Re: [Freesurfer] Permission denied error from -localGI

2022-05-02 Thread Billah, Tashrif 
No it does not exist.

-Tashrif



Douglas N. 
Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Mon, 02 May 2022 12:40:55 
-0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20220502>


Does that file exist? If so what are its perms?



From: Billah, Tashrif
Sent: Friday, April 29, 2022 3:53 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Permission denied error from -localGI

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. 
However, we ran into the same error:

>> reading filled volume...
/bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for reading
ERROR: loading 
/data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file



What can we do now?

-Tashrif


===

Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700
Can you just try it with 7.2? We had some problems at one point with 
temporary files in lGI that were fixed with 7.2

===

On 4/27/2022 9:36 AM, Billah, Tashrif wrote:
Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



 Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===


What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

It does not exist and cannot be created in a shared cluster.
Is there a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?



===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
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Re: [Freesurfer] Freesurfer on WSL2/Ubuntu 20: Could not connect to any X display

2022-05-02 Thread fsbuild 
External Email - Use Caution

Hello Maaike,
If you have not already done so, I would try,
$ export DISPLAY=:0.0
See if you get the same IP address you used below from the ip route command. 
If you don’t see the ip command is installed with,
$ which ip/bin/ip
… then sudo (or as root) to install it by doing,
$ sudo apt installiproute2
… when done you should see
$ which ip/bin/ip
Then see what you get for an IP address with the command below. Just as 
an example let’s say the result was 172.40.20.10
$ip route|awk '/^default/{print $3}'172.40.20.10
If you get a different IP address as the result from the ip command compared to 
the IP address you already tried setting in DISPLAY, then try setting DISPLAY 
with the above address - appending :0.0 to it, e.g., using my pretend IP 
address result,
$ export DISPLAY=172.40.20.10:0.0
If this does not work with Xming, then try using MobaXterm. Some people 
have found MobaXTerm to be more reliable and easier to setup compared to Xming.
https://secure-web.cisco.com/1PqVMG91VpcP_-hOrawBKaVjEi3Gmb_gU5j7isLHOirjuOJBb6M9axVUd7FFdisEeU_xC6E8klAY7qzGSIe6VaiWv5gqWjOqsuVirMl9y_jHR6ZbOqLbswju8jje3lBNxB19pWfErgC-auGbsQ352iN3DVwkwQ8oJgQP2znDNoo5p_OHoqBbAl46yr38kM1yMvEDWhQY6Hewx9UOWodPyW4Qpbg3TJspBokrhnATMJAZO7ag5_TfyRm_2YwvEAExo1b0bTRS-1D9NRtgxkxfL1Q1L2CPBgeZ0Z4O006Kdc-U0fN0uYZh85y03AjsXcVku/https%3A%2F%2Fmobaxterm.mobatek.net
FYI, if you are OK with running Freesurfer 7.2.0, then if you have not already 
done so, I would suggest you try installing and running the Ubuntu 18 
Freesurfer debian package on Ubuntu 20.
… download 
from,https://secure-web.cisco.com/1rvaTELxM79WMd_dCOCgo8HxuoY20rI0XiWNF-o3ojqojnZYIKQXKON8Je2Cq-BVRSDfY6-Q_-_g_sAS4KYopaZzd1fypbPuOXX8skf1Nb2uftw4xO6IEEt5qcir-kuPeRUeo70YBIR5ineNQK9bvkmUpE6yiV2C35gV2QlqZj51j8rc_CnWufipBxZfA7twqU7SoEyFR9XB5HE1Crv98zV009h2KKbAskGYHGCddZNw7IZmmYCQk4CH4AKYYcbB_PSF_RlCrKAMSfoakZFIob8Nk_VBWrbf4GKnyP0pMtMJv8QJ6GJqDLWCGw4LG0lTS/https%3A%2F%2Fsurfer.nmr.mgh.harvard..edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb
… then to install$ sudo apt install ./freesurfer_7.2.0_amd64.deb
- R.
On May 2, 2022, at 15:32, Maaike Oosterling 
maaikeoosterl...@hotmail.com 
wrote:External Email - Use 
CautionHello everyone,As I 
currently do not have any access to university servers, I am trying to install 
Freesurfer on my own personal Windows laptop, mostly just to experiment in 
between doing actual studies.I followed the FS7_wsl_ubuntu guide, running it on 
WSL2/Ubuntu 20 and as I am not really that good with computers at all, I was 
already impressed with myself I got this far... until I hit the error predicted 
in the guide. I followed the guide's steps to edit $DISPLAY and I have also 
edited the Xming X0.hosts file to represent my own 
localhostmaaikeo@LAPTOP-EA4GL46K:/mnt/c/Program Files (x86)/Xming$ cat 
X0.hostslocalhost172.27.128.1maaikeo@LAPTOP-EA4GL46K:~ echo 
$DISPLAY172.27.128.1:0Yet I am still getting the same error as before (although 
I feel the 'No protocol specified' is new)maaikeo@LAPTOP-EA4GL46K:~$ 
freeviewNo protocol specifiedQXcbConnection: Could not connect to display 
172.27.128.1:0Could not connect to any X display.I've looked all over and have 
found numerous threads that slightly relate to this issue, but none of the 
fixes listed there. I have double checked my Xming install and it is definitely 
running in the background.. Is there anything I might have missed? Or is this 
an indicator that my laptop is just not up for the task?Thanks in 
advance!Maaike 
Oosterling___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Average subject and head size

2022-05-02 Thread Sébastien Daligault 
External Email - Use Caution

Thank you for the answer.
So the averaged MRI has the size of the mni305.
Is there a way to give it its true size?
This can be problematic for children's MRIs.

> Le 2 mai 2022 à 21:33, Douglas N. Greve  a écrit :
> 
> It will remain in talairach space ( actually mni305)
> 
> 
> On 5/2/2022 1:08 PM, Sébastien Daligault wrote:
>> External Email - Use Caution
>> 
>> Hi support,
>> I have a naive question about the make_average_subject function.
>> I want to average MRIs to create a template.
>> This process uses the talairach transformation to average in a common space. 
>> Once averaged, is the MRI still in this space or is there an inverse 
>> transformation to return to a real size? (which would be the average size of 
>> talairach boxes).
>> Thank you in advance for your answer.
>> Sebastien
>> 
>> ___
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> 
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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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> to continue communication over unencrypted e-mail, please notify the sender 
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Re: [Freesurfer] Permission denied error from -localGI

2022-05-02 Thread Douglas N. Greve 

Does that file exist? If so what are its perms?

On 4/29/2022 3:53 PM, Billah, Tashrif wrote:
Thank you Douglas. We took our time to install FreeSurfer 7.2 and 
retry. However, we ran into the same error:


>> reading filled volume...
/bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for 
reading
ERROR: loading 
/data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz 
as MGH

Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file



What can we do now?

-Tashrif


    ===
    Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700
    Can you just try it with 7.2? We had some problems at one point 
with temporary files in lGI that were fixed with 7.2


    ===
    On 4/27/2022 9:36 AM, Billah, Tashrif wrote:
    Sorry about missing your earlier question--our FreeSurfer is 7.1.0

    We still need your help with this issue.

    Thank you,
    Tashrif



     Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

    ===


    What version of FS are you running?

    On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

        It does not exist and cannot be created in a shared cluster.
    Is there a way to define a different folder for
    /scratch/tp24093955057547375.load_mgh.m.mgh?



    ===
    Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

    Do you have permission to /scratch? Does it exist?

    ===
    Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

    Hi all,

    We are trying to run recon-all with -localGI but running into an 
unknown

    permission denied error:

    $ recon-all -s sub-1001 -localGI

    ```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
     exit
    =


    < M A T L A B (R) >
    Copyright 1984-2017 The MathWorks, Inc.
    R2017a (9.2.0.556344) 64-bit (glnxa64)
    March 27, 2017


    >> reading filled volume...
    /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission 
denied



    ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh 
for reading


    ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
     as MGH
    Struct contents reference from a non-struct array object.


    Error in make_outer_surface (line 25)
    volume=vol.vol;

    >>
    ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


    recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 
2022


    ```

    Our MATLAB environment is properly setup and we regularly run other
    FreeSurfer-MATLAB commands. So I do not think that is causing the 
issue.


    Best,
    Tashrif

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Re: [Freesurfer] Average subject and head size

2022-05-02 Thread Douglas N. Greve 
It will remain in talairach space ( actually mni305)


On 5/2/2022 1:08 PM, Sébastien Daligault wrote:
>  External Email - Use Caution
>
> Hi support,
> I have a naive question about the make_average_subject function.
> I want to average MRIs to create a template.
> This process uses the talairach transformation to average in a common space. 
> Once averaged, is the MRI still in this space or is there an inverse 
> transformation to return to a real size? (which would be the average size of 
> talairach boxes).
> Thank you in advance for your answer.
> Sebastien
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Freesurfer on WSL2/Ubuntu 20: Could not connect to any X display

2022-05-02 Thread Maaike Oosterling 
External Email - Use Caution

Hello everyone,

As I currently do not have any access to university servers, I am trying to 
install Freesurfer on my own personal Windows laptop, mostly just to experiment 
in between doing actual studies.

I followed the FS7_wsl_ubuntu guide, running it on WSL2/Ubuntu 20 and as I am 
not really that good with computers at all, I was already impressed with myself 
I got this far... until I hit the error predicted in the guide. I followed the 
guide's steps to edit $DISPLAY and I have also edited the Xming X0.hosts file 
to represent my own localhost

maaikeo@LAPTOP-EA4GL46K:/mnt/c/Program Files (x86)/Xming$ cat X0.hosts
localhost
172.27.128.1
maaikeo@LAPTOP-EA4GL46K:~ echo $DISPLAY
172.27.128.1:0

Yet I am still getting the same error as before (although I feel the 'No 
protocol specified' is new...)

maaikeo@LAPTOP-EA4GL46K:~$ freeview
No protocol specified
QXcbConnection: Could not connect to display 172.27.128.1:0
Could not connect to any X display.

I've looked all over and have found numerous threads that slightly relate to 
this issue, but none of the fixes listed there. I have double checked my Xming 
install and it is definitely running in the background.. Is there anything I 
might have missed? Or is this an indicator that my laptop is just not up for 
the task?

Thanks in advance!
Maaike Oosterling

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Re: [Freesurfer] error for qdec

2022-05-02 Thread Douglas N. Greve 

qdec has been retired and is not available in 7.2.0

On 5/2/2022 10:30 AM, Chen ZY wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to use qdec tool, but I received the following error 
when I type qdec in the terminal:


developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ qdec

Tcl_Init error: Can't find a usable init.tcl in the following 
directories:


/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 
/usr/local/freesurfer/7.2.0/lib/tcl8.4 
/usr/local/freesurfer/lib/tcl8.4 /usr/local/freesurfer/7.2.0/library 
/usr/local/freesurfer/library /usr/local/freesurfer/tcl8.4.6/library 
/usr/local/tcl8.4.6/library 
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4


This probably means that Tcl wasn't installed properly.

Error initializing Tcl.

I would be appreciated if you can help me solve this problem.

Thank you very much!

Regrads,

ZYC


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[Freesurfer] Average subject and head size

2022-05-02 Thread Sébastien Daligault 
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Hi support,
I have a naive question about the make_average_subject function.
I want to average MRIs to create a template.
This process uses the talairach transformation to average in a common space. 
Once averaged, is the MRI still in this space or is there an inverse 
transformation to return to a real size? (which would be the average size of 
talairach boxes).
Thank you in advance for your answer.
Sebastien

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Re: [Freesurfer] [ext] Re: whole brain volume measures from SynthSeg+ ??

2022-05-02 Thread jason.millw...@mdc-berlin.de 
External Email - Use Caution

Hello Eugenio,

Thanks so much for the quick response. I'm happy to hear that you are working 
on including intracranial volume in SynthSeg+, and I look forward to using 
that. I'll keep an eye on the FreeSurfer development version page to see when 
this feature has been implemented.


re. whole brain volume, indeed we are considering to just sum up the individual 
volumes to get a total, though I'm just a bit wary of doing that, in case 
something is missing. Also, in my patient population both brain and ventricle 
volumes are changing, which is why I am especially interested in ICV as a more 
stable measure.

Thanks again,

Jason.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: May 2, 2022 3:17:24 PM
To: Freesurfer support list
Subject: [ext] Re: [Freesurfer] whole brain volume measures from SynthSeg+ ??

Dear Jason,

Thank you very much for the interest in our tools.

We understand that intracranial volume (ICV) is a crucial covariate in 
volumetric analysis and are working on incorporating it into SynthSeg (and 
SynthSeg+). The good news is that we have a prototype pretty much ready and it 
should be added to the development version of FreeSurfer pretty soon.

As for the whole brain volume: it should be straightforward for users to 
compute it theirselves, and then they’re free to included or disregards eg 
ventricles as they wish. But I’m open to being convinced of the opposite. 
Either way, it’s a trivial change to the code.

Cheers,

/Eugenio


Juan Eugenio Iglesias
http://secure-web.cisco.com/1Tw1ekVUNbflV6gwSkgnFZctvx_mXX2FzQnVX3gguP9rrcusDyP1Y955McGEoM1mahXx-5XLT9h02dE2q0j4ETpLSCQ3A2DXRUoGhnnalnxIAqtFSFH27O6BN4g3a6vaIehe6IpteeVjbjUBwOA197jorlY68cG_Pax8ggVnuAzT97JQwWtNz3GbnBF08T8lAEj-9J0-oKD8d4bRQmG9EyiL_hXYAPyB-1dTul8d16WCiotYc57gEv5dmy28nv8QJ-TtUzcG1B80nwaAqJYL2giMqOKgBW4kUApMkZIneEt3GpJ3c42jPFJZ7-FLkYZf7/http%3A%2F%2Fwww.jeiglesias.com

On May 2, 2022, at 04:37, 
jason.millw...@mdc-berlin.de wrote:

External Email - Use Caution

Hello!
I am using SynthSeg (SynthSeg+), and so far testing this on my own data is 
going well.
A question I have for the forum is whether it is possible to get additional 
measures, such as whole brain volume and total intracranial volume. Both of 
these (and others) are available from FreeSurfer, but do not seem to be 
included in the SynthSeg output. I see a discussion thread from a few months 
ago referring to SamSeg, but I would really prefer to get this from SynthSeg, 
if possible – it runs much faster, and we are already implementing it

These whole brain measures are very important to our work, since we are 
measuring relative changes in patients over time, and need to normalize the 
volumes. Is there any way to get this directly from SynthSeg+? Any help is 
appreciated!
Best regards,
Jason Millward.



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[Freesurfer] error for qdec

2022-05-02 Thread Chen ZY 
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Dear FreeSurfer Developers,

I'm attempting to use qdec tool, but I received the following error when I type 
qdec in the terminal:

developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ qdec
Tcl_Init error: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 
/usr/local/freesurfer/7.2.0/lib/tcl8.4 /usr/local/freesurfer/lib/tcl8.4 
/usr/local/freesurfer/7.2.0/library /usr/local/freesurfer/library 
/usr/local/freesurfer/tcl8.4.6/library /usr/local/tcl8.4.6/library 
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Error initializing Tcl.


I would be appreciated if you can help me solve this problem.

Thank you very much!

Regrads,

ZYC

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Re: [Freesurfer] whole brain volume measures from SynthSeg+ ??

2022-05-02 Thread Iglesias Gonzalez, Juan E. 
Dear Jason,

Thank you very much for the interest in our tools.

We understand that intracranial volume (ICV) is a crucial covariate in 
volumetric analysis and are working on incorporating it into SynthSeg (and 
SynthSeg+). The good news is that we have a prototype pretty much ready and it 
should be added to the development version of FreeSurfer pretty soon.

As for the whole brain volume: it should be straightforward for users to 
compute it theirselves, and then they’re free to included or disregards eg 
ventricles as they wish. But I’m open to being convinced of the opposite. 
Either way, it’s a trivial change to the code.

Cheers,

/Eugenio


Juan Eugenio Iglesias
http://www.jeiglesias.com

On May 2, 2022, at 04:37, 
jason.millw...@mdc-berlin.de wrote:

External Email - Use Caution

Hello!
I am using SynthSeg (SynthSeg+), and so far testing this on my own data is 
going well.
A question I have for the forum is whether it is possible to get additional 
measures, such as whole brain volume and total intracranial volume. Both of 
these (and others) are available from FreeSurfer, but do not seem to be 
included in the SynthSeg output. I see a discussion thread from a few months 
ago referring to SamSeg, but I would really prefer to get this from SynthSeg, 
if possible – it runs much faster, and we are already implementing it

These whole brain measures are very important to our work, since we are 
measuring relative changes in patients over time, and need to normalize the 
volumes. Is there any way to get this directly from SynthSeg+? Any help is 
appreciated!
Best regards,
Jason Millward.



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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 
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[Freesurfer] whole brain volume measures from SynthSeg+ ??

2022-05-02 Thread jason.millw...@mdc-berlin.de 
External Email - Use Caution

Hello!
I am using SynthSeg (SynthSeg+), and so far testing this on my own data is 
going well.
A question I have for the forum is whether it is possible to get additional 
measures, such as whole brain volume and total intracranial volume. Both of 
these (and others) are available from FreeSurfer, but do not seem to be 
included in the SynthSeg output. I see a discussion thread from a few months 
ago referring to SamSeg, but I would really prefer to get this from SynthSeg, 
if possible – it runs much faster, and we are already implementing it

These whole brain measures are very important to our work, since we are 
measuring relative changes in patients over time, and need to normalize the 
volumes. Is there any way to get this directly from SynthSeg+? Any help is 
appreciated!
Best regards,
Jason Millward.


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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 
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