[Freesurfer] surface labels to volume masks in MNI space

[Alvarado,Luis R]

External Email - Use Caution

Hi all,

I am having a bit of a hard time figuring out the best option to convert 
surface labels to mni volume masks.

For my ROI FS analysis, I divided the fsaverage S1 and M1 labels into 5 
sub-labels using mris_divide_parcellation. I then used mri_label2label to map 
those labels to each of my subjects to study differences in thickness among 2 
groups.

I am now trying to map those same labels from fsaverage to mni space in order 
to use them as ROI for resting-state connectivity analysis in the conn toolbox 
pipeline. From reading The Mail Archive I have come across multiple pieces of 
advice on how one might go about doing this. These range from a) using 
mri_label2vol and mri_vol2vol; b) creating a new annotation file for fsaverage 
from the labels and using mri_aparc2aseg and then mri_vol2vol; to c) running 
mni152 through recon-all.

As you can probably tell by now, I am a bit confused about the most efficient 
and accurate way to accomplish this.

any advice would be greatly appreciated.

Luis R. Alvarado

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Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found

[Alvarado,Luis R]

External Email - Use Caution

Hi all,

Just a follow-up to report how to fix this issue.

  1.  I uninstalled my 7.2.0 tar installation
  2.  Updated my system using:
 *   sudo apt-get update && sudo apt-get upgrade && sudo apt-get 
dist-upgrade
sudo apt-get install -f
  3.  Installed xorg-dev following the isntructions from 
https://secure-web.cisco.com/1uyxJZhlPnPOIdA9nned9bq583KtYUcWz7KlVedz6uYOyn6vSVW5tygAWrdinPxsDoDzp8UEdJDRPaBtNhy8mzJ0GheEYiKH3BW5trqBwwOZ9N2u4DlUTyARL5ZfdofvF0z4GuZh_TKWP3L3rWMfsaYkrAkNEnYkggaqmNm9HczuCH4hwBt54nDSgWVbrWcTjCQl1dZfuKvQ60CuTOwbBZCHy1fkXiFtrHpr14mSCINzAFrs71YHmP4vG-tApSdSZEG-iRnkGkdP8iopbvCjMIg/https%3A%2F%2Fzoomadmin.com%2FHowToInstall%2FUbuntuPackage%2Fxorg-dev
 *   sudo apt-get update -y
sudo apt-get install -y xorg-dev
  4.  Reinstalled 7.2.0 following the instructions from fsbuild using the 
freesurfer_7.2.0_amd64.deb file.

This seems to have fixed the issue. I can now run FS binaries like mri_vol2vol 
and mri_aparc2aseg.

Best,

Luis

____
From: Alvarado,Luis R 
Sent: Tuesday, November 2, 2021 3:23 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: 
version `XCRYPT_2.0' not found


Thank you for the fast response.


I had a typo in my original message. when I said 7.1.2, I really meant 7.2. I 
originally installed it using the freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz 
archive file.  The issue with the binaries was with 7.2.0.


I uninstalled that version and I am trying to re-install it using the .deb file.


 I am getting the following error message while trying to install 
freesurfer_7.2.0_amd64.deb as suggested:


$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'freesurfer' instead of './freesurfer_7.2.0_amd64.deb'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 freesurfer : Depends: xorg-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.


any thoughts?


--Luis



From: fsbuild 
Date: Tuesday, November 2, 2021 at 7:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "Alvarado,Luis R" 
Subject: Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: 
version `XCRYPT_2.0' not found



You don't often get email from fsbu...@contbay.com. Learn why this is 
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Hello Luis,



This looks like an issue reported after people upgraded their Ubuntu systems 
causing the linker to find the wrong version of that library, e.g.,



https://secure-web.cisco.com/1EZOGxul5QsqH8V1OvHrGjhJ1TC_KmqqItKcdZhnvo3hTas0biEL7hVower8OQWE1Xg68GBFp_0vXoWuREkq88ZIwpXciC9fyqEBtVWOl49LiVJfeFCuXCrjh2U0h3dSNNwpUMYtU6KpN-jLpr0PSNAmcwQMetUFFVaq5ofyw58h011Fqt_EibbXg4htw4xBXK_WYpxwMsU-W66xnggwY2FKI-oPfIplwU4kawLHnjIC4ZES0wtdmBg7TCd5nzTnTZk_xfG0kanA1EyUJaqBADw/https%3A%2F%2Fubuntuforums.org%2Fshowthread.php%3Ft%3D2438576<https://secure-web.cisco.com/14OjrgUIXo4QO-8nDwO7pl3oHnOz71mlpCVpyMkug7wKOxiYCvIs5MVrGp0KbSNKible_Kizwj4hGAJGl1n2kw-8G9AT9Sql-jjXzZTdfRoxY2f7CWkaD38ev9InfOKHg6b-ePgCwCZ5pxnReDaavC_GOpgjAMDbQL7ntpsGPeGqmkZejrpQZLkLcIZND0QT2NyUNplOWYsrj7z8fdpLVy8F3MJxsUIM5OrjUYLBBInmqIjxHwo4_mOgN5cBI9ttPEB7mzXO0sM9S5Rz__BkmrA/https%3A%2F%2Fnam11.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fubuntuforums.org%252Fshowthread.php%253Ft%253D2438576%26data%3D04%257C01%257Cluis.alvarado%2540louisville.edu%257C06d42e638ce84c7b2d6608d99defed1c%257Cdd246e4a54344e158ae391ad9797b209%257C0%257C0%257C637714476671012879%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%26sdata%3DTZw%252F3YPeAU4%252BpnOCvOTSjTNfdwRoKv2ELZ6cvhCYFKw%253D%26reserved%3D0>



https://secure-web.cisco.com/1kFLw4bcEefcsQsueFByPn1Wq7qidxVkPcwljveeILKLPMdCUXr8tGHp71qUYm1fmDqFJdb3b8u3T-7xiVbQ4Gn1p33PX5WwTsbOxiQm-XA-SHsBQ1DCiuhFyvOG9q1EMQApicmTgakFZiHe4un2u287aHFIG2b8SXFWbjU2RRuVK49WX3tYluN9QG0PWy28yYmm6b7DEKEfypAx0YzBEyDyaIGMVE8KEm5oP4hCgmbJyAHFNDQrakz7fd71X

Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found

[Alvarado,Luis R]

External Email - Use Caution

Thank you for the fast response.

I had a typo in my original message. when I said 7.1.2, I really meant 7.2. I 
originally installed it using the freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz 
archive file.  The issue with the binaries was with 7.2.0.

I uninstalled that version and I am trying to re-install it using the .deb file.

 I am getting the following error message while trying to install 
freesurfer_7.2.0_amd64.deb as suggested:

$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'freesurfer' instead of './freesurfer_7.2.0_amd64.deb'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 freesurfer : Depends: xorg-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

any thoughts?

--Luis

From: fsbuild 
Date: Tuesday, November 2, 2021 at 7:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "Alvarado,Luis R" 
Subject: Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: 
version `XCRYPT_2.0' not found

You don't often get email from fsbu...@contbay.com. Learn why this is 
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Hello Luis,

This looks like an issue reported after people upgraded their Ubuntu systems 
causing the linker to find the wrong version of that library, e.g.,

https://secure-web.cisco.com/1Fr5vKvIOh9EoKcsWuZgJ4Hzz4M_oiQUg666wAS5dJitlCzyjAt6iKh5U0Lcyo_1Rt1sUJaT2UDwh7l9KaD4YxDXZnLQBzUF1UDJD8oENDC8udUBVMivEn9EXObhxrxhqyv8xufFDAarufr2iWbr9FKRytVdqDHeTpxT-a5IDXXp8SwulEAaXDDPiRntm7SbmyIxIzEBrIKIyMLNMD1X-WP8IO7Nnv0dXpAsGjm1k7LUcMbn53Jq0Y3KC6eWQy4p7baqdhUyyjNCTGPiB1CoxVQ/https%3A%2F%2Fubuntuforums.org%2Fshowthread.php%3Ft%3D2438576<https://secure-web.cisco.com/1vVKneNz4m9DSswGEqvtG3bXxHFwTbmc_MbNzyqfZeLDPMuXsUy2PF36uLzm0PnRpP6v6yzKxoJzKFhGclVjdSaK4X1yDo30O33iBnkPioL4aHsNwRl5_dVLrIRZFnSRMt747F0VKx--LzGcH2cuJKPZK-aP0izLKxw75ekqzo74Mm5V7_i5AtHLmP01lcnIkqq_gOx4sLJ_d564WJXGJYFrlN7tuFodnmAAlL7CtAb9ACJBvfKgA5ohJ3IUL8PIqlrwYVRNgDoWKE-MnhLtcyQ/https%3A%2F%2Fnam11.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fubuntuforums.org%252Fshowthread.php%253Ft%253D2438576%26data%3D04%257C01%257Cluis.alvarado%2540louisville.edu%257C06d42e638ce84c7b2d6608d99defed1c%257Cdd246e4a54344e158ae391ad9797b209%257C0%257C0%257C637714476671012879%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%26sdata%3DTZw%252F3YPeAU4%252BpnOCvOTSjTNfdwRoKv2ELZ6cvhCYFKw%253D%26reserved%3D0>

https://secure-web.cisco.com/1W3-M0ivO_B4lxEGqoKvPmxNe-83SJYn2jEc2w4WUDZXPlOCmnL7Olc5Nc1-bLr3HPJGt60vIS3Z5f6lEiL6sM4lZfXwIJZ_kuGQ0_q9Us16lXioKQ1td3a3M8NRCcvL9t0p61RDaV6Tbpvn49o98Aa2ZBTGFxgHyM9t9TyP-ao9pzNOXAJBuW_MfgxDxUJwwP01_EK33ZDLy449zJYXbfDnomhS6AS8or-KOnovvSXCuTu3IUI4ZjStVYf7nF279U3qUDi-yZ_KXSfZ11mufpw/https%3A%2F%2Fgithub.com%2Fpmq20%2Fruby-packer%2Fissues%2F131<https://secure-web.cisco.com/1NcSogIv1XF6Wc9uo6U9emnlRzzNT8eckWxDDjr9OLIdG5s9GsmMjoskfXOHdytLBMYWqH1i_8kD3o9Zu9G3RtNYALJzuUWfGsWtHOyexID8UgZhRnUHnDAILlJjjN3-PK_AEtII47bY52lcrXVw1XnnJSYfagVCXa7IOU5m7vcUKBO02Vvbko6dhmaA7MFN6gMKsegM33FSrqRh8MKZ-tYqWk4HBO534Ru9bHypz2H_151glAOvYXZElMe7hebGP8OAzUzTDjWEsgArgrzoi_A/https%3A%2F%2Fnam11.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fgithub.com%252Fpmq20%252Fruby-packer%252Fissues%252F131%26data%3D04%257C01%257Cluis.alvarado%2540louisville.edu%257C06d42e638ce84c7b2d6608d99defed1c%257Cdd246e4a54344e158ae391ad9797b209%257C0%257C0%257C637714476671022833%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%26sdata%3DpboxJFLmhGT81%252FAE8uKBc%252BxhqxcgwUTM8AykIEy8KZo%253D%26reserved%3D0>

As of the 7.2.0 release, there is a .deb installer package you can use if you 
have admin/root privileges.  If there is an issue with the wrong version of 
libraries on your system, running the installer might update them.

$ wget 
https://secure-web.cisco.com/1qVX_X5zYg1cIMLNAmdr0-UwTGMMwi8REx_pYUID8MKnkIqKlnDwAWjrxDZcVgGXte-Klkel_iT835mgugqLwLMb

[Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found

[Alvarado,Luis R]

External Email - Use Caution

Hi all,

I ran into issues running binaries like mri_aparc2aseg, mri_vol2vol, etc. on 
7.1.2

$ mri_vol2vol
mri_vol2vol: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not 
found (required by mri_vol2vol)
The issue is resolved when I switch back to 7.1.1.

I am running Ubuntu 18.04.5 LTS.

any help will be appreciated.

Luis R. Alvarado
Graduate Student Fellow
Department of Anatomical Sciences and Neurobiology
University of Louisville
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202
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Re: [Freesurfer] Tracula 7.2 using older structural outputs

[Alvarado,Luis R]

External Email - Use Caution

Hi all,

I am also curious about this question.

Can you run TRACULA 7.2 using the outputs from FS 6.0 and 7.1.1?

If so, is it ok to run the new segmentThalamicNuclei.sh and segmentBS.sh 7.2 
scripts on FS 6.0 recon data and feed that to TRACULA 7.2?

Best,

Luis R. Alvarado
Graduate Student Fellow
Department of Anatomical Sciences and Neurobiology
University of Louisville
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202


From: Alexopoulos, Dimitrios 
Sent: Tuesday, August 24, 2021 2:00 PM
To: Freesurfer support list 
Subject: [Freesurfer] Tracula 7.2 using older structural outputs


External Email - Use Caution

HI,



Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 
and 7.1.1?



Jim







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[Freesurfer] TRACULA configuration file for bash

[Alvarado,Luis R]

External Email - Use Caution

Hi FS and TRACULA experts,

I have a simple question. Do I need to replace:


setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs

with:


export SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs

inside the TRACULA configuration file, if my shell is bash? or should I leave 
that alone?

Best,


Luis R. Alvarado
Graduate Student Fellow
Department of Anatomical Sciences and Neurobiology
University of Louisville
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202
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Re: [Freesurfer] A question regarding a Freeview command

[Alvarado,Luis R]

External Email - Use Caution

Perfect, thank you!


Luis R. Alvarado
Graduate Student Fellow
Department of Anatomical Sciences and Neurobiology
University of Louisville
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202

From: Douglas N. Greve 
Sent: Wednesday, October 27, 2021 11:27 AM
To: Alvarado,Luis R ; Freesurfer support list 

Subject: Re: [Freesurfer] A question regarding a Freeview command


CAUTION: This email originated from outside of our organization. Do not click 
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I don't think there is anything specific for the --table option, but everything 
else is the same.

On 10/24/2021 4:31 PM, Alvarado,Luis R wrote:

External Email - Use Caution

Hi Douglas,



I was wondering if there are any “--table option” specific tutorial for the 
mri_glmfit function. I am trying to decide wheatear to export my ROI results to 
R or use the mri_glmfit function.



Best,



Luis





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[Freesurfer] fsaverage for externally preprocessed subjects.

[Alvarado,Luis R]

External Email - Use Caution

Hi all,

I have a couple of questions regarding fsaverage:


  1.  Is this file updated every time a new subject is process with recon-all?
  2.  If I obtain externally preprocessed datasets (e.g., from the 1000 
Functional Connectomes Project) should I register those subjects to my local 
fsaverage?
 *   Ultimately, I would like to conduct an ROI analysis of the differences 
between normative data from a large online biobank and locally imaged patient 
population. The workflow for such analysis recommended on 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI) suggests 
to draw ROI labels directly on fsaverage (a template to which all subjects run 
with FreeSurfer have been registered to) and then use the mri_label2label 
command to map the label to individual subjects. Would this work for both 
locally and externally preprocessed groups?
Thank you,

Luis R. Alvarado
Ph.D. Candidate
Department of Anatomical Sciences and Neurobiology
University of Louisville School of Medicine
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202


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Re: [Freesurfer] Help

[Alvarado,Luis R]

External Email - Use Caution

Please disregard this last email. I was trying to make adjustments to my mail 
list settings by following these instructions from the welcome email:

You can also make such adjustments via email by sending a message to:

  
freesurfer-requ...@nmr.mgh.harvard.edu

with the word `help' in the subject or body (don't include the
quotes), and you will get back a message with instructions.



Luis R. Alvarado
Ph.D. Candidate
Department of Anatomical Sciences and Neurobiology
University of Louisville School of Medicine
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202


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Re: [Freesurfer] Where is the BrainVolStatsFixed patch?

[Alvarado,Luis R]

External Email - Use Caution

Douglas,

Thank you for working on the patch. I didn’t mean to rush you or anything. I 
was just wondering if I was missing something. 

Thank you,

Luis R. Alvarado 

On 4/17/19, 11:26 AM, "Greve, Douglas N.,Ph.D."  wrote:

Sorry, I've been having problems getting the patch together because of 
difficulties compiling version 6 on centos 7. Should be ready today.

On 4/16/19 11:43 PM, Alvarado,Luis R wrote:
>
> External Email - Use Caution
>
> Dear Freesurfers,
>
> I just read the page about “Fixing of Morphometry Stats and Global 
> Measure of Volume” on the freesurfer website 
> 
<https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_BrainVolStatsFixed&d=DwIDaQ&c=OAG1LQNACBDguGvBeNj18Swhr9TMTjS-x4O_KuapPgY&r=KT5sx5w2OpE7yKeuKTF1DVmc3vFE73XqI2BQQQdkF3U&m=MofU2vvl6G-XNRnveua3Cug4pjt58pxUzUIDmj4OzgM&s=UhmBD3EQifBOmhXTgYPNkXjfL7tjo-Lss6ibULVBZT0&e=>.
>
> I am, however, a bit confused about the location of the 
> BrainVolStatsFixed patch. The page states “the problem has been fixed 
> and a patch put here: (To be determined)”.
>
> Does anyone know the location of the patch?
>
> Best,
>
> Luis R. Alvarado
>
> Ph.D. Candidate
>
> Department of Anatomical Sciences and Neurobiology
>
> University of Louisville School of Medicine
>
> Kentucky Spinal Cord Injury Research Center
>
> 220 Abraham Flexner Way, Suite 1500
>
> Louisville, KY 40202
>
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIDaQ&c=OAG1LQNACBDguGvBeNj18Swhr9TMTjS-x4O_KuapPgY&r=KT5sx5w2OpE7yKeuKTF1DVmc3vFE73XqI2BQQQdkF3U&m=MofU2vvl6G-XNRnveua3Cug4pjt58pxUzUIDmj4OzgM&s=8358ZHiF6S-8ihAqyU8OpyOwLonCXTXH3zyzMq1bcYw&e=






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[Freesurfer] Help

[Alvarado,Luis R]

External Email - Use Caution



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[Freesurfer] Where is the BrainVolStatsFixed patch?

[Alvarado,Luis R]

External Email - Use Caution

Dear Freesurfers,

I just read the page about “Fixing of Morphometry Stats and Global Measure of 
Volume” on the freesurfer website 
.
I am, however, a bit confused about the location of the BrainVolStatsFixed 
patch. The page states “the problem has been fixed and a patch put here: (To be 
determined)”.

Does anyone know the location of the patch?

Best,

Luis R. Alvarado
Ph.D. Candidate
Department of Anatomical Sciences and Neurobiology
University of Louisville School of Medicine
Kentucky Spinal Cord Injury Research Center
220 Abraham Flexner Way, Suite 1500
Louisville, KY 40202


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