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Today's Topics:
1. Re: Understanding ?h.sphere.reg (Salar Dini, Elaheh)
2. Re: TRACULA -bedp parallel processing (Salar Dini, Elaheh)
3. Re: ERROR: Talairach failed (Bouchra Guelib)
4. Problem with hypothalamus subunits?
(Zeng, Victor (BIDMC - Keshavan - Psychiatry))
5. Fwd: eTIV (Bouchra Guelib)
6. Re: mri_jacobian questions (Danielle Carrol)
7. Re: mri_jacobian questions (Fischl, Bruce)
8. Applying bonferroni clusterwise correction for 2spaces with
PALM F-contrast (Hye Min Shin)
9. Re: Problem with hypothalamus subunits?
(Iglesias Gonzalez, Juan E.)
10. The password request for the Freesurfer VirtualBox Image
(Nina Omejc)
----------------------------------------------------------------------
Message: 1
Date: Wed, 27 Jul 2022 17:55:33 +0000
From: "Salar Dini, Elaheh" <elaheh.salardini@yale.edu>
Subject: Re: [Freesurfer] Understanding ?h.sphere.reg
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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<BL0PR08MB467671BB49604E614465BEACF5979@BL0PR08MB4676.namprd08.prod.outlook.com>
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Hi Doug,
I found the solution to my problem, so please ignore my previous message. Thanks so much for always helping out anyway.
In case, this question ever comes up for anyone else, here is the solution:
I just used freesurfer auto-recon steps to create the files I want using co-registered images. I needed the following files:
talairach.xfm and rh.cortex.label for my pipeline, so I just the following steps of recon-all on my co-registered files:
recon-all<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://secure-web.cisco.com/1HfPVktnUOgRTFJY-mCNGr4GpEo8x9TCztlgWlyEX2jjfspgViDhhEGC-Z9f4umHvbY9N9NJ8wzYhH45BFSQmPbgu57qlA6M95j24bRmV7U6YMZXLNtPT3SRJsRC1yevK40Z11yKeAFyPBhSrREgiOVEA-UAi2Fv9ge9sXOptEx1EYbwYe_z8stAZT5A5IT-T4RCMd0k4YWBJzC8kuNH-G-SA4JxTL64rDjpSB583pXLlmoeJmxAWAK16s-ZAHEMU7zTRQC5ITfcs9ydcbqjluJuvQaBZBqmOD1hzhdLfhcASN2T1Q4Y4KFqo5uXU5IEfrcfYfmAptThmFq7NAiSKHQ/https*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frecon-all__;JSUlJSU!!BhJSzQqDqA!VD2tLA7mCu4SfPwCsZUhsourkPhZgDD4S7MTHVGin4Q776TWjxDlOmDVvt4u-GMgD_ANHxXp0oKyABbTUJK9NcwJ4CJ9-r0-n8dvhu9pSI8Y$ > -autorecon1 -subjid <subjid> -talairach<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://secure-web.cisco.com/1yX40e-pKgP2O3tNH6hEKcPzjb7Dn8B5ij5MN3lio02Uo-I_SFidef7xvuP4qAbiqAKx8zOlqxqX1YY1jcWzctzt1kJKDk1OQeUSVnYHg4SImkQsG5wcDMiS_bxqOLe1VIP0IrfIENSYbcqCwNNPJVpUCrefl3JvkIgFABRwgFQNTFdyMwuqMPJ84hKBdnx9z1Apqn2SGuY0HBWZwzWEjwcIldDkI6pJxgHlJbtMolJPZuNsg9hnbUxO280IFnwGavWzlPSGiRbGSsnXa0h6YVly-Z3-VB8g7O6ryVL0GEzyylIF2kRwwZD6KMmeuIDX0MV2IlwGcRD3CGUFEzHC8Zw/https*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Ftalairach__;JSUlJSU!!BhJSzQqDqA!VD2tLA7mCu4SfPwCsZUhsourkPhZgDD4S7MTHVGin4Q776TWjxDlOmDVvt4u-GMgD_ANHxXp0oKyABbTUJK9NcwJ4CJ9-r0-n8dvht8HnTHq$ > on post-co-registerated orig.mgz to get talairach.xfm
and recon-all<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://secure-web.cisco.com/1HfPVktnUOgRTFJY-mCNGr4GpEo8x9TCztlgWlyEX2jjfspgViDhhEGC-Z9f4umHvbY9N9NJ8wzYhH45BFSQmPbgu57qlA6M95j24bRmV7U6YMZXLNtPT3SRJsRC1yevK40Z11yKeAFyPBhSrREgiOVEA-UAi2Fv9ge9sXOptEx1EYbwYe_z8stAZT5A5IT-T4RCMd0k4YWBJzC8kuNH-G-SA4JxTL64rDjpSB583pXLlmoeJmxAWAK16s-ZAHEMU7zTRQC5ITfcs9ydcbqjluJuvQaBZBqmOD1hzhdLfhcASN2T1Q4Y4KFqo5uXU5IEfrcfYfmAptThmFq7NAiSKHQ/https*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frecon-all__;JSUlJSU!!BhJSzQqDqA!VD2tLA7mCu4SfPwCsZUhsourkPhZgDD4S7MTHVGin4Q776TWjxDlOmDVvt4u-GMgD_ANHxXp0oKyABbTUJK9NcwJ4CJ9-r0-n8dvhu9pSI8Y$ > -autorecon2 -subjid <subjid> -white on post-co-registerated aseg.presurf.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz and ?h.orig to get ?h.cortex.label
Thanks and all the best,
Ela
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Tuesday, July 26, 2022 12:45 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: Understanding ?h.sphere.reg
Hi Douglas,
It does. Thank you. Can you also help me with something else? If we coregister bunch of volume and surfaces using the same reg.lta for one subject, is there a way to safely reflect these changes in label files like rh.cortex.label or in transformation fies like talairach.xfm? In other words, can we make any changes to rh.cortex.label and talairach.xfm from pre co-registeration to make them usable with post co-registration files?
Thanks
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Douglas N. Greve<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://secure-web.cisco.com/1Sa9geD9Pn3WQS7pXoIgFzUzwLTkndP52ZiOFFA74ycdRqO4IwNK1Wy_Ed3fUyZd48SU7PTEl2on_isy_xY-UXnhkhp2NmqaoOMXHhNZeVItHidCoNqjAdO_0pF2s5GPOB31QrdS9iU5NfWrzJUs6eJCDKtjPZ3cG8blbykryh1DdEQQ_o0KCG-MLbK3VNBqkHBkqYdsCWuQI6FukiUCcXCDI1rBLKyARdu-jalsR0BjxUGrO_hUFQRuLtfja9MsG5jTpi5B95FDXtSMbPdcpp4WkYMeErmXElxacngYqyYkuS8Sm5lKAUWna5BqnhS8NpH0uVWM-10s-Mtxyf287tQ/https*3A*2F*2Fwww.mail-archive.com*2Fsearch*3Fl*3Dfreesurfer*40nmr.mgh.harvard.edu*26q*3Dfrom*3A*2522Douglas*2BN.*2BGreve*2522__;JSUlJSUlJSUlJSUlJSU!!BhJSzQqDqA!VD2tLA7mCu4SfPwCsZUhsourkPhZgDD4S7MTHVGin4Q776TWjxDlOmDVvt4u-GMgD_ANHxXp0oKyABbTUJK9NcwJ4CJ9-r0-n8dvhu7wj4S6$ > Sun, 24 Jul 2022 19:20:57 -0700<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://secure-web.cisco.com/1CZTg3v8StwDIz8ldgeKmmXwRWzysyMwI4k2NQwCM1Rkdk-ER_E0eARDrF6UsFzFRICrgy9fB7fglQV2lCsdTKeBwgofgbD49SVMC0dn-qWpVWTLkSnBiZNq1UXyHoE_wQqKNPIkkjbXsdUt0TVD1lvdl2eMY9Jsp8WkXS7YQTtJod3SOkpga1NYGz-yY8t1BIyI2kNGvEX1N9995ME9YUWM9lkt_rjFCePu2AFq5xO2zlwn8_bFx748WcZSNKlQvLpqE_DH90o3Y9lAIbwFAlryqIIEV2kMyWZ50MPg8gLU6gxfZfcWiEGxTgRHpl_CZ-zBb3E2pbEhLA0f1LQ3qog/https*3A*2F*2Fwww.mail-archive.com*2Fsearch*3Fl*3Dfreesurfer*40nmr.mgh.harv__;JSUlJSUlJQ!!BhJSzQqDqA!VD2tLA7mCu4SfPwCsZUhsourkPhZgDD4S7MTHVGin4Q776TWjxDlOmDVvt4u-GMgD_ANHxXp0oKyABbTUJK9NcwJ4CJ9-r0-n8dvhjY-BmI4$
ard.edu%26q%3Ddate%3A20220724>
The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To apply a spherical registration, a point on one spherical mesh is mapped to the closest point on the other spherical mesh. not sure if that answers your question ...
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Thursday, July 21, 2022 5:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Understanding ?h.sphere.reg
Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay
. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct?
I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough.
Thank you for your help and time.
Ela
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------------------------------
Message: 2
Date: Wed, 27 Jul 2022 18:03:50 +0000
From: "Salar Dini, Elaheh" <elaheh.salardini@yale.edu>
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
To: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>, Freesurfer
support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BL0PR08MB46760ACCCB12EC49138A8D05F5979@BL0PR08MB4676.namprd08.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
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Hi all,
A nice gentleman, a doctor working as program analyst at James J. Peters Dept. of Veterans Administration Medical Center (OOMH) has kindly emailed me about this with a solution, whose name I won't mention for privacy reasons. I'm sharing it here in case it is helpful to others one day:
1) edit pre.Parallel.docx
bedpostx_preproc.sh takes 2 arguments. Add a 2nd argument 0 at the end
bedpostx_preproc.sh /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri 0
bedpostx_preproc.sh /home2/am2359/fs6_data/TRACULA/subjects_dir/58/dmri 0
2) create nodif_brain_mask.nii.gz link in dmri
cd /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri
ln -s ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz nodif_brain_mask.nii.gz
3) create dirs
dmri.bedpostX/diff_slices
dmri.bedpostX/logs/monitor
dmri.bedpostX/xfms
in /home2/am2359/fs6_data/TRACULA/subjects_dir/57
same for 58
This worked like a charm.
Thank you the anonymous helper and all,
Regards,
Ela
________________________________
From: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Tuesday, June 14, 2022 9:23 PM
To: Salar Dini, Elaheh <elaheh.salardini@yale.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
Unfortunately it's not something we've been able to replicate here ?
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Tuesday, June 14, 2022 8:53 PM
To: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
External Email - Use Caution
I tried to troubleshoot this, but I couldn't. I just want to follow-up and make sure no other solutions come to your mind. If not, we will run it out of cluster which seems to work just fine.
Thanks and all the best,
Ela
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Wednesday, June 8, 2022 3:32 PM
To: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
Thanks Paul.
bedpostx_preproc.sh is the first job that is I submit to my cluster. My input file is attached to this email.
Thanks,
Ela
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Subject:Re: TRACULA -bedp parallel processing
Hi Ela,
It looks to me like line 79 of bedpostx_preproc.sh is:
if [ ${gflag} -eq 1 ]; then
Which is consistent with the error:
-eq: unary operator expected
What this error is saying is that the variable `gflag` has not been set, so the
script does not know how to perform the comparison.
`gflag` is set a few lines above to the second parameter passed when executing
`bedpostx_preproc.sh`. I would investigate how `bedpostx_preproc.sh` is being
invoked to chase down the cause of this error.
-Paul
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Wednesday, June 8, 2022 12:32 PM
To: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
That actually helps but not solving all the problems. So, what happens is that if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a directory). However, the second error still exists: a.k.a. (home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And when I try to run Parallel lines, I still get the error (dmri.bedpostX/logs/log0000: No such file or directory). So, my guess is, it still doesn't copy the whole needed package for some reason. So, what we end up having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.
I can always manually copy all needed file from fsl folder to our subjects folder, but I am curious why we get the error and why everything is not copied automatically. I also don't know what files we need to manually copy.
Thanks again,
Ela
________________________________
From: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Tuesday, June 7, 2022 2:46 PM
To: Salar Dini, Elaheh <elaheh.salardini@yale.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
What if you create the directory (that shows up in the "not a directory" error)?
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
External Email - Use Caution
Hi Anastasia,
FSL version is 6.0.5.1
Thanks,
Ela
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To: Salar Dini, Elaheh <elaheh.salardini@yale.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processin
Hi Ela - Which version of FSL are you using?
Anastasia.
________________________________
From: Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
Thanks for the reply. I'm not sure if you are looking for this: we use a small cluster with 40 nodes, 512 CPU cores. We are still using PBS.
Thanks,
Ela
________________________________
From: Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh <elaheh.salardini@yale.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: TRACULA -bedp parallel processing
What kind of cluster are you running the parallel processes on?
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
External Email - Use Caution
Thank you for the guidance.
When it tries to run pre.ParallelI , I'll get this:
Copying files to bedpost directory
cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected
Done
This happens for all subjects.
After this, when I check the subject 57 folder in subjects_dir, there is a file named "dmri.bedpostX.nii.gz".
However, when it tries to run Parallel lines, these errors coming up:
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0000: No such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No such file or directory
...
If I run trac-all -bedp -c <Cinfig File> , and not try to process parallelly, it runs without any errors to the end.
Do you have any thoughts what goes wrong?
Thanks again,
Ela
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You run them in that order. First the pre, then the parallel, then the post.
You can queue them that way, so that the parallel jobs wait for the pre to
finish, and the post waits for all the parallel jobs to finish.
________________________________
From: Salar Dini, Elaheh
Sent: Friday, June 3, 2022 3:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: TRACULA -bedp parallel processing
Hello,
I have tried to create a text file with command lines that can be run in parallel by using trac-all -bedp -c <config file> -jobs Parallel.
When I use this command three text files are produced named: pre.Parallel, post.Parallel, and Parallel. Should I just use Parallel as a source for command lines? What are pre.Parallel and post.Parallel for? I am attaching my Configuration file, pre.Parallel, post.Parallel, and Parallel to this message as well.
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your help.
Kindly,
Ela
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------------------------------
Message: 3
Date: Wed, 27 Jul 2022 19:27:57 +0100
From: Bouchra Guelib <bouchra.guelib@univ-constantine2.dz>
Subject: Re: [Freesurfer] ERROR: Talairach failed
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CALRi-dzPugcRPszcCE4deRzyKUKZdiMntRO3o8qq23b4o_0b7g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
It is clear now thank you.
Le mer. 27 juil. 2022 ? 14:13, Douglas N. Greve <dgreve@mgh.harvard.edu> a
?crit :
> recon-all does not change the space to mni305 (it just "conforms" it).
>
> On 7/26/2022 10:22 AM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> The problem was That I transferred my MRI to mni 305 space before the
> recon-all. Still, when I read the documentation on your website, I found
> that changing the space is a step of the recon-all, so I used recon-all
> directly on my original data without any space changing. Thank you so
> much for your answer.
>
> Le lun. 25 juil. 2022 ? 03:40, Douglas N. Greve <dgreve@mgh.harvard.edu>
> a ?crit :
>
>> did you see where it said "see *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__http://secure-web.cisco.com/1Gz_6qC6AfoxAkFmHB1wHgUcoxuYfNh7T2q2fiAktR1qt2txv5liygRCoYcH__ASEFBrgsa-YCgdFD1qAo6qPxc9L3tXuWvoXnpwd42oq1fWCXinQXrRQEgTP0zPGXqoTnWE8Plnm8xYtffeS1VyozB_L12jfeV0PLZOwcNbjyb6dBArvo9G7O5dsjRS8jV8nqdo4dA6olahBYSdqOsDOfWOPOyn-KljS3ZsPcE6uiR-5RTA3pOTcpwZSNh5fx77aPPeh2FmklfUXTFcjY03jnMfBvN_N0pQpqtARGooSXPgnX1Ir0pYqsgzF78EzCuZ3X8gi_WYpcu3PxKYOEWoahg/http*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FFsTutorial*2FTalairach__;JSUlJSUl!!BhJSzQqDqA!VD2tLA7mCu4SfPwCsZUhsourkPhZgDD4S7MTHVGin4Q776TWjxDlOmDVvt4u-GMgD_ANHxXp0oKyABbTUJK9NcwJ4CJ9-r0-n8dvhl-Yq7I4$
>> <