MGH -- Dec 6th and 7th
Date:   Wed, 17 Nov 2021 19:31:48 -0500
From:   Wighton, Paul 
To: Greve, Douglas N.,Ph.D. 



Hi Doug,

I was hoping you could forward this to anyone you think may be 
interested.  Thanks.


We are hosting a hackathon on Dec 6th and 7th in close collabration with 
the OpenNeuroPET group (openneuropet.github.io).


The goal of the Hackathon is to educate researchers about the new 
BIDS-PET standard, to help researchers curate BIDS-PET datasets and to 
discuss how to build and execute pipelines that can operate on BIDS 
datasets.  We are also super interested in multi-modal imaging more 
generally.


Details can be found here: 
https://github.com/openneuropet/outreach/tree/main/Brainhack-MGH2021. 
 Please reach out to Paul Wighton (pwigh...@mgh.harvard.edu) if you 
have any questions or would like to give a talk or have a project you 
would like to propose.  If you'd like to attend some or all of the talks 
either virtually, or in person (for MGH employees only due to COVID) but 
don't have the bandwidth to give a talk or work on a project, that's ok too!


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Re: [Freesurfer] Fwd: Base correction, longitudinal analysis

[Douglas N. Greve]

That is just part of the way the long stream works. When you run a base 
subject, you have to spec all the cross tps that go into it. I agree, it 
is not elegant.


On 8/8/2021 8:03 PM, Eszter Boros wrote:


External Email - Use Caution

Dear FreeSurfer Team,

I am working on a longitudinal pipeline and after correcting the Cross 
and generating the Base, I can still see some pial problems 
sometimes (on the Base).
I read on the Freesurfer website that it is possible to correct and 
regenerate only the Base, but when I use this command:


recon-all -base OAS2_0057 -autorecon-pial

/where OAS2_0057 is the name of the Base/

I get the following error message:

ERROR: must specify subjects for base subject using -base-tp


Why is this not working? I am using Freesurefer 7.1.1.
Thank you so much!

All the best,
Eszter Boros


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[Freesurfer] Fwd: [Neuroimaging] [Nibabel] Discourse category for Surface API discussions

[Satrajit Ghosh]

External Email - Use Caution

fyi

-- Forwarded message -
From: Christopher Markiewicz 
Date: Mon, Aug 9, 2021 at 5:01 PM
Subject: [Neuroimaging] [Nibabel] Discourse category for Surface API
discussions
To: neuroimag...@python.org 


Hi all,

I'm starting to work on the Surface API portion of the Nibabel grant.

I've created a category on the Discourse here:
https://secure-web.cisco.com/1fZyTqmwozZU5Qoa2utEX0kDdW_8B7XIMEFga96aHR-YctDChh-Zx9cN1SO_1ZHs_xdWuUetZM5VK1uRC1XNJBe7RRgeb09fdKqZK7Fuo0tuUTJMBM9IcuCrTnAKvXvP8FOiP-L0VcuCluMnufN4nIwJJpS50EG8jsc8IDz4bpGskjHV6kESUnY9QF89xoapABaPugxAFVyfRw5wyE8ru4jIh8QQf5T3PUc5iZJ_HgutYCfKx_ovrEaWBk0fMvy_tphmUp6jFt46JB17z8AlX2A/https%3A%2F%2Fnipy.discourse.group%2Fc%2Fsurface-api%2F10

And I've started some initial notes here mostly laying out the problem:
https://secure-web.cisco.com/1qQtCe4EJSW0O7Z_CBMnNittP03bU4FYzr1xy2YZOTw_oawdHMw3nJVKmZQBvF8O3rErC-ZpG0VuwIxcIWO0IgTTPnlkKqCPj5oRMRa8qQfwhcw_iEOc_tD1yHlmjQu2Eztu4hU1rdMCmbHxLgddtj27C5RBrLpK2dYBjLhs-3LWhMVuKovrE_19eEDzEFRrFOg0g-EwwmjAjmAExOHABver1Hfbz5nl0ON7KVhr_lTPmWVaA4Z9kmSxljiBBW2W-P4r9ExaW0nrhdMoaMPJsiw/https%3A%2F%2Fnipy.discourse.group%2Ft%2Fpreliminary-notes-on-surface-representations%2F57

The next steps are going to be to identify use cases for people working
with surface data, which will also involve finding people who I may not
know about, so please forward this on to people who might be interested in
joining the discussion.

--
Christopher J. Markiewicz, PhD
Center for Reproducible Neuroscience
Stanford University
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[Freesurfer] Fwd: Base correction, longitudinal analysis

[Eszter Boros]

External Email - Use Caution

Dear FreeSurfer Team,

I am working on a longitudinal pipeline and after correcting the Cross and
generating the Base, I can still see some pial problems sometimes (on the
Base).
I read on the Freesurfer website that it is possible to correct and
regenerate only the Base, but when I use this command:

recon-all -base OAS2_0057 -autorecon-pial

/where OAS2_0057 is the name of the Base/

I get the following error message:

ERROR: must specify subjects for base subject using -base-tp


Why is this not working? I am using Freesurefer 7.1.1.
Thank you so much!

All the best,
Eszter Boros
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[Freesurfer] Fwd: TRACULA FS 7.2.0 Error: domainname: Command not found. Too many )'s.

[juergen.haenggi]

External Email - Use Caution

Dear R, dear Anastasia

thanks for your answer.
there is indeed no domainname command in /usr/bin.
I am working on a Mac and I am wondering why this error did not occur if using 
TRACULA in FS 7.1.1 if this command is not available on my Mac.
please can you explain in more detail how I can fix this problem on a Mac if 
using tcsh?

Thanks in advance
Regards
Jürgen

Am 23.07.2021 um 08:17 schrieb fsbuild 
mailto:fsbu...@contbay.com>>:

Hello Jürgen,

/bin/domainname should be installed as part of the base distribution on a linux 
machine.  Maybe it was not in your PATH before you ran the freesurfer shell 
setup script?   You could test this by starting with a basic PATH, e.g., on 
CentOS,

$ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
$ which domainname
/usr/bin/domainname

… then add in anything else to PATH  …

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

… output deleted …

$ which domainname
/usr/bin/domainname

- R.

On Jul 23, 2021, at 01:50, 
juergen.haen...@upd.unibe.ch wrote:

domainname: Command not foundDear TRACULA experts

I am trying to run the new version of TRACULA implemented in FS 7.2.0 on a Mac 
and the following error occurred at the beginning of trac-all -prep:

trac-all -prep -c 
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/tracula_config_IPS_all_example_DICOMs_FS720.txt
domainname: Command not found.
Too many )'s.
ERROR: Syntax error in configuration file 
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/tracula_config_IPS_all_example_DICOMs_FS720.txt

I checked the configuration file with respect to the brackets, but did not find 
too many )’s.

What does it mean "domainname: Command not found.“ and could it be that this 
error is related to "Too many )’s."?

The config file is attached and no log file is produced.

Any advise is greatly appreciated

Thanks in advance

Regards
Jürgen



# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects


# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = 
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Results_DICOMs_FS720


# Subject IDs (n = 130 incl. IPS_SZ_024, excl. IPS_SZ_028 & IPS_SZ_068 due to 
missing fieldmap)
#
set subjlist = (IPS_CO_007)


# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
set runlist = (1)


# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = 
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/00_TRACULA_Prepared_DICOMs_FS720
set dcmlist = (IPS_CO_007/DTI/32863323.dcm)


# Diffusion gradient tables (file names can be relative to dcmroot)
# Must be specified only if they cannot be read from the DICOM headers
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
#set bveclist = (TRACULA_Prepared/IPS_CO_007/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_009/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_010/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_012/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_013/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_020/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_027/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_031/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_034/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_039/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_050/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_051/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_058/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_059/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_071/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_072/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_074/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_080/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_087/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_088/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_091/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_094/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_097/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_099/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_102/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_103/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_108/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_111/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_114/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_115/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_116/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_121/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_124/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_125/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_126/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_128/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_131/DTI/bvecs.bvec 
TRACULA_Prepared/IPS_CO_132/DTI/bvecs.bvec 

[Freesurfer] Fwd: Fwd: Yeo atlas for children!

[Martin Juneja]

External Email - Use Caution

Dear Thomas and FreeSurfer experts,

Here I am just reposting my question below - just in case this was missed
by the experts. Any help would be really appreciated.

-- Forwarded message -
From: Martin Juneja 
Date: Sat, Jul 10, 2021 at 3:45 PM
Subject: Re: [Freesurfer] Fwd: Yeo atlas for children!
To: Freesurfer support list 


Dear Thomas,

Thanks for your response.

I have one more question here: I was looking at the Schaefer parcellation
paper where authors have 100, 200, 300, 500...1000 areas parcellation. Is
there a way to choose among these parcellations (i.e., what's the basic
difference/justification/significance of each of these parcellations over
one another) for cortical structure analysis?

Thanks!

On Thu, Jun 24, 2021 at 7:24 PM Thomas Yeo  wrote:

> External Email - Use Caution
>
> Hi Martin,
>
> With regards to adolescents versus adults, there's obviously differences
> between the two age groups. In our experience, when we re-estimate
> parcellations from this study (*MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1imRwMSixADMoOIgpdpY29jXpDOLeSGli2a22XCxZWFbr2XZcnxO2KDrRbNMcsCgQMkiZ1MsPEXG3o-3E9Y8PqOAA_WXMSVytHVXo0IghuduA56nI9K7IG2cxiGQ_6nU-TWPhPW-etqRzG5uQOkyA64SXMxYawNeZNm5ggMchWgpwYLmUPctZnCmo5pQTBNUxJVA-pQ6-EihauZbmWBsHMIqTlPg1U5vnpftP9B9whY1fRvPAL2YtklY-zX6zcEdUx_jAncDqCVT0lDpZ1ciI5A/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101
> <https://secure-web.cisco.com/1TF7OmC5fKijUUx5uZkr1n5IUfkGr1RFX7MO-EmdsI3fo1_9zP0Jp-ETRw5NAjxS8BJDa6kKcSMMpJ2sdiX-ot-j-5QFedPJw2Pv_w_Lx09S2qip068nmS_qYJ7jPemY60cjnwP8Sv5YsnioL9TmWNC25owkxNqJp4Z23siRPlxWMF6odSKRD90PbJNM9pQK60dgMUgk07qeKbxs2PfIzD7evz-QcmOcS6NgyV6QttV9sTK7p2YtU6VOPRTXrkqV29tPjdaVkUQg-0QMGTS-45w/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101>)
> in kids (ABCD), the parcellations are not better based on various metrics
> we computed, so I suspect it won't matter much. But the kids results are
> not in our paper, so I am not sure the reviewer will buy this argument. For
> this issue, you could reapply the Yeo2011 algorithm (*MailScanner has
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
> be*
> https://secure-web.cisco.com/1TRaCda3Ajq2cSPkyOdjhs-iDjMQqQpE0pfWxMyCDpAO5VRbGYtKOT3ESGeNIkcwZ3mCdJhReWuzhWi9pXY1grfJSeKsSmO-OkwTvwN9ji0-lW8jAdGenRsKwBA7v5mgvFY_fzJo8AWJ223pcmruUzdI5R-Dhb-eLfDUtqAxn0Ck8lp3PhZmPBc27-snFbAikXbe9ZlzLVPdJyPmXQyvKeo3GhIDUbbE9J8uq_cgSgK727TvQLtqTArCX1ZPbDFIMNadY2RHLMtyxLZJf2OoiWA/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering
> <https://secure-web.cisco.com/1Z2srwkLUjJ_Dnco-Ccq_78ppkQhV3eTVmdR3bkvuvg64MLymHCpblVH7s3BbaYqCgmBhjfn2fLmvOxE52eTv_pNlqqJU66mrQ_kyS9r5xo7vnpF49mnl1CurnSQ-g0lBHQrOu-r1VaMu4bdeod4wOunBUn8z0Ilju3bxxxEVIBwddrah-4RY6d0MV-0qlYnFyxyw5vpq66r2twE7Xzv--mIsL85psoPahHst1Vto9_q39hxhT94w3fNtgOpITnrC9jSZStJGUBEPMuLDb7fWgQ/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering>)
> to your sample and estimate cohort-specific networks and repeat your
> analysis. We have also developed individual-specific versions of the
> Yeo2011 networks (*MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1uqONT3oR5bPf0SnEdMW-1CdNAMyYxLbz75N5HGX7ryuRL5BtKUre5JkOu_xWBiMu_7SE5xf0aYHXK_YbkZORrCStIQKqz9-pVg38BsiqqAP1ovmM-smi2l9ELT95KkAE9W1ErC0eDnRQvCYR4aoatuT2EfPobOkfxk7-TDdW-xaWuZiaBdZBA2Qs39dCKia-pDrE92rVfPquYg8jm1JhOhfxFPmV4NBmIvCpuOwb8hrzFDfWKd5LB_n4hn3CQRo4WkRwVaaaUPg5hSnPJe0AZw/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM
> <https://secure-web.cisco.com/1ja6ZcGwaTlynHGpv68CpBe5wYiryA6Cd9PoPXavhiQcOfiz9Dqk182Jm1NOGknuS5V4LN5APd8rzUErhPpJ6N8fmbPbU1ofhucuPYirEkxbiN-f7KwiyDUiW26HQYY_APS_F3PptKP35VM14zsTm7TwwBSzRZcp1x2GUabhSkC2Uwedw4JQXh_Wned1PegQitYecAZLY0yG_RxpEISUp9zo-MvBV5DdGwVNYsVx8cRr1imnAjiZgQ241c3ZHSKJsuA3WlEi0QZmaYA9NYNL2Ng/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM>),
> which you might find helpful, although it's probably not necessary based on
> the reviewer's comments.
>
> The other issue is whether a functional atlas might be appropriate for
> structural data. I think that really depends on your question. For example,
> if your question is whether default network cortical thickness might be
> different between adolescents and adults, I think it's reasonable to use a
> functional atlas where the default network is well defined. If you use a
> structural atlas like the Desikan-Kiliany atlas, then you will still need
>

Re: [Freesurfer] Fwd: Yeo atlas for children!

[Martin Juneja]

External Email - Use Caution

Dear Thomas,

Thanks for your response.

I have one more question here: I was looking at the Schaefer parcellation
paper where authors have 100, 200, 300, 500...1000 areas parcellation. Is
there a way to choose among these parcellations (i.e., what's the basic
difference/justification/significance of each of these parcellations over
one another) for cortical structure analysis?

Thanks!

On Thu, Jun 24, 2021 at 7:24 PM Thomas Yeo  wrote:

> External Email - Use Caution
>
> Hi Martin,
>
> With regards to adolescents versus adults, there's obviously differences
> between the two age groups. In our experience, when we re-estimate
> parcellations from this study (*MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1IudlKj4RIkQs10Z1MVq-qyzXMK1KFK6wvN63xEvKi24e5rl_nD07TnliMPHz--sVPiuLtdjF5Uno-ntkj7ShCgpDd-_pVOfDTwPs8v3BORNcCYGYEXuKEHapxMGFDUqBsB1r3--Tugb7rj2pJnb_D5_Tw5S5K5JM-LcIY5CNtaPGZbvPi-7aaQDLDXnRWP3HMnGNdWAq0DAiiZMkdJMSgBVBoPz0iYOScBVBAqBIp1ZjYY3oIpqcaEWeeAa38udpWOxVKFsCc4ICNMHiGfFl3Q/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101
> )
> in kids (ABCD), the parcellations are not better based on various metrics
> we computed, so I suspect it won't matter much. But the kids results are
> not in our paper, so I am not sure the reviewer will buy this argument. For
> this issue, you could reapply the Yeo2011 algorithm (*MailScanner has
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
> be*
> https://secure-web.cisco.com/1STyuALGZ52-UjmmBJfV1CdFGDZwA6RF_hF3zsYX0GWpLCkfj7qHKlydSNtvsgrAASfMxhmLzmr3J-WKESy3vHHsZoPLJbyPXLThqjBLazJASUShD8mcGT64jgsTszFPmjOtCrPVkDxiN2pPTCGnzmu4uI5v0aFfFnqbvKIDbcoewtYhubdrVxz8ddVqXcctwzu-GiXKZ_gjDc8qLAPkGmUmXXt4UPbtoFtGErM5Ptv8lk5pxxp1cW_1-if-y6RZRVbR5FdClkm47EOECT1n67w/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering
> )
> to your sample and estimate cohort-specific networks and repeat your
> analysis. We have also developed individual-specific versions of the
> Yeo2011 networks (*MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1uV4DGwqj8a1p5Y1x2Tqm4bmH1OC1GsJDtJUxazbhQpCeX1Qh0-XvjJnEtrLykJPVtB4ziclalH5902_91LzNCbxKGu7ZaIV34auBzznywx381WKsyrgP2YpXikFUQyDllBeRtHICEOnRPUu_5Yu3Tv-ZfH_e8nX5AxRSCp5OiQ-vi_29IpAFk2Gi8A751cW_9Iqrs7-ZHXZ9HeXoIZe6o-svzW4bxhDn5jh-g7nwQ5II4TUJJ-h-lccKF-wrrC1Byy4xETMzfisO5YAfxns15A/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM
> ),
> which you might find helpful, although it's probably not necessary based on
> the reviewer's comments.
>
> The other issue is whether a functional atlas might be appropriate for
> structural data. I think that really depends on your question. For example,
> if your question is whether default network cortical thickness might be
> different between adolescents and adults, I think it's reasonable to use a
> functional atlas where the default network is well defined. If you use a
> structural atlas like the Desikan-Kiliany atlas, then you will still need
> to use a functional atlas to roughly assign the Desikan-Kiliany parcels to
> the default network, which does not seem that great either.
>
> Regards,
> Thomas
>
> On Fri, Jun 25, 2021 at 12:52 AM Martin Juneja  wrote:
>
>> External Email - Use Caution
>>
>>
>> Hi all,
>>
>> I am reposting my concerns below. I would really appreciate any help.
>>
>> -- Forwarded message -
>> From: Martin Juneja 
>> Date: Fri, Jun 18, 2021 at 6:16 PM
>> Subject: Yeo atlas for children!
>> 

Re: [Freesurfer] Fwd: Yeo atlas for children!

[Thomas Yeo]

External Email - Use Caution

Hi Martin,

With regards to adolescents versus adults, there's obviously differences
between the two age groups. In our experience, when we re-estimate
parcellations from this study 
(https://secure-web.cisco.com/1TF7OmC5fKijUUx5uZkr1n5IUfkGr1RFX7MO-EmdsI3fo1_9zP0Jp-ETRw5NAjxS8BJDa6kKcSMMpJ2sdiX-ot-j-5QFedPJw2Pv_w_Lx09S2qip068nmS_qYJ7jPemY60cjnwP8Sv5YsnioL9TmWNC25owkxNqJp4Z23siRPlxWMF6odSKRD90PbJNM9pQK60dgMUgk07qeKbxs2PfIzD7evz-QcmOcS6NgyV6QttV9sTK7p2YtU6VOPRTXrkqV29tPjdaVkUQg-0QMGTS-45w/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101)
 in
kids (ABCD), the parcellations are not better based on various metrics we
computed, so I suspect it won't matter much. But the kids results are not
in our paper, so I am not sure the reviewer will buy this argument. For
this issue, you could reapply the Yeo2011 algorithm (
https://secure-web.cisco.com/1Z2srwkLUjJ_Dnco-Ccq_78ppkQhV3eTVmdR3bkvuvg64MLymHCpblVH7s3BbaYqCgmBhjfn2fLmvOxE52eTv_pNlqqJU66mrQ_kyS9r5xo7vnpF49mnl1CurnSQ-g0lBHQrOu-r1VaMu4bdeod4wOunBUn8z0Ilju3bxxxEVIBwddrah-4RY6d0MV-0qlYnFyxyw5vpq66r2twE7Xzv--mIsL85psoPahHst1Vto9_q39hxhT94w3fNtgOpITnrC9jSZStJGUBEPMuLDb7fWgQ/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering)
to your sample and estimate cohort-specific networks and repeat your
analysis. We have also developed individual-specific versions of the
Yeo2011 networks (
https://secure-web.cisco.com/1ja6ZcGwaTlynHGpv68CpBe5wYiryA6Cd9PoPXavhiQcOfiz9Dqk182Jm1NOGknuS5V4LN5APd8rzUErhPpJ6N8fmbPbU1ofhucuPYirEkxbiN-f7KwiyDUiW26HQYY_APS_F3PptKP35VM14zsTm7TwwBSzRZcp1x2GUabhSkC2Uwedw4JQXh_Wned1PegQitYecAZLY0yG_RxpEISUp9zo-MvBV5DdGwVNYsVx8cRr1imnAjiZgQ241c3ZHSKJsuA3WlEi0QZmaYA9NYNL2Ng/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM),
which you might find helpful, although it's probably not necessary based on
the reviewer's comments.

The other issue is whether a functional atlas might be appropriate for
structural data. I think that really depends on your question. For example,
if your question is whether default network cortical thickness might be
different between adolescents and adults, I think it's reasonable to use a
functional atlas where the default network is well defined. If you use a
structural atlas like the Desikan-Kiliany atlas, then you will still need
to use a functional atlas to roughly assign the Desikan-Kiliany parcels to
the default network, which does not seem that great either.

Regards,
Thomas

On Fri, Jun 25, 2021 at 12:52 AM Martin Juneja  wrote:

> External Email - Use Caution
>
>
> Hi all,
>
> I am reposting my concerns below. I would really appreciate any help.
>
> -- Forwarded message -
> From: Martin Juneja 
> Date: Fri, Jun 18, 2021 at 6:16 PM
> Subject: Yeo atlas for children!
> To: Freesurfer support list 
>
>
> Dear experts,
>
> I used Yeo's 17-network parcellation to study the association between
> network-wise cortical volume and a clinical variable in adolescents. I
> received the following two questions from the reviewers regarding the use
> of Yeo's atlas. I would really appreciate if someone could help us in
> addressing these questions:
>
>
>
> *1) Could the author justify their choice to use a functional parcellation
> on structural data? How is using this parcellation helpful in understanding
> the brain? All in all, the authors need to justify the superiority of using
> Yeo's 17-area parcellations on structural data over other methods of
> parcellation/analysis. *
> *2) One issue with Yeo's parcellation also stems from the fact that this
> parcellation was derived from adult connectomes. Could the authors also
> address this issue and provide examples that justify their approach.*
>
> Thanks.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1vYwj4u8tnnloAFkq4GNee0aO8bp4AJUBz-f6_rsP7s37_gWii9gsMI3T4i80MIoKCmaAbgSDavMI9Bra-Qk7FqwHAR__FBeRuuC3XCpet50brzAn5-A8K5-0JOTdZXjrfA1qCqFs04yCTLQy1mTe7wOXzmWFuHfI7dyoNfQpgcuJM0neywH2WO4quKfZx9e2C_pm4ronht7RD98Axtw5iLCfeiE4ofV57OGHobrbOveEjP3csgYMC7ZS_59V7Kxia-b8F9Ct_3ip4R_Lpq0PyA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Fwd: Yeo atlas for children!

[Martin Juneja]

External Email - Use Caution

Hi all,

I am reposting my concerns below. I would really appreciate any help.

-- Forwarded message -
From: Martin Juneja 
Date: Fri, Jun 18, 2021 at 6:16 PM
Subject: Yeo atlas for children!
To: Freesurfer support list 


Dear experts,

I used Yeo's 17-network parcellation to study the association between
network-wise cortical volume and a clinical variable in adolescents. I
received the following two questions from the reviewers regarding the use
of Yeo's atlas. I would really appreciate if someone could help us in
addressing these questions:



*1) Could the author justify their choice to use a functional parcellation
on structural data? How is using this parcellation helpful in understanding
the brain? All in all, the authors need to justify the superiority of using
Yeo's 17-area parcellations on structural data over other methods of
parcellation/analysis. *
*2) One issue with Yeo's parcellation also stems from the fact that this
parcellation was derived from adult connectomes. Could the authors also
address this issue and provide examples that justify their approach.*

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

[Freesurfer] Fwd: Running FreeSurfer with fmriprep

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Dear Freesurfer's experts,

I have run recon-all all to one subject with fmriprep.

The work finished without errors. However, after inspecting the results, I
have seen that there are some *grey regions* (mainly frontal and temporal
ones) that have not been fully covered.

I wonder how I could proceed in order to improve the segmentation.

Kind regards,
Rosie
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Fwd: confirm 8038f95159942b876b5e8f8110930301c8222d61

[Andrew Raines]

External Email - Use Caution

Hi there,


I really need some help…I have experienced a mild/moderate head injury in 1997 
which caused me to go into seizures (no family history of epilepsy) I have had 
MRI recently done as my cognitive function and memory have declined rapidly 
over the years, after the accident I apparently changed from very happy and a 
large group of friends to being grumpy and short with people and making 
inappropriate comments... i also lost all my friends at the time as my mood 
changed and i have struggled to retain friendships (even new ones) since the 
accident. I have tried to follow your instructions of how to install free 
surfer but despite once being proficient on c basic programming I have been 
unable to follow instruction on how to install run and process my MRI data.

I was hoping that you may have an angel that would be able to uplift my MRI 
data from dropbox, process and send it back to me, in lou of being able to use 
my MRI for any research,  the neurologist only look at the MRI data with the 
naked eye and say i look normal…im hoping that freesurfer will show evidence 
otherwise so that the government based accident coverage can get me sent to 
australia for analysis as there is no way the hundreds of falls and head injury 
i have had can leave me “normal” yet barely functional

thank you for any help you may be able to give


Kind Regards


Andrew Raines

> Begin forwarded message:
> 
> From: Andrew Raines 
> Subject: Re: confirm 8038f95159942b876b5e8f8110930301c8222d61
> Date: 25 May 2021 at 11:04:46 AM NZST
> To: freesurfer-requ...@nmr.mgh.harvard.edu
> 
> 
> 
>> On 25/05/2021, at 11:03 AM, freesurfer-requ...@nmr.mgh.harvard.edu 
>>  wrote:
>> 
>> confirm 8038f95159942b876b5e8f8110930301c8222d61
> 

___
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Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Fwd: Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug,

Did you have a chance to look at this subject ?

Thanks a lot,
Julie

-- Forwarded message -
From: Julie Ottoy 
Date: Thu, 18 Mar 2021 at 13:08
Subject: Re: [Freesurfer] Failed tissue type check {Disarmed}
To: Freesurfer support list 


Hi Doug

I upload the files on the server, see subject_ottoy.tar.gz

thanks a lot!
Julie

On Tue, 16 Mar 2021 at 12:03, Douglas N. Greve 
wrote:

> I don't know. Can you upload the data so I can take a look? Instructions
> are below. I'd need both the anatomical data (output of recon-all) and
> input.nii.gz and PET.lta
>
> From the linux command line,
> Create the file you want to upload, eg,
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
>
> On 3/8/2021 11:47 AM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug,
>
> Any other suggestions I could try? It seems to be only an issue with the
> non-pvc data.
>
> Thanks
> Julie
>
> On Tue, 2 Feb 2021 at 11:10, Julie Ottoy  wrote:
>
>> Hi Doug,
>>
>> I tried these fixes but they still give me the error message below. I did
>> replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab
>> in the aux folder ?
>>
>> Thanks,
>> Julie
>>
>> On Tue, 12 Jan 2021 at 10:37, Julie Ottoy 
>> wrote:
>>
>>> Hi Doug
>>>
>>> I tried that as well but getting the same error as with --replace 29 3.
>>>
>>> ERROR: CTABpruneCTab(): ctab does not have segid 2
>>>
>>>
>>> Thanks,
>>> julie
>>>
>>> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>>
 Try using --replace 29 2


 On 12/29/2020 12:48 PM, Julie Ottoy wrote:

 External Email - Use Caution
 Hi Doug

 Thanks for your reply. I tried both your suggestions, but it seems as
 though they both ran into an error.

 For your first suggestion, i.e. adding --replace 29 3 to the command
 line of gtmpvc, I get the error:

 Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz

 Loading seg ctab 057_S_5295re/mri/gtmseg.ctab

 Reading 057_S_5295re/mri/gtmseg.lta

 Replacing 19

 Pruning ctab

 ERROR: CTABpruneCTab(): ctab does not have segid 3


 For your second suggestion, i.e. I replaced the following line in the
 ctab:

   29  Left-undetermined   135 206 2350  -1

 ==> replaced by:  29  Left-undetermined   135 206 2350
 3


 I get the error:

 Computing Seg in input space

 Building GTM DoVoxFracCor=0

 ERROR: creating region for nthseg=12, segid=29, Left-undetermined

 It may be that there are no voxels for this seg when mapped into the
 input space.

 Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
 registration

  Build time 5.9690, err = 1


 Thank you,

 Julie

 On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
 dgr...@mgh.harvard.edu> wrote:

> You can use the fix from my previous email or you can add the
> following line any were into the gtmseg.ctab file:
>  29  Left-undetermined   135 206 235 0 3
>
>
> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Sorry I would like to correct my previous post. The subject also
> failed with PVC.
> I see now that the issue is happening during the gtm seg stage where
> it gives the error: WARNING: segid   29 Left-undetermined tissue type is
> not set.
> For your information: I ran the standard FS and petsurfer pipeline as
> outlined on the wiki. I tried two gtm seg commands:
> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
> --subseg-cblum-wm
>
> Thank you for your help,
> Julie
>
> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
> wrote:
>
>> External Email - Use Caution
>> Dear Doug,
>>
>> I have the same issue as the people below. I was wondering if this
>> was solved in the meantime.
>>
>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC
>> and got the following error in only one of my subjects. When I ran the 
>> same
>> subject with PVC and specified psf, it did run fine.
>>
>> $Id: mri_gtmpvc.c,-
>> setenv -
>> cd -
>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
>> 

[Freesurfer] Fwd: Three researcher positions (doctoral candidates) in visual perception and educational neuroscience

[Mareike Grotheer]

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The Educational Neuroscience Lab at the Philipps Universität Marburg 
(Germany) is currently recruiting up to three Doctoral Candidates. Two 
positions are aimed at candidates who are interested in simultaneously 
pursuing their doctorate as well as training as a child and adolescent 
psychotherapists. These two positions are described here: 
https://secure-web.cisco.com/1u41B3o1_wCuZdmyXcMyyhvPMvChH9Gk-uVYt5UJ5WOx7sVoOZdGP7xhPr8uscUr9VKZyJzTe7XOuydsk6PaVsESkajzNZMoiJsNWygnlcM6W-mEALXwUVnatcba-94RKILSnnBDcT_aJJLxDG1cp5QidYPHQ0jjfZCANlQRcJbBTDQ0a7-wTiOCqveaFRw_lhvIQI-VT0gbUywJdpKbpgyrgAnkS_5Z5Ymei12X-LQ5upTobZxbhWctqJCDSSkD9dPGOsOugJxvp8stSKOix1w/https%3A%2F%2Fwww.psychjob.eu%2Fde%2Fjob%2F1-2-stipendien-im-rahmen-des-marburger-modells-neuronale-grundlagen-13241 
. 
The third position is focused on research only and is described below.


In the Department of Psychology and the Center for Mind Brain and 
Behavior (CMBB), the Education Neuroscience Lab headed by Junior Group 
Leader Dr. Mareike Grotheer is currently accepting applications for a 
*Researcher (Doctoral Candidate)*.


The position is offered for a period of 3 years, if no former times of 
qualification must be considered. The starting date is as soon as 
possible. The position is part-time (65 % of regular working hours) with 
salary and benefits commensurate with a public service position in the 
state Hessen, Germany (TV-H E 13, 65 %).


The successful candidate will be highly motivated to conduct research on 
the neural substrates of visual perception as well as reading and 
mathematical cognition. The lab strives to employ a multimodal approach 
and the successful candidate will therefore have the opportunity to 
acquire multiple cutting-edge MRI techniques, such as functional, 
diffusion and quantitative MRI. By combining these tools with behavioral 
measures as well as computational models, the successful candidate will 
explore the interplay of brain function and structure, learning-induced 
changes in the brain and/or brain development. The successful candidate 
will plan, carry out and analyze experiments as well as prepare 
publications and conference presentations of their work. The lab is part 
of a larger research network, with excellent links to scientists in 
Europe and the US. Marburg is a beautiful university town, located just 
90 km north of Frankfurt, right in the heart of Germany.


The position is limited to a time period deemed adequate for the 
completion of a doctoral degree. As part of the assigned duties, there 
will be ample opportunity to conduct the independent scientific research 
necessary for the completion of a doctorate. The limitation complies to 
§ 2, 1 WissZeitVG.


The successful applicant will hold an MSc-degree (or equivalent) in 
Psychology, Neuroscience, Biology, Computer Science, or related fields. 
The applicant will further be keen to learn new techniques and to expand 
their quantitative and programming skills. He/she should also enjoy 
working in a team, as well as, independently. Experience with MRI, 
programming in Matlab or Python and good written and verbal English 
skills are desirable. Disposition to own scientific qualification (e.g. 
a doctorate project in the area of Education Neuroscience) is expected.


Feel free to contact Dr. Mareike Grotheer at 
groth...@staff.uni-marburg.de for more information.


We actively support the professional development of junior researchers, 
e.g. by the offers of Marburg Research Academy (MARA), the International 
Office, the Higher Education Didactics Office and the Human Resources 
Development Office.


We support women and strongly encourage them to apply. In areas where 
women are underrepresented, female applicants will be preferred in case 
of equal qualifications. Applicants with children are welcome – 
Philipps-University is certified as a family-friendly university. 
Sharing a full-time position (§ 8 Abs. 2 S. 1 HGlG) as well as a 
reduction of working time is possible. Applicants with a disability as 
described in SGB IX (§ 2 Abs. 2, 3) will be preferred in case of equal 
qualifications. Application and interview costs can not be refunded.


Please send your application mentioning registration number 
fb04-0025-wmz-2021 as a single PDF file to 
groth...@staff.uni-marburg.de, before the 9th of April, 2021.


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Re: [Freesurfer] Fwd: label to surface

[Douglas N. Greve]

I've never done it in FS, but you might be able to do it with 
mris_convert using -c option and specifying a gifti as an output


On 2/1/2021 8:19 PM, Sam W wrote:


External Email - Use Caution

Hi!
Just pinging. Is there a way to get the surface+overlay file as 
mentioned above using freesurfer? Thank you!

Best regards,
Sam


-- Forwarded message -
From: *Sam W* mailto:samf...@gmail.com>>
Date: Fri, Jul 10, 2020 at 9:05 PM
Subject: Re: [Freesurfer] label to surface
To: Freesurfer support list >



Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However 
probtrackx requires a file that contains both the whole surface file 
(eg, lh.pial) as well as the overlay (the scalar values associated 
with the vertices of the roi).
I can create such a file with FSL's label2surf command which creates a 
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running 
probtrackx with the overlay from mri_label2label --outmask does not 
work. It also needs the associated pial or white surface.

Best regards,
Sam


On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


what do you mean merge with the pial?

On 7/9/2020 8:07 PM, Sam W wrote:


External Email - Use Caution

It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay
with mri_label2label using --outmask as you suggested, but now
I'd like to merge that overlay with the pial surface (lh.pial).
Is there a tool I can use to achieve that result?
Best regards,
Sam


On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Use mri_label2label with the --outmask option

On 7/8/2020 10:14 PM, Sam W wrote:


External Email - Use Caution

Hi,
Is there a way to convert a label file into a
surface/overlay? Thank you!
Best regards,
Sam

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[Freesurfer] Fwd: label to surface

[Sam W]

External Email - Use Caution

Hi!
Just pinging. Is there a way to get the surface+overlay file as mentioned
above using freesurfer? Thank you!
Best regards,
Sam


-- Forwarded message -
From: Sam W 
Date: Fri, Jul 10, 2020 at 9:05 PM
Subject: Re: [Freesurfer] label to surface
To: Freesurfer support list 


Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However
probtrackx requires a file that contains both the whole surface file (eg,
lh.pial) as well as the overlay (the scalar values associated with the
vertices of the roi).
I can create such a file with FSL's label2surf command which creates a
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running
probtrackx with the overlay from mri_label2label --outmask does not work.
It also needs the associated pial or white surface.
Best regards,
Sam


On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve 
wrote:

> what do you mean merge with the pial?
>
> On 7/9/2020 8:07 PM, Sam W wrote:
>
> External Email - Use Caution
> It works great Doug, thanks a lot!
> Can I ask you a follow up question please? I created the overlay with
> mri_label2label using --outmask as you suggested, but now I'd like to merge
> that overlay with the pial surface (lh.pial). Is there a tool I can use to
> achieve that result?
> Best regards,
> Sam
>
>
> On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve 
> wrote:
>
>> Use mri_label2label with the --outmask option
>>
>> On 7/8/2020 10:14 PM, Sam W wrote:
>>
>> External Email - Use Caution
>> Hi,
>> Is there a way to convert a label file into a surface/overlay? Thank you!
>> Best regards,
>> Sam
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/14Le9F02YSqeepBlENPo9ukq6i4TYc7zAHc-GwEnBTCPsLMW-ksg83S9TsBRlTTTfp41tpf009gzFnQ_H__V-4VIo_7E5lXSfrrsM_V9q8Xwy5nfXyAu1OV-ZHwwsvohy4LQk0ZHbtgAUlaj_l1Zxv2xxI4TqSGtD2iTjFEll2fSIZn3hEWtZEBkM_rv-hQscN6_6VLxq8XxTPuTbC_PdtEcuFJhEKdxlcqTzynCaRegvb68Zn54YpLBpqN8fc6_uLZQ_IiAUHwQow-_FmIiIDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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[Freesurfer] Fwd: SAMSEG longitudinal processing questions

[Douglas N. Greve]

Forwarding Stefano's answers...


 Forwarded Message 
Subject:Re: [Freesurfer] SAMSEG longitudinal processing questions
Date:   Thu, 28 Jan 2021 16:45:39 +
From:   Stefano Cerri 
To: Douglas N. Greve 
CC: Koen Van Leemput 



External Email - Use Caution


1) SAMSEG long should compute more consistent longitudinal structural 
volumes than SAMSEG while detecting better volumetric group differences 
(cf. Table 1 and Fig 3 of https://arxiv.org/pdf/2008.05117.pdf). Yes, 
using SBTIV for correcting volume changes from different scanners would 
be beneficial and most probably necessary.


2) The lesion version of SAMSEG long is available in the development 
version. Enabling the lesion extension can be done by adding the same 
flag(s) as for the cross-sectional lesion version (--lesion, see the 
Wiki for details: https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg)


3) We never conducted extensive experiments for the number of burn-in 
and samples for the MCMC scheme, but we found that 50 burn-in and 50 
samples lead to robust and replicable lesion segmentation results. 
Increasing these two numbers might increase the lesion segmentation 
performance, although differences might be minimal and the overall 
computational cost high. We suggest to not decrease these two numbers as 
lesion performance could potentially decrease.


Best,
Stefano




*From:* Douglas N. Greve 
*Sent:* 28 January 2021 16:30
*To:* Koen Van Leemput; Stefano Cerri
*Subject:* Fwd: [Freesurfer] SAMSEG longitudinal processing questions

 Forwarded Message 
Subject:[Freesurfer] SAMSEG longitudinal processing questions
Date:   Thu, 28 Jan 2021 09:37:32 -0500
From:   XY XY 
Reply-To:   Freesurfer support list 
To: freesurfer@nmr.mgh.harvard.edu



External Email - Use Caution
Hi FreeSurfers,

Thank you for sharing the new SAMSEG tool, which I consider a major 
breakthrough in image processing!

I have a few questions about using SAMSEG vs SAMSEG_Long:

1. What volumetric differences should I expect between running SAMSEG on 
individual images, vs. using SAMSEG_Long for the longitudinal analysis? 
Could I use SBTIV to adjust differences between scans?

(all images are FLAIRs preprocessed using mrI_robust_template)

2. Is there currently a way to integrate lesion segmentation into the 
SAMSEG_long’s longitudinal analysis?


3. What is the expected impact of increasing or decreasing -Burn-In and 
-Sample numbers for lesion segmentation?



Thank you for all the help!

Best,

Dave Kamson

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[Freesurfer] Fwd: Password for Virtual Machine {Disarmed}

[Miguel Hornero]

External Email - Use Caution

-- Forwarded message -
De: Miguel Hornero 
Date: lun, 14 dic 2020 a las 14:08
Subject: Password for Virtual Machine
To: 


Hi!I wanted to try out FreeSurfer and
followed the install guide from
https://secure-web.cisco.com/1aVjrKMkEJV_BmsbE4Zk5EdoFrDeZFRXS4LAWnl9PPwS1hVW7b5zKt4vDrcqS08Nj3qzguSc0AXKLgr_PtXRRtlSW7Dd472GdE5aC9dDdpev7SydOFv3y-Y9PrN4pPbm3anoJ3_QhxEowpVYxwbzNPbow_LFuoHXuyyBahX4vazb504mAb19EI0bMTLz5F1fgoP9_bgIHmrvZPosHI-1DVm4rkeAc0NI79ZKNf67vUcchj7c96yzepWvIGDz8EVTBR86D9DcAnXDZnQM9tjWiVw/https%3A%2F%2Fsurfer.nmr..mgh.harvard.edu%2Ffswiki%2FVM_67_win
 with the
linkedUbuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded
2020-12-14).However, upon startup of the virtual machine, the Ubuntu
installation asks me for my user credentials with a preselected
"developer" user (seescreenshot
attached). According to the install guide, the virtual machine should
just boot up to Desktop without requiring a password.Is there a
default password I am supposed to use (I tried leaving the password
field blank, "freesurfer", "FreeSurfer", "developer" but none of those
worked)

Thank you in advance,

Miguel
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Re: [Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

[Fischl, Bruce]

Hi Paul

Have you tried using the wmseg?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of miracle ozzoude
Sent: Wednesday, December 2, 2020 1:35 PM
To: Douglas N Greve 
Subject: [Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and 
centrum semiovale


External Email - Use Caution
Any help with this will be greatly appreciated.
Thanks.
-- Forwarded message -
From: miracle ozzoude mailto:miracoo...@gmail.com>>
Date: Fri, Nov 27, 2020 at 9:28 AM
Subject: extracting mask for basal ganglia, deep grey, and centrum semiovale
To: Douglas N Greve 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Hello Experts,

I did like to create a mask for basal ganglia, deep grey matter, and centrum 
semiovale. I know how to extract the mask for the first 2 (using aseg.mgz) 
however, how do I extract the last one. What mask should I use to extract the 
centrum semiovale? I don't want to include the cerebellar white matter.

Thanks.

Best,
Paul
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[Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

[miracle ozzoude]

External Email - Use Caution

Any help with this will be greatly appreciated.
Thanks.

-- Forwarded message -
From: miracle ozzoude 
Date: Fri, Nov 27, 2020 at 9:28 AM
Subject: extracting mask for basal ganglia, deep grey, and centrum semiovale
To: Douglas N Greve 


Hello Experts,

I did like to create a mask for basal ganglia, deep grey matter, and
centrum semiovale. I know how to extract the mask for the first 2 (using
aseg.mgz) however, how do I extract the last one. What mask should I use to
extract the centrum semiovale? I don't want to include the cerebellar white
matter.

Thanks.

Best,
Paul
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Re: [Freesurfer] Fwd: Issue with custom label

[Greve, Douglas N.,Ph.D.]

Try --i mri/aparc+aseg.mgz instead of --c

On 11/30/2020 7:28 PM, Catherine Tallman wrote:

External Email - Use Caution

Hello,

I was wondering if there were any updates on this question?

Thank you,
Catherine

-- Forwarded message -
From: Catherine Tallman mailto:ctall...@ucsd.edu>>
Date: Thu, Nov 19, 2020 at 8:57 AM
Subject: Issue with custom label
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello,

After running mri_vol2label I created a custom label named test.label. When I 
try to load the label onto lh.pial, I receive the following error: "Could not 
load label from ". The file is saved within the path folder itself. 
Within the terminal I receive the warning "label has not been mapped to 
surface". I was wondering what might be causing this issue? Attached is the 
label file.

mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.test.label

Thank you,
Catherine
--

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego


--

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego



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[Freesurfer] Fwd: Issue with custom label

[Catherine Tallman]

External Email - Use Caution

Hello,

I was wondering if there were any updates on this question?

Thank you,
Catherine

-- Forwarded message -
From: Catherine Tallman 
Date: Thu, Nov 19, 2020 at 8:57 AM
Subject: Issue with custom label
To: Freesurfer support list 


Hello,

After running mri_vol2label I created a custom label named test.label. When
I try to load the label onto lh.pial, I receive the following error: "Could
not load label from ". The file is saved within the path folder
itself. Within the terminal I receive the warning "label has not been
mapped to surface". I was wondering what might be causing this issue?
Attached is the label file.

mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.test.label

Thank you,
Catherine

-- 

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego


-- 

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego


test.label
Description: Binary data
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[Freesurfer] Fwd: Longitudinal pipeline

[vittal korann]

External Email - Use Caution

Hello FS experts

Thank you for your kind response.
This is regarding my previous mail.

I think we need to talk about the design matrix X first (sorry, I did not
look at your xlsx file; I think it's probably better to send simple csv
files if at all).
I attached longitudinal data in csv format.

Besides the covariates that you mention, the matrix needs to contain an
intercept, a variable for ?time?, a variable for ?group? (assuming you have
a control group also), and a group-by-time interaction term in order to
asses differential change over time (again, if you have a control group).
I do not have a control group. Right now I have only schizophrenia patients
who underwent 2 scans: the first is the baseline and the second one is
after 3 months of yoga therapy. Wish to know how can I proceed with my
available data.

Just to make sure: ?age? should be ?age at baseline? (i.e. constant across
time per subject), otherwise, it will be confounded with time.
Yes, I used the same across the study.

Could you review (and possibly adapt) your design matrix X with respect to
which columns it contains, and write it in the reply?
I tried but couldn't get there.

Looking forward to your response.

Thanks,
Vittal
fsid	fsid-base	years	Age	Years_of_education	Gender	ICV
SATM002	SATM002_LG	0	34	17	0	1567441.51469
SATM-002-2-PS-Structural.nii	SATM002_LG	0.2493	34	17	0	1567441.51469
SATM003	SATM003_LG	0	39	12	0	1295542.26469
SATM-003-NMR-2-Strctural.nii	SATM003_LG	0.2465	39	12	0	1295542.26469
SATM004	SATM004_LG	0	25	17	0	1450161.12103
SATM-004-M-2-Structural.nii	SATM004_LG	0.2794	25	17	0	1450161.12103
SATM005	SATM005_LG	0	32	15	0	1179683.61415
SATM-005-VRS-2-Structural.nii	SATM005_LG	0.2712	32	15	0	1179683.61415
SATM-007-DPN-2-Structural.nii	SATM007_LG	0	35	17	0	1440474.71762
SATM-007-DPN-3-Structural.nii	SATM007_LG	0.2301	35	17	0	1440474.71762
SATM009	SATM009_LG	0	41	15	1	1285164.31808
SATM-009-M-2-Structural.nii	SATM009_LG	0.3065	41	15	1	1285164.31808
SATM010	SATM010_LG	0	30	15	1	1220618.55741
SATM-010-S-2-Structural.nii	SATM010_LG	0.2493	30	15	1	1220618.55741
SATM-012-VR-1-Structural.nii	SATM012_LG	0	40	17	0	1469767.32763
SATM-012-VR-2-Structural.nii	SATM012_LG	0.241	40	17	0	1469767.32763
SATM-014-TNR-2-Structural.nii	SATM014_LG	0	27	12	1	1466066.7893
SATM-014-3-Structural.nii	SATM014_LG	0.2657	27	12	1	1466066.7893
SATM-015-K-1-Structural.nii	SATM015_LG	0	35	8	1	1435185.12278
SATM-015-2-Structural.nii	SATM015_LG	0.4246	35	8	1	1435185.12278
SATM-016-1-Structural.nii	SATM016_LG	0	41	15	1	1266770.55794
SATM-017-RP-1-Structural.nii	SATM017_LG	0	31	17	1	1324830.23846
SATM-018-TS-1-Structural.nii	SATM018_LG	0	25	15	1	1316362.99533
SATM-018-TS-2-Structural.nii	SATM018_LG	0.3945	25	15	1	1316362.99533
SATM-019-2-Structural.nii	SATM019_LG	0	25	17	0	1750898.15
SATM-019-3-AR-Structural.nii	SATM019_LG	0.2274	25	17	0	1750898.15
SATM020	SATM020_LG	0	40	10	0	1247960.37357
SATM-021-1-Structural.nii	SATM021_LG	0	37	15	0	1357985.77226
SATM-021-2-RKS-Structural.nii	SATM021_LG	0.2301	37	15	0	1357985.77226
SATM-022-1-Structural.nii	SATM022_LG	0	26	12	0	1531212.64485
SATM-022-2-Structural.nii	SATM022_LG	0.2603	26	12	0	1531212.64485
SATM025	SATM025_LG	0	31	14	0	1308825.22921
SATM-025-2-Structural.nii	SATM025_LG	0.326	31	14	0	1308825.22921
SATM026-1	SATM026_LG	0	31	14	1	1206803.63083
SATM-026-2-AS-Structural.nii	SATM026_LG	0.2712	31	14	1	1206803.63083
SATM027	SATM027_LG	0	44	14	0	1220690.03978
SATM-027-2-Structural.nii	SATM027_LG	0.2685	44	14	0	1220690.03978
SATM028	SATM028_LG	0	22	10	0	1269044.33237
SATM029	SATM029_LG	0	39	12	0	1428819.02641
SATM030-1	SATM030_LG	0	23	12	0	1402325.35666
SATM030-2	SATM030_LG	0.3671	23	12	0	1402325.35666
SATM032-1	SATM032_LG	0	27	12	1	1272099.28885
SATM032-2	SATM032_LG	0.3205	27	12	1	1272099.28885
SATM033-2	SATM033_LG	0	27	15	1	1404410.98645
SATM033-3	SATM033_LG	0.3342	27	15	1	1404410.98645
SATM036-1	SATM036_LG	0	33	12	0	1327686.87066
SATM036-2	SATM036_LG	0.2603	33	12	0	1327686.87066

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[Freesurfer] Fwd: Error in longitudinal pipeline {Disarmed}

[vittal korann]

External Email - Use Caution

-- Forwarded message -
From: vittal korann 
Date: Tue, Nov 17, 2020 at 1:16 PM
Subject: Error in longitudinal pipeline
To: 


Hi FreeSurfer experts

Recently I started working on the longitudinal data.
I followed the pipeline described in the below link.
Also, I attached my longitudinal table along with freesurfer data.

https://secure-web.cisco.com/1tkYny6yViIok4HHSJ4fdMQL186SjX1A72s5pbjDlpttjtAFE-0v8RFBy_Lk2cKKs4MGT9RFKv5HsAu_7F8jM2TtWaxqsyoMQW-CTzq3bhcMd-7Wo2S3eNWwTudolPJ-_WhLmM5DVNO_0ULMkb1h-pHwkm8fwNvCyLDEyh7IHl2De94ETqs1YrtsWn7VrIdDRrcbsCTnG4tUkpn5RdBwzkgouQ6YY06qwKUlG7AaN5jsrJRE5-yYMXoqWijHvYICv-yhXkkpuox_SkoU4u-4lcA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels

I got the error while executing the following commands:

CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];

F_lhstats = lme_mass_F(lhstats,CM);

And the Matlab threw an error shown below

>> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1]
> zeros(3,5)];
> >> F_lhstats = lme_mass_F(lhstats,CM);
> Error using lme_mass_F (line 50)
> The number of colums in the contrast matrix CM(1).C is different from the
> corresponding number of fixed effects in stats(1).Bhat


Any help would be appreciated!

With regards
Korann


long.qdec.table.dat.xlsx
Description: MS-Excel 2007 spreadsheet
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[Freesurfer] Fwd: Error in longitudinal pipeline {Disarmed}

[vittal korann]

External Email - Use Caution

Hi FreeSurfer experts

Recently I started working on the longitudinal data.
I followed the pipeline described in the below link.
Also, I attached my longitudinal table along with freesurfer data.

https://secure-web.cisco.com/10GeKQWbNwmdQQgtn3lkt2V_V6CbZVv7dzOuHKANAfbzRAGomTtlFNhDzA4pY4ZQuLB5OKutRoWZmuTIiRZq8s8dHrF_8jP9_YwiAcYhWc2_nJ1F7j6KtRcLuBUeRd8AEwLty9yAMeJlyYLagWgXBRfs9aYywbcF4h7qbXbfe1Fp6tkTjAhKB7KqEvstqt7f-PV9c2yCvmZdmgnQTe8ZOr5036aKU2v0XgzyYpMep8-97LMopdyYsudhNkLZFuWdv82PEMhJPNLAupP3KrdD04Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels

I got the error while executing the following commands:

CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];

F_lhstats = lme_mass_F(lhstats,CM);

And the Matlab threw an error shown below

>> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1]
> zeros(3,5)];
> >> F_lhstats = lme_mass_F(lhstats,CM);
> Error using lme_mass_F (line 50)
> The number of colums in the contrast matrix CM(1).C is different from the
> corresponding number of fixed effects in stats(1).Bhat


Any help would be appreciated!

With regards
Korann


long.qdec.table.dat.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}

[Douglas N. Greve]

The caudate segmentation would not affect the surface placement. Is the 
surface placement ok? Can you send a pic of the caudate error?


On 11/6/2020 9:58 AM, Donatienne Van Weehaeghe wrote:


External Email - Use Caution

Dear,

Would there be another option to fix this?

Kind regards
Donatienne


Op do 5 nov. 2020 om 17:38 schreef Donatienne Van Weehaeghe 
>:


The subcortical structures were not delineated correctly,
especially the nucleus caudatus which had a lot of atrophy in this
particular patient group.

Kind regards
Donatienne

Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>:

I don't think CAT creates white or pial surfaces, so no. What
is wrong with your FS analysis?

On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote:


External Email - Use Caution

Dear,

The segmentation using Freesurfer was incorrect, however we
have a good segmentation from Cat 12. Can we use this
segmentation for PVC in PETsurfer?

Kind regards
Donatienne

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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}

[Donatienne Van Weehaeghe]

External Email - Use Caution

Dear,

Would there be another option to fix this?

Kind regards
Donatienne


Op do 5 nov. 2020 om 17:38 schreef Donatienne Van Weehaeghe <
donatiennevanweehae...@gmail.com>:

> The subcortical structures were not delineated correctly, especially the
> nucleus caudatus which had a lot of atrophy in this particular patient
> group.
>
> Kind regards
> Donatienne
>
> Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve <
> dgr...@mgh.harvard.edu>:
>
>> I don't think CAT creates white or pial surfaces, so no. What is wrong
>> with your FS analysis?
>>
>> On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote:
>>
>> External Email - Use Caution
>> Dear,
>>
>> The segmentation using Freesurfer was incorrect, however we have a good
>> segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer?
>>
>> Kind regards
>> Donatienne
>>
>> ___
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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}

[Donatienne Van Weehaeghe]

External Email - Use Caution

The subcortical structures were not delineated correctly, especially the
nucleus caudatus which had a lot of atrophy in this particular patient
group.

Kind regards
Donatienne

Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve :

> I don't think CAT creates white or pial surfaces, so no. What is wrong
> with your FS analysis?
>
> On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
> Dear,
>
> The segmentation using Freesurfer was incorrect, however we have a good
> segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer?
>
> Kind regards
> Donatienne
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC

[Douglas N. Greve]

I don't think CAT creates white or pial surfaces, so no. What is wrong 
with your FS analysis?


On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote:


External Email - Use Caution

Dear,

The segmentation using Freesurfer was incorrect, however we have a 
good segmentation from Cat 12. Can we use this segmentation for PVC in 
PETsurfer?


Kind regards
Donatienne

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[Freesurfer] Fwd: using CAT12 segmentation for PVC

[Donatienne Van Weehaeghe]

External Email - Use Caution

Dear,

The segmentation using Freesurfer was incorrect, however we have a good
segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer?

Kind regards
Donatienne
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[Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list {Disarmed}

[Nicholas BH NG (NUHS)]

External Email - Use Caution

Dear Free Surfer

I followed the excellent video step by step instructions. At the last part of 
putting the code/ key into the terminal, I encountered the error message as 
below: no such file or directory. As such I think my set up was not complete.

Kindly advice.

Thank you
Nicholas

Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or 
directory
Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or 
directory
Nicholass-MacBook-Pro:~ Nic$




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Date: 5 November 2020 at 11:56:45 AM SGT
To: mailto:nicholas_bh...@nuhs.edu.sg>>

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Re: [Freesurfer] Fwd: Freesurfer edits

[Douglas N. Greve]

It looks like the image darkens a lot at the top. Try putting control 
points in the WWM near the start of the gyrus. make sure they are truly 
in WM!


On 10/25/2020 9:03 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Any comments from FS users to best best tackle these manual edits?

Jim

Get Outlook for Android 


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, 
Dimitrios 

*Sent:* Tuesday, October 20, 2020, 10:25 AM
*To:* Freesurfer support list
*Subject:* [Freesurfer] Freesurfer edits

** External Email - Caution **

External Email - Use Caution

Hi freesurfer editing experts.

Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old 
run through FS 7.1.1


I’m hoping for feedback on the best way to make the relevant edits to 
the three blue-circled regions.


1.In the superior regions I think control points will help to pick up 
some WM to help fuill


2.In the left hemisphere medial prefrontal (gyrus rectus) regions, the 
WM is overestimated. I presume removing WM voxels from the wm.mgz is 
the best approach?


3.The left temporal pole region is missing GM/cortex and there really 
isn’t any WM that would help with controls points or adding WM voxels. 
How can I add GM to this area?




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[Freesurfer] Fwd: Freesurfer edits

[Alexopoulos, Dimitrios]

External Email - Use Caution

Any comments from FS users to best best tackle these manual edits?

Jim

Get Outlook for Android


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Tuesday, October 20, 2020, 10:25 AM
To: Freesurfer support list
Subject: [Freesurfer] Freesurfer edits

* External Email - Caution *

External Email - Use Caution
Hi freesurfer editing experts.

Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run 
through FS 7.1.1
I’m hoping for feedback on the best way to make the relevant edits to the three 
blue-circled regions.


1.   In the superior regions I think control points will help to pick up 
some WM to help fuill

2.   In the left hemisphere medial prefrontal (gyrus rectus) regions, the 
WM is overestimated. I presume removing WM voxels from the wm.mgz is the best 
approach?

3.   The left temporal pole region is missing GM/cortex and there really 
isn’t any WM that would help with controls points or adding WM voxels. How can 
I add GM to this area?

[cid:image007.jpg@01D6A6CB.3399D5E0][cid:image008.jpg@01D6A6CB.3399D5E0]


[cid:image009.jpg@01D6A6CB.3399D5E0][cid:image010.jpg@01D6A6CB.3399D5E0]




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Information or other information of a sensitive nature. If you are not the 
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Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Douglas N. Greve]

Yes, that is correct

On 9/30/2020 3:12 PM, Martin Juneja wrote:


External Email - Use Caution

Dear Doug,


*--sumwf * seems to work fine - it gives subjectwise values and values 
seems of to be of volume:



11262.26605
 9294.07182
12673.14610
12601.33416
11141.31917






Whenever you get a chance, could you please confirm if --sumwf is the 
correct flag here?



Thanks.



On Wed, Sep 30, 2020 at 1:04 PM Martin Juneja > wrote:


Dear Doug,

Yes, that gives me subjectwise values if I run the following
command, but now the output doesn't seem to be the volume values,
it gives very small subjectwise values as following:

mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0
--i lh.HC_GAD.vol.10.mgh --accumulate --avgwf volumesum1.table


Output:
    1.49360
    1.71227
    1.84950
    1.58922
    1.98355
    1.49314
    1.37157
    1.77108
    1.87064
    2.08438
    1.87076
    1.61026
    2.42607
    1.69756
    1.65158
    1.61560

On Wed, Sep 30, 2020 at 12:58 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Use the --avgwf output.table instead of --sum

On 9/30/2020 1:48 PM, Martin Juneja wrote:


External Email - Use Caution

Dear Doug,

Thanks for your response. I created a binary mask and ran the
following command, but the output gives me only one value of
volume as follows. I was wondering how I can extract the
values for each subject.

mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid
0 --i lh.HC_GAD.vol.10.mgh --accumulate --sum volumesum.dat



.

.

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean
StdDev Min Max Range
  1   1      6126     6126.0  Seg0001 11262.2666   0.5353    
0.9159     3.4016     2.4857

On Wed, Sep 30, 2020 at 9:17 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

If you have a binary mask or cluster mask, you can use
mri_segstats, like
mri_segstats --seg binary-or-clustermask.mgz --excludeid
0 --i volumestack.mgz --accumulate --sum volumesum.dat
where volumestack.mgz is a stack of the subjects volume
(eg, created by mris_preproc)


On 9/29/2020 1:32 PM, Martin Juneja wrote:


External Email - Use Caution

Dear Doug and FreeSurfer team,

Any help with this on an urgent basis would be really
appreciated. Sorry for being a little impatient :(.
Thank you so much !

-- Forwarded message -
From: *Martin Juneja* mailto:mj70...@gmail.com>>
Date: Mon, Sep 28, 2020 at 5:42 PM
Subject: Extraction of subject-wise values after
permutation test !
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello everyone,

I have significant group differences in volume (controls
> patients) for one of the clusters (say C1) -
calculated after permutation test using PALM, which
gives me following outputs:

*_clustere_tstat_fwep.mgz (this is significant at p <
0.05, number of voxels = 1105)
*_clustere_tstat.mgz
*_dpv_tstat_fwep.mgz
*_dpv_tstat_uncp.mgz
*_dpv_tstat.mgz

I was wondering if there is a way to calculate volume
values of C1 for each subject (i.e., controls and patients).

Thanks.

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Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Martin Juneja]

External Email - Use Caution

Dear Doug,


*--sumwf * seems to work fine - it gives subjectwise values and values
seems of to be of volume:


11262.26605
 9294.07182
12673.14610
12601.33416
11141.31917






Whenever you get a chance, could you please confirm if --sumwf is the
correct flag here?


Thanks.



On Wed, Sep 30, 2020 at 1:04 PM Martin Juneja  wrote:

> Dear Doug,
>
> Yes, that gives me subjectwise values if I run the following command, but
> now the output doesn't seem to be the volume values, it gives very small
> subjectwise values as following:
>
> mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i
> lh.HC_GAD.vol.10.mgh --accumulate --avgwf volumesum1.table
>
> Output:
> 1.49360
> 1.71227
> 1.84950
> 1.58922
> 1.98355
> 1.49314
> 1.37157
> 1.77108
> 1.87064
> 2.08438
> 1.87076
> 1.61026
> 2.42607
> 1.69756
> 1.65158
> 1.61560
>
> On Wed, Sep 30, 2020 at 12:58 PM Douglas N. Greve 
> wrote:
>
>> Use the --avgwf output.table instead of --sum
>>
>> On 9/30/2020 1:48 PM, Martin Juneja wrote:
>>
>> External Email - Use Caution
>> Dear Doug,
>>
>> Thanks for your response. I created a binary mask and ran the following
>> command, but the output gives me only one value of volume as follows. I was
>> wondering how I can extract the values for each subject.
>>
>> mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i
>> lh.HC_GAD.vol.10.mgh --accumulate --sum volumesum.dat
>>
>>
>>
>> .
>>
>> .
>> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min
>> Max Range
>>   1   1  6126 6126.0  Seg0001 11262.2666 0.5353 0.9159
>>   3.4016 2.4857
>>
>> On Wed, Sep 30, 2020 at 9:17 AM Douglas N. Greve 
>> wrote:
>>
>>> If you have a binary mask or cluster mask, you can use mri_segstats, like
>>> mri_segstats --seg binary-or-clustermask.mgz --excludeid 0 --i
>>> volumestack.mgz --accumulate --sum volumesum.dat
>>> where volumestack.mgz is a stack of the subjects volume (eg, created by
>>> mris_preproc)
>>>
>>>
>>> On 9/29/2020 1:32 PM, Martin Juneja wrote:
>>>
>>> External Email - Use Caution
>>> Dear Doug and FreeSurfer team,
>>>
>>> Any help with this on an urgent basis would be really appreciated. Sorry
>>> for being a little impatient :(.
>>> Thank you so much !
>>>
>>> -- Forwarded message -
>>> From: Martin Juneja 
>>> Date: Mon, Sep 28, 2020 at 5:42 PM
>>> Subject: Extraction of subject-wise values after permutation test !
>>> To: Freesurfer support list 
>>>
>>>
>>> Hello everyone,
>>>
>>> I have significant group differences in volume (controls > patients) for
>>> one of the clusters (say C1) - calculated after permutation test using
>>> PALM, which gives me following outputs:
>>>
>>> *_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of
>>> voxels = 1105)
>>> *_clustere_tstat.mgz
>>> *_dpv_tstat_fwep.mgz
>>> *_dpv_tstat_uncp.mgz
>>> *_dpv_tstat.mgz
>>>
>>> I was wondering if there is a way to calculate volume values of C1 for
>>> each subject (i.e., controls and patients).
>>>
>>> Thanks.
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>>
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>>
>>
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Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Martin Juneja]

External Email - Use Caution

Dear Doug,

Yes, that gives me subjectwise values if I run the following command, but
now the output doesn't seem to be the volume values, it gives very small
subjectwise values as following:

mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i
lh.HC_GAD.vol.10.mgh --accumulate --avgwf volumesum1.table

Output:
1.49360
1.71227
1.84950
1.58922
1.98355
1.49314
1.37157
1.77108
1.87064
2.08438
1.87076
1.61026
2.42607
1.69756
1.65158
1.61560

On Wed, Sep 30, 2020 at 12:58 PM Douglas N. Greve 
wrote:

> Use the --avgwf output.table instead of --sum
>
> On 9/30/2020 1:48 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear Doug,
>
> Thanks for your response. I created a binary mask and ran the following
> command, but the output gives me only one value of volume as follows. I was
> wondering how I can extract the values for each subject.
>
> mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i
> lh.HC_GAD.vol.10.mgh --accumulate --sum volumesum.dat
>
>
>
> .
>
> .
> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min
> Max Range
>   1   1  6126 6126.0  Seg0001 11262.2666 0.5353 0.9159
> 3.4016 2.4857
>
> On Wed, Sep 30, 2020 at 9:17 AM Douglas N. Greve 
> wrote:
>
>> If you have a binary mask or cluster mask, you can use mri_segstats, like
>> mri_segstats --seg binary-or-clustermask.mgz --excludeid 0 --i
>> volumestack.mgz --accumulate --sum volumesum.dat
>> where volumestack.mgz is a stack of the subjects volume (eg, created by
>> mris_preproc)
>>
>>
>> On 9/29/2020 1:32 PM, Martin Juneja wrote:
>>
>> External Email - Use Caution
>> Dear Doug and FreeSurfer team,
>>
>> Any help with this on an urgent basis would be really appreciated. Sorry
>> for being a little impatient :(.
>> Thank you so much !
>>
>> -- Forwarded message -
>> From: Martin Juneja 
>> Date: Mon, Sep 28, 2020 at 5:42 PM
>> Subject: Extraction of subject-wise values after permutation test !
>> To: Freesurfer support list 
>>
>>
>> Hello everyone,
>>
>> I have significant group differences in volume (controls > patients) for
>> one of the clusters (say C1) - calculated after permutation test using
>> PALM, which gives me following outputs:
>>
>> *_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of
>> voxels = 1105)
>> *_clustere_tstat.mgz
>> *_dpv_tstat_fwep.mgz
>> *_dpv_tstat_uncp.mgz
>> *_dpv_tstat.mgz
>>
>> I was wondering if there is a way to calculate volume values of C1 for
>> each subject (i.e., controls and patients).
>>
>> Thanks.
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Douglas N. Greve]

Use the --avgwf output.table instead of --sum

On 9/30/2020 1:48 PM, Martin Juneja wrote:


External Email - Use Caution

Dear Doug,

Thanks for your response. I created a binary mask and ran the 
following command, but the output gives me only one value of volume as 
follows. I was wondering how I can extract the values for each subject.


mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i 
lh.HC_GAD.vol.10.mgh --accumulate --sum volumesum.dat




.

.

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   1      6126     6126.0  Seg0001 11262.2666     0.5353   0.9159   
  3.4016     2.4857


On Wed, Sep 30, 2020 at 9:17 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


If you have a binary mask or cluster mask, you can use
mri_segstats, like
mri_segstats --seg binary-or-clustermask.mgz --excludeid 0 --i
volumestack.mgz --accumulate --sum volumesum.dat
where volumestack.mgz is a stack of the subjects volume (eg,
created by mris_preproc)


On 9/29/2020 1:32 PM, Martin Juneja wrote:


External Email - Use Caution

Dear Doug and FreeSurfer team,

Any help with this on an urgent basis would be really
appreciated. Sorry for being a little impatient :(.
Thank you so much !

-- Forwarded message -
From: *Martin Juneja* mailto:mj70...@gmail.com>>
Date: Mon, Sep 28, 2020 at 5:42 PM
Subject: Extraction of subject-wise values after permutation test !
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello everyone,

I have significant group differences in volume (controls >
patients) for one of the clusters (say C1) - calculated after
permutation test using PALM, which gives me following outputs:

*_clustere_tstat_fwep.mgz (this is significant at p < 0.05,
number of voxels = 1105)
*_clustere_tstat.mgz
*_dpv_tstat_fwep.mgz
*_dpv_tstat_uncp.mgz
*_dpv_tstat.mgz

I was wondering if there is a way to calculate volume values of
C1 for each subject (i.e., controls and patients).

Thanks.

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Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Martin Juneja]

External Email - Use Caution

Dear Doug,

Thanks for your response. I created a binary mask and ran the following
command, but the output gives me only one value of volume as follows. I was
wondering how I can extract the values for each subject.

mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i
lh.HC_GAD.vol.10.mgh --accumulate --sum volumesum.dat



.

.
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
  1   1  6126 6126.0  Seg0001 11262.2666 0.5353 0.9159
3.4016 2.4857

On Wed, Sep 30, 2020 at 9:17 AM Douglas N. Greve 
wrote:

> If you have a binary mask or cluster mask, you can use mri_segstats, like
> mri_segstats --seg binary-or-clustermask.mgz --excludeid 0 --i
> volumestack.mgz --accumulate --sum volumesum.dat
> where volumestack.mgz is a stack of the subjects volume (eg, created by
> mris_preproc)
>
>
> On 9/29/2020 1:32 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear Doug and FreeSurfer team,
>
> Any help with this on an urgent basis would be really appreciated. Sorry
> for being a little impatient :(.
> Thank you so much !
>
> -- Forwarded message -
> From: Martin Juneja 
> Date: Mon, Sep 28, 2020 at 5:42 PM
> Subject: Extraction of subject-wise values after permutation test !
> To: Freesurfer support list 
>
>
> Hello everyone,
>
> I have significant group differences in volume (controls > patients) for
> one of the clusters (say C1) - calculated after permutation test using
> PALM, which gives me following outputs:
>
> *_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of
> voxels = 1105)
> *_clustere_tstat.mgz
> *_dpv_tstat_fwep.mgz
> *_dpv_tstat_uncp.mgz
> *_dpv_tstat.mgz
>
> I was wondering if there is a way to calculate volume values of C1 for
> each subject (i.e., controls and patients).
>
> Thanks.
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Douglas N. Greve]

If you have a binary mask or cluster mask, you can use mri_segstats, like
mri_segstats --seg binary-or-clustermask.mgz --excludeid 0 --i 
volumestack.mgz --accumulate --sum volumesum.dat
where volumestack.mgz is a stack of the subjects volume (eg, created by 
mris_preproc)



On 9/29/2020 1:32 PM, Martin Juneja wrote:


External Email - Use Caution

Dear Doug and FreeSurfer team,

Any help with this on an urgent basis would be really appreciated. 
Sorry for being a little impatient :(.

Thank you so much !

-- Forwarded message -
From: *Martin Juneja* mailto:mj70...@gmail.com>>
Date: Mon, Sep 28, 2020 at 5:42 PM
Subject: Extraction of subject-wise values after permutation test !
To: Freesurfer support list >



Hello everyone,

I have significant group differences in volume (controls > patients) 
for one of the clusters (say C1) - calculated after permutation test 
using PALM, which gives me following outputs:


*_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of 
voxels = 1105)

*_clustere_tstat.mgz
*_dpv_tstat_fwep.mgz
*_dpv_tstat_uncp.mgz
*_dpv_tstat.mgz

I was wondering if there is a way to calculate volume values of C1 for 
each subject (i.e., controls and patients).


Thanks.

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[Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

[Martin Juneja]

External Email - Use Caution

Dear Doug and FreeSurfer team,

Any help with this on an urgent basis would be really appreciated. Sorry
for being a little impatient :(.
Thank you so much !

-- Forwarded message -
From: Martin Juneja 
Date: Mon, Sep 28, 2020 at 5:42 PM
Subject: Extraction of subject-wise values after permutation test !
To: Freesurfer support list 


Hello everyone,

I have significant group differences in volume (controls > patients) for
one of the clusters (say C1) - calculated after permutation test using
PALM, which gives me following outputs:

*_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of
voxels = 1105)
*_clustere_tstat.mgz
*_dpv_tstat_fwep.mgz
*_dpv_tstat_uncp.mgz
*_dpv_tstat.mgz

I was wondering if there is a way to calculate volume values of C1 for each
subject (i.e., controls and patients).

Thanks.
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Re: [Freesurfer] Fwd: non-white matter hypointensity

[L]

External Email - Use Caution

Thank you so much for the response from both of you. I guess I should
upload the  T1 brain image in fsaverage to show the hypointensity spots?

Best,

Lihong





On Fri, Sep 18, 2020 at 11:35 AM Douglas N. Greve 
wrote:

> I think these usually show up in putamen/pallidum, in which case they are
> probably mineralization, a virchow-robin space, or maybe a subcortical
> stroke.
>
> On 9/18/2020 11:28 AM, L wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
>
>
> I am wondering what the non-white matter hypointensity refers to. Does it
> refer to hypointensity in subcortical regions or all brain regions except
> white matter? When we do data analysis using volume results from ROI
> tables, we found a greater volume of non-wm hypointensity in depressed
> subjects with- than without high vascular risk factors. However, I am not
> sure where the non-white matter hypointensity ROI covers, and it is
> possible to visually display the non-wm hypointensity regions in freeview?
>
>
> Appreciate your guidance in advance.
>
>
> Lihong
>
>
>
> ___
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>
>
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Re: [Freesurfer] Fwd: non-white matter hypointensity

[Fischl, Bruce]

Yes, they are typically in gray matter, although I’m not sure we see them very 
often (sometimes in the basal ganglia I think)


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of L
Sent: Friday, September 18, 2020 11:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: non-white matter hypointensity


External Email - Use Caution
Dear experts,

I am wondering what the non-white matter hypointensity refers to. Does it refer 
to hypointensity in subcortical regions or all brain regions except white 
matter? When we do data analysis using volume results from ROI tables, we found 
a greater volume of non-wm hypointensity in depressed subjects with- than 
without high vascular risk factors. However, I am not sure where the non-white 
matter hypointensity ROI covers, and it is possible to visually display the 
non-wm hypointensity regions in freeview?

Appreciate your guidance in advance.

Lihong

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Re: [Freesurfer] Fwd: non-white matter hypointensity

[Douglas N. Greve]

I think these usually show up in putamen/pallidum, in which case they 
are probably mineralization, a virchow-robin space, or maybe a 
subcortical stroke.


On 9/18/2020 11:28 AM, L wrote:


External Email - Use Caution

Dear experts,

I am wondering what the non-white matter hypointensity refers to. Does 
it refer to hypointensity in subcortical regions or all brain regions 
except white matter? When we do data analysis using volume results 
from ROI tables, we found a greater volume of non-wm hypointensity in 
depressed subjects with- than without high vascular risk factors. 
However, I am not sure where the non-white matter hypointensity ROI 
covers, and it is possible to visually display the non-wm 
hypointensity regions in freeview?



Appreciate your guidance in advance.


Lihong



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[Freesurfer] Fwd: non-white matter hypointensity

[L]

External Email - Use Caution

Dear experts,



I am wondering what the non-white matter hypointensity refers to. Does it
refer to hypointensity in subcortical regions or all brain regions except
white matter? When we do data analysis using volume results from ROI
tables, we found a greater volume of non-wm hypointensity in depressed
subjects with- than without high vascular risk factors. However, I am not
sure where the non-white matter hypointensity ROI covers, and it is
possible to visually display the non-wm hypointensity regions in freeview?


Appreciate your guidance in advance.


Lihong
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Re: [Freesurfer] Fwd: Whole Thalamus Volume

[Iglesias Gonzalez, Juan E.]

They’re different  modules with different algorithms, which give different yet 
very highly correlated results. So, whatever you use the volumes for further 
down the stream, the results should be very similar with either version.
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Al Qadi, Ameen" 

Reply-To: Freesurfer support list 
Date: Monday, September 7, 2020 at 14:37
To: "Fischl, Bruce" , Freesurfer support list 

Subject: [Freesurfer] Fwd: Whole Thalamus Volume


External Email - Use Caution

-- Forwarded message -
From: Al Qadi, Ameen 
mailto:ameen.alq...@icahn.mssm.edu>>
Date: Fri, Sep 4, 2020 at 6:09 PM
Subject: Whole Thalamus Volume
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Dear Freesurfer Developers,

I noticed a significant disparity in the left and right whole thalamus volumes 
between aseg.stats generated from recon-all and 
ThalamicNuclei.v12.T1.volumes.txt generated from the thalamic nuclei 
segmentation. Which set of volumes is the correct one to use?

Best,
Ameen

--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu<mailto:ameen.alq...@icahn.mssm.edu>


--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu<mailto:ameen.alq...@icahn.mssm.edu>
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[Freesurfer] Fwd: Whole Thalamus Volume

[Al Qadi, Ameen]

External Email - Use Caution

-- Forwarded message -
From: Al Qadi, Ameen 
Date: Fri, Sep 4, 2020 at 6:09 PM
Subject: Whole Thalamus Volume
To: Freesurfer support list 


Dear Freesurfer Developers,

I noticed a significant disparity in the left and right whole thalamus
volumes between *aseg.stats *generated from recon-all and
*ThalamicNuclei.v12.T1.volumes.txt
*generated from the thalamic nuclei segmentation. Which set of volumes is
the correct one to use?

Best,
Ameen

-- 
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu


-- 
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu
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[Freesurfer] Fwd: using own skull stripped t1

[Julie Ottoy]

External Email - Use Caution

Hi Freesurfer team

I was wondering if you’d have some time to take a look at question below.
Thanks!

-- Forwarded message -
From: Julie Ottoy 
Date: Thu, 30 Jul 2020 at 13:22
Subject: using own skull stripped t1
To: Freesurfer support list 


Dear freesurfer team

I'm trying to use my own skull stripped T1 when running recon-all. For
this, I'm doing following steps:
1) run recon-all with -autorecon-1 -noskullstrip
2) mri_convert --in_type nii --out_type mgz -rl
./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz
./FreeSurfer/ID/mri/brainmask.mgz
3) run recon-all with -autorecon-2 and autorecon-3

My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore,
when transforming to the size of brainmask.mgz (256x256x256), it deforms. I
tried nearest, cubic, and interpolate, but none of them gives actually a
good result in terms of retaining the contrast. I was wondering if it is
important to keep a good contrast for brainmask.mgz , or whether this
brainmask.mgz is just used to determine the brain borders for segmentation.
(ie.: in which steps of recon-all is the brainmask.mgz actually used?)

Any recommendations?

Thank you!
Julie
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Re: [Freesurfer] Fwd: Re: Segmentation with FreeSurfer 7.1

[Douglas N. Greve]

Here is the page on topo defects
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefectV6.0

I can't answer your other questions because the previous emails are not 
in this one. If you repost with previous correspondance, then I can answer.


On 7/24/2020 8:12 AM, Sara PONTICORVO wrote:


External Email - Use Caution

Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1
Message-ID >



Hi, thanks a lot.
What do you mean for topological default?
We have checked our data, and there aren't any visible artifacts (if 
you were referring to this kind of things). Actually we have seen 
these problems in about 50% of the already acquired data.
If it can be useful for you we can also send you the raw DICOM images 
to check yourself.
It is possible that there are some default settings in the 7.1 
recon-all pipeline that we can adjust?


Thanks again,
Sara


--
Sara Ponticorvo
PhD Student
Departement of Medicine Surgery and Dentistry, University of Salerno

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[Freesurfer] Fwd: Re: Segmentation with FreeSurfer 7.1

[Sara PONTICORVO]

External Email - Use Caution

Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1
Message-ID 


Hi, thanks a lot.
What do you mean for topological default?
We have checked our data, and there aren't any visible artifacts (if you
were referring to this kind of things). Actually we have seen these
problems in about 50% of the already acquired data.
If it can be useful for you we can also send you the raw DICOM images to
check yourself.
It is possible that there are some default settings in the 7.1 recon-all
pipeline that we can adjust?

Thanks again,
Sara


-- 
Sara Ponticorvo
PhD Student
Departement of Medicine Surgery and Dentistry, University of Salerno
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