Re: [Freesurfer] VirtualBox pass code

[fsbuild]

External Email - Use Caution

Sending the info to your email shortly.
- R.On Apr 27, 2022, at 21:54, JESS WOOLF  
wrote:   External Email - Use Caution 
   Hello,Will you please send me the 
pass code for the Virtual Box  ova.7z file?Thank 
you,Jess___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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 .
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Re: [Freesurfer] Cortical depth at each cortical voxel

[Fotiadis, Panagiotis]

External Email - Use Caution

Hi Iman,

That is exactly what I was looking for, thank you!!

Best,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Aganj, Iman 

Date: Tuesday, April 26, 2022 at 9:40 AM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Hi Panos,

Please see my responses interleaved.

Best,
Iman


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Monday, April 25, 2022 10:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Iman,

Apologies for the follow up! I had a couple questions concerning the software:


  1.  Concerning the MLI_thickness.m function: I used a binary mask of the 
cortical ribbon (= I) as its first input and L (where L = 
makeLineSegments(round(.2*size(I,1)) ) as the second input (similarly to the 
suggestion in EXAMPLE.m file). I tried different radii as well for the 
makeLineSegments function and the thickness results are highly linear to each 
other. Do those inputs seem reasonable in this case (i.e., for real 3D MRI 
scans), in your opinion?

In makeLineSegments, you may want to use a radius that is a few voxels larger 
than the maximum thickness that you expect (voxels being the unit of the 
measured thickness).


  1.  Concerning the cortical depth calculation for each voxel: Unless I’m 
mistaken, the (cortical depth = Thickness/2 – SkeletonDistance) equation would 
give me the cortical depth of each voxel from the closest surface layer, right? 
 So for instance, if my voxel of interest were “above” the skeleton (i.e., the 
middle layer of the cortical ribbon), then the above equation would give out 
its distance from the surface layer that is also above the skeleton, whereas if 
my voxel were “below” the skeleton, then the aforementioned equation would give 
its distance from the surface layer that is also below the skeleton, right?



That is correct.


Would there be, however, a way to compute the cortical depth of each cortical 
voxel from the outer surface layer of the cortical ribbon? I believe that would 
be distance t1(v) mentioned in the equations and text in p. 3199 of your paper, 
but I unfortunately wasn’t able to pinpoint that variable in the scripts. Is 
that variable hard-coded in the scripts, or would you recommend that I follow a 
different approach to calculate that (for instance set up a conditional 
argument where I use cortical depth = Thickness/2 – SkeletonDistance if the 
voxel is above the skeleton layer, and cortical depth = Thickness/2 + 
SkeletonDistance if the voxel is below the skeleton layer)?


t1(v) is the oneSidedThickness_partial variable in the MLI_thickness function. 
The algorithm, however, works pretty locally and cannot really distinguish 
between the inner and outer surfaces of the cortical ribbon. So, In order to 
use t1(v) for your purpose (or your other suggested approach), you would need a 
label for each voxel that says which surface the voxel is closer to. If you 
have masks for the subcortical areas (e.g. the white-matter mask) and the 
beyond-pial area (~(GM | WM)), you could create such a label by comparing the 
distance transform maps created from the two masks (by Matlab’s bwdist 
function). In fact, the distance transform from the latter mask might just give 
you the cortical depth that you are looking for.


Thank you again very much for your time and help!

Best,
Panos

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aganj, Iman 
mailto:iag...@mgh.harvard.edu>>
Date: Thursday, April 21, 2022 at 1:02 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Of course! Please let me know if you have any questions about the toolbox.

Best,
Iman

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21, 2022 12:32 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Iman,

That is extremely helpful, thank you very much (also the paper is a great read)!

Best,
Panos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aganj, Iman 
mailto:iag...@mgh.harvard.edu>>
Date: Thursday, April 21, 2022 at 12:06 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Hi Panos,

You can do such a volumetric analysis using this toolbox:

Code:  
https://secure-web.cisco.com/1Ieq0hfM465RoCoCk9wco5SWF8BC_F38Rs0ZRDkBh73dame7pnE-S99qyCsNJCATUXij

Re: [Freesurfer] FreeSurfer 7Zip archive passcode

[Katharina Hense]

External Email - Use Caution

Dear FreeSurfer team,
 
Thank you for providing the passwords and some instructions for the 
installation.
However, I encountered a problem while unzipping the file. Both 7zip and WinRAR 
show me that something is wrong with the file or
the password is wrong. I tried to enter the provided password by copy+paste and 
as manual input. I also deleted the file and
downloaded it again from the FreeSurfer homepage and tried this on a different 
computer. Unfortunately, none of this worked.

Attached you will find the error message from WinRAR.

C:\Users\user\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z: Checksum error in the 
encrypted file
C:\Users\user\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z. Corrupt file or wrong 
password.

 

Best regards,
Katharina


>>> Katharina Hense 25.04.2022, 10:59 >>>

Hello,
 
I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Can I 
get the passcode for
FS_7_2_0_Ubuntu_18_04_06.ova.7z?
 
Sincerely,
Katharina
___
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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] FreeSurfer 7Zip archive passcode

[fsbuild]

External Email - Use Caution

I will send you an alternate way to download the file.
- R.

On Apr 28, 2022, at 04:15, Katharina Hense 
 
wrote:External Email - Use 
CautionDear FreeSurfer 
team, Thank you for providing the passwords and some instructions for the 
installation.However, I encountered a problem while unzipping the file. Both 
7zip and WinRAR show me that something is wrong with the file or the password 
is wrong. I tried to enter the provided password by copy+paste and as manual 
input. I also deleted the file and downloaded it again from the FreeSurfer 
homepage and tried this on a different computer. Unfortunately, none of this 
worked.Attached you will find the error message from 
WinRAR.C:\Users\user\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z: Checksum error 
in the encrypted file C:\Users\user\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z. 
Corrupt file or wrong password. Best regards,Katharina>>> 
Katharina Hense 25.04.2022, 10:59 >>>Hello, I'm trying to expand 
the 7Zip archive for FreeSurfer on the VirtualBox. Can I get the passcode for 
FS_7_2_0_Ubuntu_18_04_06.ova.7z? Sincerely,Katharina___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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] Mri Convert Bruker MGRE files dicom to nii error

[Mateo Jean]

External Email - Use Caution

Hi, 

Thanks! 
It works I guess. 
I didn't manage to use setenv in the command line before using mri_convert 
(command not found) 

But I did the following modifications and mri_convert works now (it doesn't put 
the error message anymore and I have the nifti file at the end) : 

 
Opening ubuntu 

> $cd then > $ nano .bashrc 

And I write just before the source /path/freesurfer/7.2.0/SetUpFreeSurfer.sh 
the line : export FS_LOAD_DWI=0 

Then I change the directory to freesurfer : > $ cd /path//freesurfer/7.2.0 and 
open the csh : > $nano SetUpFreeSurfer.csh 
I add setenv FS_LOAD_DWI before the line source 
$FREESURFER_HOME/FreeSurferEnv.csh 

 
I suppose this locks the DWI to zero and I need to remodify it if one day I 
want to use Diffusion data. 

So mri_convert for Bruker data now works. The last problem (and I might create 
an other post) is that negative values were not kept. When I compared phase 
imagec converted in nifti with 3D slicer and phase image converted in nifti 
with mri_convert, 3D slicer's nifti have values ranging from - 32 766 to 32 766 
while mri_convert's nifti only have values ranging from 0 to 32 767. 

How can I set mri_convert to convert values in signed- 16 bits ? 

Thank you for your previous answer !!! 

Best Regards, 

Mateo 



De: "Huang, Yujing"  
À: "freesurfer"  
Envoyé: Mercredi 27 Avril 2022 15:20:37 
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error 



I’m assuming you didn’t source .bashrc after editing it. 



You can actually set it on the command line before submitting mri_convert. So, 
the setting only affect that window. You can use echo $FS_LOAD_DWI to verify 
the setting. 



Here is an example for csh: 



>echo $FS_LOAD_DWI 

FS_LOAD_DWI: Undefined variable. 

>setenv FS_LOAD_DWI 0 

>echo $FS_LOAD_DWI 

0 

>mri_convert … 



I’m hoping it will solve your problem by setting the environment variable. 



Best, 



Yujing 




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mateo Jean 
Sent: Wednesday, April 27, 2022 8:16 AM 
To: freesurfer  
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error 




External Email - Use Caution 


Thank you for your answer. 





Even though I don't need the DTI values, I can't avoid this message : 




"ERROR: the number of frames * number of slices does not equal the number of 
dicom files." 



I'm not very familiar with Ubuntu too so I might have made a mistake : 





I try to set the environnement variable ‘ export FS_LOAD_DWI = 0 ’ in bash (I 
use the command $cd then $nano .bashrc and write after 

export FS_LICENSE=/home/jeanmri/license.txt 

export FREESURFER_HOME=/home/jeanmri/freesurfer/7.2.0 

the line export FS_LOAD_DWI = 0 ) 





Then I open with nano the FreeSurferEnv.csh and add setenv FS_LOAD_DWI 0 at the 
end but when I use mri_convert on my bruker dicom files, the same error 
reappeared. 





Did I miss something ? 






Best Regards, 






Mateo 






De: "Huang, Yujing" < [ mailto:yhuan...@mgh.harvard.edu | 
yhuan...@mgh.harvard.edu ] > 
À: "freesurfer" < [ mailto:freesurfer@nmr.mgh.harvard.edu | 
freesurfer@nmr.mgh.harvard.edu ] > 
Envoyé: Mardi 26 Avril 2022 21:22:28 
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error 





Hi Mateo, 



It looks like mri_convert terminated prematurely when you tried to convert 
those 512 dicom files. 



Those error messages are printed when mri_convert wasn’t able to retrieve DTI 
information from dicom. If you don’t need the DTI values, you can ignore those 
error messages. 



Also, looking at the codes, I think if you set environment variable FS_LOAD_DWI 
to 0 before running mri_convert, it should finish convert all 512 dicom files. 
To set the environment variable, you do ‘export FS_LOAD_DWI = 0’ in bash, and 
‘setenv FS_LOAD_DWI 0’ in csh. 



Can you give it a try? 



Thanks. 



Yujing 






From: [ mailto:freesurfer-boun...@nmr.mgh.harvard.edu | 
freesurfer-boun...@nmr.mgh.harvard.edu ] < [ 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu | 
freesurfer-boun...@nmr.mgh.harvard.edu ] > On Behalf Of Mateo Jean 
Sent: Tuesday, April 26, 2022 7:51 AM 
To: freesurfer < [ mailto:freesurfer@nmr.mgh.harvard.edu | 
freesurfer@nmr.mgh.harvard.edu ] > 
Subject: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error 




External Email - Use Caution 


Hello FreeSurfer Developers 





I hope i don't spam, if anyone has a clue... 








I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to 
my Bruker multi gradient echo phase files then enter the following command : 


mri_convert MRIm001.dcm phaseMGE.nii 





Here is the first message : 

Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

[Huang, Yujing]

Hi Mateo,

I’m glad mri_convert works for you now.

I’m little confused about the value ranges you saw. We map DT_SIGNED_SHORT 
(-32766~32766) to signed short.  mri_info should give ‘type: SHORT (4)’.

In Freesurfer 7.2, we don’t support DT_UINT16. We map DT_UINT16 (0~65535) to 
signed short. You will see value maxed at 32766 for DT_UINT16. Is this what you 
were experiencing?

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mateo Jean
Sent: Thursday, April 28, 2022 6:06 AM
To: freesurfer 
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error


External Email - Use Caution
Hi,

Thanks!
It works I guess.
I didn't manage to use setenv in the command line before using mri_convert 
(command not found)

But I did the following modifications and mri_convert works now (it doesn't put 
the error message anymore and I have the nifti file at the end) :

Opening ubuntu

>$cd then >$ nano .bashrc

And I write just before the source /path/freesurfer/7.2.0/SetUpFreeSurfer.sh
the line : export FS_LOAD_DWI=0

Then I change the directory to freesurfer : >$ cd /path//freesurfer/7.2.0 and 
open the csh : >$nano SetUpFreeSurfer.csh
I add setenv FS_LOAD_DWI before the line source 
$FREESURFER_HOME/FreeSurferEnv.csh

I suppose this locks the DWI to zero and I need to remodify it if one day I 
want to use Diffusion data.

So mri_convert for Bruker data now works. The last problem (and I might create 
an other post) is that negative values were not kept. When I compared phase 
imagec converted in nifti with 3D slicer and phase image converted in nifti 
with mri_convert, 3D slicer's nifti have values ranging from - 32 766 to 32 766 
while mri_convert's nifti only have values ranging from 0 to 32 767.

How can I set mri_convert to convert values in signed-16 bits  ?

Thank you for your previous answer !!!

Best Regards,

 Mateo



De: "Huang, Yujing" mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mercredi 27 Avril 2022 15:20:37
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

I’m assuming you didn’t source .bashrc after editing it.

You can actually set it on the command line before submitting mri_convert. So, 
the setting only affect that window. You can use echo $FS_LOAD_DWI to verify 
the setting.

Here is an example for csh:

>echo $FS_LOAD_DWI
FS_LOAD_DWI: Undefined variable.
>setenv FS_LOAD_DWI 0
>echo $FS_LOAD_DWI
0
>mri_convert …

I’m hoping it will solve your problem by setting the environment variable.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mateo Jean
Sent: Wednesday, April 27, 2022 8:16 AM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error


External Email - Use Caution
Thank you for your answer.

Even though I don't need the DTI values, I can't avoid this message :

"ERROR: the number of frames * number of slices does not equal the number of 
dicom files."

I'm not very familiar with Ubuntu too so I might have made a mistake :

I try to set the environnement variable  ‘export FS_LOAD_DWI = 0’ in bash (I 
use the command $cd then $nano .bashrc and write after
export FS_LICENSE=/home/jeanmri/license.txt
export FREESURFER_HOME=/home/jeanmri/freesurfer/7.2.0
the line export FS_LOAD_DWI = 0)

Then I open with nano the FreeSurferEnv.csh and add  setenv FS_LOAD_DWI 0  at 
the end but when I use mri_convert on my bruker dicom files, the same error 
reappeared.

Did I miss something ?

Best Regards,

 Mateo


De: "Huang, Yujing" mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mardi 26 Avril 2022 21:22:28
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

Hi Mateo,

It looks like mri_convert terminated prematurely when you tried to convert 
those 512 dicom files.

Those error messages are printed when mri_convert wasn’t able to retrieve DTI 
information from dicom. If you don’t need the DTI values, you can ignore those 
error messages.

Also, looking at the codes, I think if you set environment variable FS_LOAD_DWI 
to 0 before running mri_convert, it should finish convert all 512 dicom files. 
To set the environment variable, you do ‘export FS_LOAD_DWI = 0’ in bash, and 
‘setenv FS_LOAD_DWI 0’ in csh.

Can you give it a try?

Thanks.

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:fr

Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

[Huang, Yujing]

Hi Mateo,

Sorry, I’m confused by your question.

Can you try to rerun mri_convert by passing it additional flag 
‘--rescale-dicom’, or setting environment variable FS_RESCALE_DICOM to 1?

Hope that will solve your problem. Repost your question in a different thread 
is a good idea since it is a different problem now.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Thursday, April 28, 2022 10:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

Hi Mateo,

I’m glad mri_convert works for you now.

I’m little confused about the value ranges you saw. We map DT_SIGNED_SHORT 
(-32766~32766) to signed short.  mri_info should give ‘type: SHORT (4)’.

In Freesurfer 7.2, we don’t support DT_UINT16. We map DT_UINT16 (0~65535) to 
signed short. You will see value maxed at 32766 for DT_UINT16. Is this what you 
were experiencing?

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mateo Jean
Sent: Thursday, April 28, 2022 6:06 AM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error


External Email - Use Caution
Hi,

Thanks!
It works I guess.
I didn't manage to use setenv in the command line before using mri_convert 
(command not found)

But I did the following modifications and mri_convert works now (it doesn't put 
the error message anymore and I have the nifti file at the end) :

Opening ubuntu

>$cd then >$ nano .bashrc

And I write just before the source /path/freesurfer/7.2.0/SetUpFreeSurfer.sh
the line : export FS_LOAD_DWI=0

Then I change the directory to freesurfer : >$ cd /path//freesurfer/7.2.0 and 
open the csh : >$nano SetUpFreeSurfer.csh
I add setenv FS_LOAD_DWI before the line source 
$FREESURFER_HOME/FreeSurferEnv.csh

I suppose this locks the DWI to zero and I need to remodify it if one day I 
want to use Diffusion data.

So mri_convert for Bruker data now works. The last problem (and I might create 
an other post) is that negative values were not kept. When I compared phase 
imagec converted in nifti with 3D slicer and phase image converted in nifti 
with mri_convert, 3D slicer's nifti have values ranging from - 32 766 to 32 766 
while mri_convert's nifti only have values ranging from 0 to 32 767.

How can I set mri_convert to convert values in signed-16 bits  ?

Thank you for your previous answer !!!

Best Regards,

 Mateo



De: "Huang, Yujing" mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mercredi 27 Avril 2022 15:20:37
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

I’m assuming you didn’t source .bashrc after editing it.

You can actually set it on the command line before submitting mri_convert. So, 
the setting only affect that window. You can use echo $FS_LOAD_DWI to verify 
the setting.

Here is an example for csh:

>echo $FS_LOAD_DWI
FS_LOAD_DWI: Undefined variable.
>setenv FS_LOAD_DWI 0
>echo $FS_LOAD_DWI
0
>mri_convert …

I’m hoping it will solve your problem by setting the environment variable.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mateo Jean
Sent: Wednesday, April 27, 2022 8:16 AM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error


External Email - Use Caution
Thank you for your answer.

Even though I don't need the DTI values, I can't avoid this message :

"ERROR: the number of frames * number of slices does not equal the number of 
dicom files."

I'm not very familiar with Ubuntu too so I might have made a mistake :

I try to set the environnement variable  ‘export FS_LOAD_DWI = 0’ in bash (I 
use the command $cd then $nano .bashrc and write after
export FS_LICENSE=/home/jeanmri/license.txt
export FREESURFER_HOME=/home/jeanmri/freesurfer/7.2.0
the line export FS_LOAD_DWI = 0)

Then I open with nano the FreeSurferEnv.csh and add  setenv FS_LOAD_DWI 0  at 
the end but when I use mri_convert on my bruker dicom files, the same error 
reappeared.

Did I miss something ?

Best Regards,

 Mateo


De: "Huang, Yujing" mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mardi 26 Avril 2022 21:22:28
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

Hi Mateo,

It

[Freesurfer] Request for 7 zip password VM_67

[Bastola, Subrat]

External Email - Use Caution

Hi,


 I just need a passcode to archive the zip folder for file
FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install free surfer virtual disk.



Regards,
Subrat




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[Freesurfer] segmentHA_T1, mri_segstats: How can I get the PVC uptake for amygdalar nuclei?

[Tun, Samantha]

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Hello Freesurfer Devs!

I am attempting to extract the tau uptake in the amygdalar segmentations. I ran 
this command:
mri_segstats --seg
rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i anat_resliced.mgz --sum
rHA_stats.dat
to try and calculate the tau uptake.

I was able to get an output, but I am unsure how to proceed from here. I 
basically want to get the pvc uptake of the amygdalar and hippocampal subfields 
scaled to the pons. I don't think I can run the mri_gtmpvc command, so if you 
had any insight on how to calculate the scaled uptake of tau in the subfields, 
let me know!

Best,
Samantha
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