Re: [Freesurfer] Help Download FreeSurfer Windows VM

[fsbuild]

External Email - Use Caution

We don’t expect things to work reliably with 8G total RAM for the machine. 
The host machine itself will always consume some memory when running its 
OS, probably up to a few Gig, leaving even less than 8G to be used for 
running the VM with freesurfer.
The Virtualbox VM is no longer available because the security/login credentials 
were compromised on this list.
Since you are on Windows, you could try using the windows OS built in Windows 
Subsystem for Linux (WSL). We have some notes about setting that up at,
https://secure-web.cisco.com/15CztkRxVJ7Ddir4MS_9Arksy0DkD_t2mgoGcHYmhJKK5Lsyhn9OQQF2n11zmSLeqbeGjffl8JiKJspStS5BIEqDeW4hwjubpORcz_WfM_QelzOOGCbo0-yxIrw5CRp9OTe6G_opwaoTix1AU6qWdzQ84fN4r922b3CXNohHY0nfJE_R1L5EMyO6V8j9OBROkgqBF4F3YCyusFxnCekqZ6zfNabw_pTnvaJDgwZR0JLlJ5nw84ZNy4DAJEMie-rQ8TdAxUT8Hafmh1q3BlprlvLyJxQ9QWTHDvp0ztYKxEOP5KBlgWyaJl3eak96w5YgK1ETj64k1_2sTQtEOkUs3sQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
But you would still likely run into the same issues consistent with having less 
than 8G of RAM to run Ubuntu Linux in WSL (instead of VirtualBox) + running 
freesurfer.
- R.
On Feb 6, 2024, at 08:54, lioudadraca...@gmail.com 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. 
But I have few problems.First, I do not have the access to the compressed VM 
Image file (FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to 
have an access to that ?Second, I've seen that it also requires a login 
password for the "Developer" account. Is it possible to also have the password 
?Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be able to 
run Freesurfer ?Thank you for your help.Best 
regards,Liouda___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[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!
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[Freesurfer] Using funcroi-sess with per-run analysis

[Akkoyunlu, Beyza]

External Email - Use Caution

Hi,

We are trying to do % signal change within a ROI. However, when we run 
funcroi-sess function (after funcroi-config), we get following output in 
terminal

set: variable name must begin with a letter

When we run the function with -debug, we saw that the function cannot find 
meanfunc file. This is because we do our analysis performed as per-run and 
therefore meanfunc files are not in the following path 
$SUBJECTS_DIR//bold//meanfunc but exists in 
$SUBJECTS_DIR//bold//pr001/meanfunc for each 
run.

Could you please help us with this problem? I add the -debug output as an 
attachment.

FYI: We use version 7.2 but tried it also with 7.5, problem persists there

Best, Beyza

set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
foreach grp ( $grpdefs )
foreach grp ( )
goto check_params ;
goto check_params
if ( $#SessList == 0 ) then
if ( 1 == 0 ) then
if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif
goto check_params_return ;
goto check_params_return
set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end
set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )
set errs = 0 ;
set errs = 0
set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( sub-201_post-task )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./sub-201_post-task
if ( -d $stst ) then
if ( -d ./sub-201_post-task ) then
if ( ! -r $stst ) then
if ( ! -r ./sub-201_post-task ) then
pushd $stst > /dev/null ;
pushd ./sub-201_post-task
set tmp = ( $tmp `$PWDCMD` ) ;
set tmp = ( `$PWDCMD` )
pwd
popd > /dev/null ;
popd
endif
endif
end
end
set nfound = ( $#tmp ) ;
set nfound = ( 1 )
if ( $nfound == 0 ) then
if ( 1 == 0 ) then
if ( $nfound > 1 ) then
if ( 1 > 1 ) then
set SessPath = ( $SessPath $tmp ) ;
set SessPath = ( /sub-201_post-task )
end
end
set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /sub-201_post-task )
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /sub-201_post-task )
endif
endif
end
end
echo $SessPath
echo /sub-201_post-task
exit $errs ;
exit 0
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#SessList == 0 ) then
if ( 1 == 0 ) then
if ( $#roicfg == 0 ) then
if ( 1 == 0 ) then
set roiname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'`
set roiname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'`
awk {if($1 == "roiname") print $2}
cat rh.V1
set label = `cat $roicfg | awk '{if($1 == "label") print $2}'`
set label = `cat $roicfg | awk '{if($1 == "label") print $2}'`
awk {if($1 == "label") print $2}
cat rh.V1
set annot = `cat $roicfg | awk '{if($1 == "annot") print $2}'`
set annot = `cat $roicfg | awk '{if($1 == "annot") print $2}'`
awk {if($1 == "annot") print $2}
cat rh.V1
if ( $#annot ) then
if ( 0 ) then
set segvol = `cat $roicfg | awk '{if($1 == "seg") print $2}'`
set segvol = `cat $roicfg | awk '{if($1 == "seg") print $2}'`
awk {if($1 == "seg") print $2}
cat rh.V1
if ( $#segvol ) then
if ( 0 ) then
set fillthresh = `cat $roicfg | awk '{if($1 == "fillthresh") print $2}'`
set fillthresh = `cat $roicfg | awk '{if($1 == "fillthresh") print $2}'`
awk {if($1 == "fillthresh") print $2}
cat rh.V1
set analysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'`
set analysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'`
awk {if($1 == "analysis") print $2}
cat rh.V1
set contrast = `cat $roicfg | awk '{if($1 == "contrast") print $2}'`
set contrast = `cat $roicfg | awk '{if($1 == "contrast") print $2}'`
awk {if($1 == "contrast") print $2}
cat rh.V1
set sign = `cat $roicfg | awk '{if($1 == "sign") print $2}'`
set sign = `cat $roicfg | awk '{if($1 == "sign") print $2}'`
awk {if($1 == "sign") print $2}
cat rh.V1
set thresh = `cat $roicfg | awk '{if($1 == "thresh") print $2}'`
set thresh = `cat $roicfg | awk '{if($1 == "thresh") print $2}'`
awk {if($1 == "thresh") print $2}
cat rh.V1
set pct = `cat $roicfg | awk '{if($1 == "pct") print $2}'`
set pct = `cat $roicfg | awk '{if($1 == "pct") print $2}'`
awk {if($1 == "pct") print $2}
cat rh.V1
set map = `cat $roicfg | awk '{if($1 == "map") print $2}'`
set map = `cat $roicfg | awk '{if($1 == "map") print $2}'`
awk {if($1 == "map") print $2}
cat rh.V1
set frame = `cat $roicfg | awk '{if($1 == "frame") print $2}'`
set frame = `cat $roicfg | 

Re: [Freesurfer] calculation of sulcal depth

[Linn Christin Bonaventure Norbom]

External Email - Use Caution

OK perfect, thank you so much for the clarification!


Kind regards Linn


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

Sent: 06 February 2024 15:35:16
To: Freesurfer support list
Subject: Re: [Freesurfer] calculation of sulcal depth

Hi Linn

The text you cite is how we measure it. It is the signed distance each points 
moves to get from the white to the inflated surface, where outwards movement is 
positive (along the surface normal direction) and inwards distance is negative.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Linn Christin Bonaventure 
Norbom
Sent: Tuesday, February 6, 2024 8:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] calculation of sulcal depth


External Email - Use Caution
Dear experts,

I am assessing different morphological aspects of the cortex including sulcal 
depth but am struggling to understand how this is calculated in FreeSurfer. I 
see that a previous correspondence 
(https://secure-web.cisco.com/17UFKrNEsAz2sbufihMcQDONUJK07Rabz1hBwgQnCV0_4DajbF3NqxA5kgpRM5ovJ4vRJmIPQHei7X9XdasF1bte2lyQ71-A-5GKxU3fbmNanz5puJBz69Osj5--WnkO-wsOPdhTpXgofRDgz1V-sGN7MBkIISqARus8Rr84v8TRlHduYNCCKYan7TZjUr08C55rudnWe0J62gdV9XA3S700OMt0-B2jcS2fpqwOmD2FgN3uTJVzMWX32dBqTeVWv_nTiXx4YUMbpK16PWwd_BC7pI6LuqZD78jDSc-XIoVGK2T67ghvPB1Fhelj-o8OI51xLSbuuPVFVY9KZXynZoA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg43772.html)
 points to this being described on page 199 within the “Cortical surface-based 
analysis II” – paper, by Fischl et al. but to my understanding it only 
describes the inflation process. Is it so that as concave areas like sulci move 
outward, while convex areas like gyri move inward during this process, this 
movement is somehow quantified and used to calculate sulcal depth? I also see a 
previous article stating that “..Freesurfer's sulcal depth measurement measures 
how far a vertex moves during an inflation operation”, also referencing the 
same Fischl paper.

While other folding measures like LGI (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/15zaRhNC9Gz2IJ5YjV7AwLqUoAjKhY6J96nEnBm8vCDW7OBl-YIlEkJOzvbHYJeA_0rL8egGENUXZ3veETJsyWfIiS2CywlB0id7iGmCknuVS4tm7_y0CHjlJmjgASOMWdwxcaFtHy17tKRjHWeFi7AiHLP-Qpy30BMFnoj1V-ytnWwYRXA2gAXcfREN1Ny-DIgE6XevdKMDJmnHO4dtFDOZ-Mmk95eEuWe3AOvL_FC1E9_n81xD8aIgbl5b8B5Bc5nyWbF1CBNyz6v40R9kCFOYcR4JE8V3vp6wHxlzR3uuBiDLpr2QUr_3PzduVQDEZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLGI
 and curvature (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1-7akPiNVTlNC9KxMTovd50a0rRROLiMJCFH9KZ2F4r4_XhgtYWbahcZ_7W5dwrrnGqSw-LoAag9IVa8xcxFZMZRQ97KtAUy1ZoReo6rJVm1XVGH3cWN0G9Jau0Hii0tQiIpjPAJ-nR0dnY6YOQAg7yWc8qcdwh_F1W1BSctJxUcbn8ufc2srurRMkCfF1EhIcZuhZKSB6umdohfzHkXM7tKKYNtgHNdq7NxLTv_3_4QthaBjVsUKQNx2Ujsqorf7wWqgrI-9EZaYwvo_TlZh5FZhGLKrIrROulJguXR4Hnv572q0j_tNC4R5HySziPob/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMeanCurvature)
 are neatly covered, I unfortunately could not find the same descriptions for 
sulcal depth. Any clarifications would be greatly appreciated.

Thank you in advance!

Kind regards Linn Norbom

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Re: [Freesurfer] calculation of sulcal depth

[Fischl, Bruce R.,PHD]

Hi Linn

The text you cite is how we measure it. It is the signed distance each points 
moves to get from the white to the inflated surface, where outwards movement is 
positive (along the surface normal direction) and inwards distance is negative.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Linn Christin Bonaventure 
Norbom
Sent: Tuesday, February 6, 2024 8:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] calculation of sulcal depth


External Email - Use Caution
Dear experts,

I am assessing different morphological aspects of the cortex including sulcal 
depth but am struggling to understand how this is calculated in FreeSurfer. I 
see that a previous correspondence 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43772.html) 
points to this being described on page 199 within the "Cortical surface-based 
analysis II" - paper, by Fischl et al. but to my understanding it only 
describes the inflation process. Is it so that as concave areas like sulci move 
outward, while convex areas like gyri move inward during this process, this 
movement is somehow quantified and used to calculate sulcal depth? I also see a 
previous article stating that "..Freesurfer's sulcal depth measurement measures 
how far a vertex moves during an inflation operation", also referencing the 
same Fischl paper.

While other folding measures like LGI (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
 and curvature (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/MeanCurvature)
 are neatly covered, I unfortunately could not find the same descriptions for 
sulcal depth. Any clarifications would be greatly appreciated.

Thank you in advance!

Kind regards Linn Norbom

___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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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Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

[Huang, Yujing]

I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the 
script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? 
I’m hoping it will give some hints.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sven Kühn
Sent: Sunday, February 4, 2024 12:09 PM
To: Greve, Douglas N.,Ph.D. ; 
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat


External Email - Use Caution

Hi Dr. Greve, hi all

I have tried your code. I copied it from the website into a text file and 
replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable 
but aborts after a few lines with no indication of a cause. The following 
output is generated:



xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir 
--cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum
cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C 
Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex 
--glmdir rh.volume.DCS.10.glmdir
SURFACE: fsaverage rh
Unmatched `.

Even if I run --help, only some of the lines appear:

mri_glmfit-sim --help

 --glmdir glmdir
 --cwp cwthresh : cluster-wise p-value threshold (.05)

Use pre-computed z-based monte-carlo simulations (see mri_mcsim)
 --mczsim vwthreshold sign
If you have run your own simulations (mri_mcsim), then specify
   --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor
   --mczsim-label label : default is cortex

Use permutation simulation
 --perm nsim CFT sign : permutation simulation with nsim iterations
Unmatched ".

Do you have any idea why this might be?
Like Xiaoxu before me, I have already tried to convert the file with dos2unix. 
However, without the desired effect.

I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.

I would be very grateful for any tips.

Best regards



sven
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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 
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 .
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[Freesurfer] Help Download FreeSurfer Windows VM

[lioudadracacci]

   External Email - Use Caution


Hello FreeSurfer Developers,


I am attempting to start Ubuntu via VirtualBox 7.0 on Windows 10. But I 
have few problems.


First, I do not have the access to the compressed VM Image file 
(FS_7_3_2_course_ubuntu_18_04_06.ova.7z), is it still possible to have 
an access to that ?


Second, I've seen that it also requires a login password for the 
"Developer" account. Is it possible to also have the password ?


Finally, I have a 8Go RAM, even if a 16Go is recommended, will it be 
able to run Freesurfer ?



Thank you for your help.

Best regards,

Liouda
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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. 

Re: [Freesurfer] if: Expression Syntax - preproc-sess

[Huang, Yujing]

Not sure where this happened. Does it produce any log files that you can share? 
Maybe both logs with and without the -nomc option.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stefano Delli Pizzi
Sent: Saturday, February 3, 2024 2:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] if: Expression Syntax - preproc-sess


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to run preproc-sess with -nomc option



preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest

-per-run -sliceorder up -force

if: Expression Syntax.



This error occurred before to create the file with slice timing correction



The error did not occur when I run the preproc-sess command line without the

-nomc option.



I've searched the list and no similar errors have been reported. Does anyone

have any thoughts on how to trouble-shoot this one?



FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460

Platform: Darwin Kernel Version 21.6.0
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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. 

Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 9

[Huang, Yujing]

It looks like your recon-all was killed. Is it possible that your recon-all ran 
out of the job limit (time, memory, ...).

I also noticed you have these options to recon-all '-3T -no-isrunning'. Make 
sure you don't have other instance of recon-all running on the same subject.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lucas Alexis Ronat
Sent: Tuesday, February 6, 2024 12:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: mri_ca_register with non-zero status 9


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Hello FreeSurfer developers,

I'm trying to process structural MRI (T1w.nii) using the recon-all command but 
I get the following error:
ERROR: mri_ca_register with non-zero status 9

Similar errors have been reported but I am unable to resolve this problem. Do 
you have any details on how to fix this? I have also attached the latest 
recon-all.log file in case it is useful.

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
2) Platform: Alliance Canada Graham cluster (via MobaXterm terminal)
3) uname -a : Linux gra-login2 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 
15:41:52 UTC 2023 x86_64 GNU/Linux
4) recon-all.log : see attached

I got a similar error on the Niagara cluster using FreeSurfer version 7.1.0 
(ERROR: mri_ca_register with non-zero status 24)

Thanks for your help

Lucas Ronat
Postdoctoral Fellow
Douglas Research Center, Montreal, Canada
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[Freesurfer] calculation of sulcal depth

[Linn Christin Bonaventure Norbom]

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Dear experts,

I am assessing different morphological aspects of the cortex including sulcal 
depth but am struggling to understand how this is calculated in FreeSurfer. I 
see that a previous correspondence 
(https://secure-web.cisco.com/130Tf81zvPk_603DeJ5a0ZZo4MNfYCZ60im_ZWCS7hPT0Boh03RcosHar-VFCAEsXxp8DP0KbJ3PcQplwB_8w36CyyD-mLjT9upNz28bLQH_7N8OwIfg-aWBDPQ56GH8N_KLqZD8x5iRCvx8VrbvV_o9uly23JxJwE5BKM0nv55XY2UeUv0Tu1oQMN_XvWQ1irmsE2b0gPa1igaVIQx7cls7ZUiOsgaZ-OTmbCH_q7LOl6qyRRhYbxg8Zyeiye7JIFmm6Ca2JzpSDCsP7gF7-pBdbgRNzHFlfbV93cwmlJpajxIIrgsbKnbSy8RYSkKuuj2x3Xg0mpbyjGxQP00-zdA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg43772.html)
 points to this being described on page 199 within the “Cortical surface-based 
analysis II” – paper, by Fischl et al. but to my understanding it only 
describes the inflation process. Is it so that as concave areas like sulci move 
outward, while convex areas like gyri move inward during this process, this 
movement is somehow quantified and used to calculate sulcal depth? I also see a 
previous article stating that “..Freesurfer's sulcal depth measurement measures 
how far a vertex moves during an inflation operation”, also referencing the 
same Fischl paper.

While other folding measures like LGI 
(https://secure-web.cisco.com/1rZbD04F-L_WBb_-7dP8B298OK6uZo1zDlLneMBGyND_ivL2gPkiZTug0WyglfVkOxxiC02F2Fh9blwiaSive2lw9mQNXXar3KvM6viLVnbE0k8g7scdmmyXJnbPb5wzV7dorN16_yT8hpRYKkSnOgVJPTiYFr6imCXCw0oqSa3vw69icYlZlp0nrJEZ8CQI6THyg7T7c18tXbLwhC255w6lGcKFdcqQrkDtTxdDJ2m2rKsF8kH0AyALHcPwzFqoW5lVOAgzmbhZXo18NET-ucEVyQLZkek29qz2zU84XKJGF_9yRPSlYxRMomM5dW00gbbDpAYbhEk1jwn-WXxTb6w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLGI
 and curvature 
(https://secure-web.cisco.com/1bY39JsrtiDKpPFJNg4aHhIchmGuug1PSRGvTczzLFMkNC8ifemRnYXnUDdmvRVVZ4BQmPxQvIJYXoUo14A2_GWqoJNuEnMk1x13Nj6Nu8dkE12w8VdN62Wvy5k2ihHSWjarOV9aYXxP7z56hbzOv-OIIfyD4jdXX65nYsgl0gy63HZMpxvtIe7E4aREI07xP6OJiWKOkIBQcg4rhaXvSYofqQl930k1EpdawV8TMZBGr7tPI8p4Q8x99pg9LtQAkPs9_1zpMUeiIRrajetzyPwuc597BofExcrVipWR3eBC0nVk_aC7UjmoHJciUUPE-q2SMcd8zX2FMOXGT2RJfng/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMeanCurvature)
 are neatly covered, I unfortunately could not find the same descriptions for 
sulcal depth. Any clarifications would be greatly appreciated.

Thank you in advance!

Kind regards Linn Norbom

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[Freesurfer] Cortical WM parcellation for DKT atlas?

[Hamied Haroon]

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Hello Freesurfer Gurus,

Is it possible to obtain "wmparc" but for the DKT cortical atlas, please?

Many thanks.

Best wishes,

Hamied


Dr Hamied A Haroon [he/him/his], MSc, PhD, MInstP
Research Fellow in Quantitative Biomedical MR Imaging
The University of Manchester

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