[Freesurfer] Fusion of PET and T1 weighted

[Amar Shukla]

External Email - Use Caution

Dear Freesurfer Community.

I want to do image fusion (PET+T1) = T' weighted image. Then I want to go
for the feature extraction from this T1 modality which I will get from the
fusion.So how i can go for this.

Questions are:

1) Do I have to use PET Surfer for this? Does Pet Surfer support the fusion
of the two different modality.
2) I am in the perception that I want  PET+ T = T' , or does it justify the
multimodality approach for the detection of disease.
3) If i extract features from the different modality and then i combine it.
Can we say that this is the multimodality approach of Image Fusion.

Please advise me and provide the approach or the tool which will help me
for the multimodality.




-- 
With Regards,
Amar Shukla
Assistant Professor,
M tech AI ANN(2014-2016),
Centre Of Information Technology,
UPES
Contact :+91 897 977 8016
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[Freesurfer] mghread : cannot open the file

[priya padma]

External Email - Use Caution

Hello Team,

I am trying to find the volume of WM, GM, CSF separately and I came
across this command namely
"mri_compute_volume_fractions"

Looking through all the email archives I gave the following line as the
command after setting the paths

$ mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz

but I get the following error

user-MacBook-Pro:sub-AD003S1059S61129 user$ mri_compute_volume_fractions
--o test --regheader tester /mri/norm.mgz

 supposed to be reproducible but seed not set


7.3.2

sysname  Darwin

hostname user-MacBook-Pro.local

machine  x86_64

user 

setenv SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects

cd /Applications/freesurfer/7.3.2/subjects/sub-AD003S1059S61129

mri_compute_volume_fractions --o test --regheader tester /mri/norm.mgz

outstem test

regfile (null)

regtype 0

segfile aseg.mgz

wsurf white

psurf pial

TempVolFile /mri/norm.mgz

USF 2

Reading in aseg and surfs from
/Applications/freesurfer/7.3.2/subjects/tester

Loading /Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz

error: mghRead(/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz,
-1): could not open file



I set all the paths so why am I not able to read the mgz file?


Could anyone help me with this ?


Thank you
-- 
Best Regards
Padma Priya
*AI Developer *

*PhenoMx, Inc.*
*pr...@phenomx.ai  | (+82)10-5405-2685*
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Re: [Freesurfer] Running recon-all in parallel

[priya padma]

External Email - Use Caution

thank you for your reply, I got the issue resolved.

On Thu, Oct 13, 2022 at 12:02 AM Wighton, Paul 
wrote:

> Hi Padma,
>
> It looks like tcsh isn't installed.  Can you try installing it by running
>
> ```
> sudo apt update
> sudo apt install tcsh
> ```
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of priya padma <
> pr...@phenomx.ai>
> *Sent:* Wednesday, October 12, 2022 3:16 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] Running recon-all in parallel
>
>
> External Email - Use Caution
>
> Hello team,
>
> As freesurfer takes lot of time for processing one subject, I was
> searching on how to run recon-all for multiple subjects in parallel and I
> found the following in Andy's brain book doc
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1dnYvwJNSItIjaPsftdGIbD2HV040qoka4qQwTE8_MjR3zZAzEN5dFgASY5lpVSyqWiatxoOClMZYnZXmHWnRdyIRfN4hVdDAlu2GQd02ooOCXd2iCGk3j9tPOr1hfKVXEQlwJWt0GDLVac6536UspcCVTXaKnkSQFjBkVuDDBGP7c-XrNv3XR8tly8BmI2zR4YCoNWI5-9EVWhby58oYrqzDNPPokQuYsxQYjTl9eyJy_SZwbB6uMH2MYjmxw3TvJMM4DiYfCwTCbHMSSvydg7ReTdFbaM0fHhgOAL8-hxZMBQeKC4xWPBkhsDRyqO6jG_KOc7gR90dMXprnUooLFQ/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_04_ReconAllParallel.html
> 
>
> and ran
>
> $ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache
>
> and I get the error "/usr/bin/bash:
> /home/***/***/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such
> file or directory "
>
> I believe that this is not the right command for linux, ubuntu 20 OS but I
> am not sure.
>
> Could anyone help me with this?
>
> Thank you
>
> --
> Best Regards
> Padma Priya
> *AI Developer *
>
> *PhenoMx, Inc.*
> *pr...@phenomx.ai  | (+82)10-5405-2685*
>
>
> ___
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> Brigham Compliance HelpLine at
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>  .
> 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.
>


-- 
Cheers
Priya
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Re: [Freesurfer] Extract single time frame

[Proulx, Jean Sebastien]

Hello,

Specifying a single volume frame with # is great, but how to specify a range or 
multiple arbitrary choosen frames?
Something like #0..9 would be nice for the 1st to the 10th frame, and #0,2,4 
for the 1st, 3rd and 5th frames.

Thanks for the help and
Have a very good day!
Sebastien
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[Freesurfer] Issue with rotation during longitudinal base creation

[Nathan Kindred (PGR)]

External Email - Use Caution

Hi,

I have been processing longitudinal data using the longitudinal processing 
stream but for some subjects I am having getting this error when creating the 
base:

Input rotation's max deviation from rotation is: 0.000258493
MyMatrix::RotationMean input(s) not rotation

What would be the best way to fix this?

Best,
Nathan
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Re: [Freesurfer] Running recon-all in parallel

[Wighton, Paul]

Hi Padma,

It looks like tcsh isn't installed.  Can you try installing it by running

```
sudo apt update
sudo apt install tcsh
```

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of priya padma 

Sent: Wednesday, October 12, 2022 3:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Running recon-all in parallel


External Email - Use Caution

Hello team,

As freesurfer takes lot of time for processing one subject, I was searching on 
how to run recon-all for multiple subjects in parallel and I found the 
following in Andy's brain book doc

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_04_ReconAllParallel.html

and ran

$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache

and I get the error "/usr/bin/bash: /home/***/***/freesurfer/bin/recon-all: 
/bin/tcsh: bad interpreter: No such file or directory "

I believe that this is not the right command for linux, ubuntu 20 OS but I am 
not sure.

Could anyone help me with this?

Thank you

--
Best Regards
Padma Priya
AI Developer
[https://secure-web.cisco.com/1XLVnI0aLlqbfbCotrXgyfGAqS76ynzDA16AK0UPYPBFVyMmcGdjYw13PRbu_GL-p855BsKJU9SklwJQSakQKpxHv5eMf2-laEUBjeva9dcHFAZapnnIf93hWg8pRAWbVcg-2MydVNiXmXBj-YmWq-bH0WE41eoRC00Ckz8H1it778wY8pz28_aRWuDtNfpUn8HQutOjBgPcWHG3LdEfx0Kd7gMeX1I6sOkQq-0Z8G_WOM8MvElrz2q3TpU2zG9XFRelH-mh5Reodau1XKrdoVh54-bfua-fWehURa_uA1CwdSxNM_-9MyX9uYRF1sRe6-R7mEFWx1h4ogvwU4F4RuQ/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4ykzpaZA1H7XsTn4HQ_Fs4hZSuCC45PmDIn7lgswekFx_3X0rBTeiaRDv_vFG8eJpfL5ziZS8s]
PhenoMx, Inc.
pr...@phenomx.ai | (+82)10-5405-2685


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Re: [Freesurfer] Entering MRISpositionSurface error

[fsbuild]

External Email - Use Caution

Not sure what your container is running for Freesurfer.   I would 
check you are running the latest version = 7.3.2 compiled for Ubuntu 20 from, 
https://secure-web.cisco.com/1HfVaiagqDrkuTglakaaQb9f9tkuN3NAisGLhceeHTxDiD0odIXl0a53to4D1tzSxi99Zu6h2l0doReev94ReBIeQEGtOPoXOZJgp63v4x5-EVtKLNpORaAiPbJSk2VWwH8Kzby8yTKLGiLSlwVLFUoqYrDYiCSyDL1DrDrrzSw5n3DRZe2mvPqSJuyNOMM5-jwLXDwI9nEJGYd3wQHYDO1WKcsnsDlPtcCwB9a33Xv-nqqX2KSDRnC41-V87S7vLX1mf3NzKpZteRhp0fZ5a6BurpOUVFJqty59VRBnDce-E5QD0eSZcTX63fnFt12hw_Cy_1u1X9q5spIIrHVYj0g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer_ubuntu20-7.3.2_amd64.deb

Looks like recon-all crashed with a core dump while 
running MRISpositionSurface()Segmentation fault (core dumped)Linux 
2824b6974774 5.15.0-48-generic #54~20.04.1-Ubuntu SMP Thu Sep 1 16:17:26 UTC 
2022 x86_64 x86_64 x86_64 GNU/LinuxCould be the docker container does not have 
adequate run time resources, e.g., RAM.  Maybe you could send along the 
core dump file.
- R.

On Oct 12, 2022, at 02:46, 梁群君  
wrote:
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[Freesurfer] Running recon-all in parallel

[priya padma]

External Email - Use Caution

Hello team,

As freesurfer takes lot of time for processing one subject, I was searching
on how to run recon-all for multiple subjects in parallel and I found the
following in Andy's brain book doc

https://secure-web.cisco.com/1MEMXaE4I_nNiI-Rew0Vd8aEQB5KqBzrJ54sB6YQjjf_p8mYy6QKljeDcXuzbfx_nGEh14jSussDu49EGjDdEtDy9i7nDhGycEoHv-C2WdqjEmvt-sDEUJM-T9VjrR0zRNIhfY7ECdqIaqaG2WkqiywZzfdJZhHpjGK9swf1GFUb_-eEozUbvipLWVN8IAFcqY4aWeE3uWj5lMUxf0M1XqbbZ9TyAVLjHStOCwXvzLFIPWu48DBHirGnhI9VbENX2WHXdoy9URKf61mD3lkWRUTZbWfSLFh29HXyQGOxfD4F6Rg6lRhPNX1ZVN4110JWOGtMVqTIrqq2zR3MHV-vbYw/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_04_ReconAllParallel.html

and ran

$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache

and I get the error "/usr/bin/bash: /home/***/***/freesurfer/bin/recon-all:
/bin/tcsh: bad interpreter: No such file or directory "

I believe that this is not the right command for linux, ubuntu 20 OS but I
am not sure.

Could anyone help me with this?

Thank you

-- 
Best Regards
Padma Priya
*AI Developer *

*PhenoMx, Inc.*
*pr...@phenomx.ai  | (+82)10-5405-2685*
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 .
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