Re: [Freesurfer] hippocampal-subfields-T1 error

[Duvnjak, Aleksandar]

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Dear Juan,

Thank you so much. This has sorted our issue. You're a lifesaver.

Kind regards,
Aleks Duvnjak

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: 27 March 2020 19:07
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal-subfields-T1 error


This email from jiglesiasgonza...@mgh.harvard.edu originates from outside 
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Dear Aleks,

Please try:  chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/*

Cheers,

/Eugenio





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







From:  on behalf of "Duvnjak, 
Aleksandar" 
Reply-To: Freesurfer support list 
Date: Friday, March 27, 2020 at 14:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal-subfields-T1 error



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Dear FreeSurfer Experts,



FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL



Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields



Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.



We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.



I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.



Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Iglesias Gonzalez, Juan E.]

Dear Aleks,
Please try:  chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/*
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Duvnjak, 
Aleksandar" 
Reply-To: Freesurfer support list 
Date: Friday, March 27, 2020 at 14:39
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal-subfields-T1 error


External Email - Use Caution
Dear FreeSurfer Experts,

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL

Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.

We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.

I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.

Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] hippocampal-subfields-T1 error

[Duvnjak, Aleksandar]

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To clarify, upon copying the entire FreeSurfer 6.0 package to our personal 
directory, we have then downloaded the matlab runtime MCRv80 folder to that 
directory and the issue does not appear to be the hippocampal-subfields-T1 
pipeline accessing that.

Regards,
Aleks Duvnjak

From: Duvnjak, Aleksandar
Sent: 27 March 2020 18:38
To: freesurfer@nmr.mgh.harvard.edu 
Subject: hippocampal-subfields-T1 error

Dear FreeSurfer Experts,

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platform: Secure Shell port of a high performance computer (HPC) accessed via 
Ubuntu 18.04 WSL

Having processed a cohort of 1mm^3 MRI images via the recon-all command, we 
have had issues processing the hippocampal subfield command as described: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Although we eventually want to run the command in array, we are currently 
attempting it on individual subjects to ensure a good output. Upon running the 
command we receive a "permission denied" error. The HPC is a shared cluster, 
and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot 
edit, and thus couldn't download the Matlab runtime to.

We initially thought this may be the issue, and so tried multiple workarounds, 
including copying the entirety of the FreeSurfer installation package from the 
shared directory to our own directory, within which we have editing 
permissions. This didn't help, even when setting our personal directory as the 
FREESURFER_HOME. As you can see from the end of the recon-all.log file, we 
tried numerous attempts with various workarounds and all have the same outcome.

I appreciate this may still be more of an issue with running FreeSurfer via a 
secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, 
but I'm sure you have many research labs asking questions regarding using HPC 
systems to run FreeSurfer, so any recommendations or thoughts would be welcome.

Kind Regards,
Aleks Duvnjak
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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

[Bruce Fischl]

glad it worked out
Bruce
On Fri, 13 Sep 2019, 3 6 wrote:



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Hi Bruce,
I checked the alias, I really aliased mv to “mv -i”, and it worked
automatically, after I unaliased.

Thanks for your help.

Best regards,
Guodong

  在
  2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu
  写道：

Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)



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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

[3 6]

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Hi Bruce,

I checked the alias, I really aliased mv to “mv -i”, and it worked 
automatically, after I unaliased.

Thanks for your help.

Best regards,
Guodong

> 在 2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道：
> 
> Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)

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Re: [Freesurfer] Hippocampal-subfields-T1 interruption

[Bruce Fischl]

Hi Guodong

Hmmm, not sure what is doing that, but my guess is you have mv aliased. Can 
you type:


which mv

and see if you have it aliased to "mv -i" or some such?

cheers
Bruce


On Thu, 12 Sep 2019, 
3 6 wrote:


   External Email - Use Caution 


Hello FreeSurfer Developers,

I'm attempting to analyze hippocampal subfields for T1 scan, but when I run the command recon-all -s subjects -hippocampal-subfields-T1, I always get interrupted by the warning : 


mv: overwrite ‘imageDump.mgz’?

It keep running only when I type Y or N.

I've searched the list and no similar request have been submitted. Does anyone have any thoughts on how to make it automatically running? Also, I’ve attached the hippocampal-subfields-T1.log in case it's of any use. 


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
2) Platform: CentOS release 7 
3) recon-all.log: see attached


Best regards,
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Re: [Freesurfer] hippocampal subfields - T1

[Rizvi, Batool]

Got it, thanks for the help!

Batool

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, February 23, 2017 4:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields - T1

Hi Batool,
It’s not ideal, but if FreeSurfer does a decent job with the recon, something 
decent should come out of the subfields.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 23 Feb 2017, at 20:11, Rizvi, Batool 
<br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote:

Hi,
I was wondering if the hippocampal subfields analysis can still run on a lower 
resolution T1 scan than 1mm? One of our datasets has T1 scans with these 
dimensions: .93 x .93 x 1.3 .

Would it still run on this dataset, if it's not the standard 1mm to begin with?

Thanks!
Batool
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Re: [Freesurfer] hippocampal subfields - T1

[Iglesias Gonzalez, Eugenio]

Hi Batool,
It’s not ideal, but if FreeSurfer does a decent job with the recon, something 
decent should come out of the subfields.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 23 Feb 2017, at 20:11, Rizvi, Batool 
> wrote:

Hi,
I was wondering if the hippocampal subfields analysis can still run on a lower 
resolution T1 scan than 1mm? One of our datasets has T1 scans with these 
dimensions: .93 x .93 x 1.3 .

Would it still run on this dataset, if it's not the standard 1mm to begin with?

Thanks!
Batool
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[Freesurfer] hippocampal subfields - T1

[Rizvi, Batool]

Hi,
I was wondering if the hippocampal subfields analysis can still run on a lower 
resolution T1 scan than 1mm? One of our datasets has T1 scans with these 
dimensions: .93 x .93 x 1.3 .

Would it still run on this dataset, if it's not the standard 1mm to begin with?

Thanks!
Batool
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[Freesurfer] -hippocampal-subfields-T1

[Daniele Orlandi]

dear all,
I'm running analysis with the new FS-v6.0 using the flag
-hippocampal-subfields-T1 and  I get the following error:

none
  Matrix:
-3.3 0 0
0 0 -3.3
0 3.3 0
  Offset: [-34.0783, 128.423, -71.9905]
  Center: [0, 0, 0]
  Translation: [-34.0783, 128.423, -71.9905]
  Inverse:
-0.3 0 0
0 0 0.3
0 -0.3 0
  Singular: 0
I am WriteImage and I'm running!
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Error using zeros
NaN and Inf not allowed.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1396)

MATLAB:nonaninf


How I can solve it?

Best,
Daniele
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Re: [Freesurfer] -hippocampal-subfields-T1

[Eugenio Iglesias]

Hi Daniele, 
do you think you could send us the subject? norm.mgz, wmparc.mgz and aseg.mgz 
should be enough. 
Also, have you experienced this problem with other subjects? 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Daniele Orlandi" <daniele.orlandi@gmail.com> 
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 
Sent: Wednesday, November 18, 2015 10:20:10 AM 
Subject: [Freesurfer] -hippocampal-subfields-T1 

dear all, 
I'm running analysis with the new FS-v6.0 using the flag 
-hippocampal-subfields-T1 and I get the following error: 

none 
Matrix: 
-3.3 0 0 
0 0 -3.3 
0 3.3 0 
Offset: [-34.0783, 128.423, -71.9905] 
Center: [0, 0, 0] 
Translation: [-34.0783, 128.423, -71.9905] 
Inverse: 
-0.3 0 0 
0 0 0.3 
0 -0.3 0 
Singular: 0 
I am WriteImage and I'm running! 
Wrote image to file asmr2.mgz 
This file does not contain MRI parameters 
Error using zeros 
NaN and Inf not allowed. 

Error in segmentSubjectT1_autoEstimateAlveusML (line 1396) 

MATLAB:nonaninf 


How I can solve it? 

Best, 
Daniele 


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properly 
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