[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I am trying to run hippocampal subfield segmentation on our subjects on 
FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an 
error relatively early:

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found

When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, 
kvlAutoCrop.bin was located there, as expected. When I tried to run the step 
manually, it produced the correct output, but the next step gave me the similar 
error: command not found. I looked into 
/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other 
binaries were there, as well. The binaries are correctly exported on my PATH. I 
also made sure to download the Matlab compiler runtime and made sure they were 
on my PATH.

I am running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is 
greatly appreciated.

Thanks,
Ryan

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Re: [Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Ryan, 
This is weird! I am safely assuming that you sourced FreeSurfer, etc? What was 
the command you ran?
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 25/04/2018, 19:12, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Nillo, Ryan Michael R"  wrote:

External Email - Use Caution

Hello FreeSurfer users,

I am trying to run hippocampal subfield segmentation on our subjects on 
FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an 
error relatively early:

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 
3: kvlAutoCrop.bin: command not found

When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, 
kvlAutoCrop.bin was located there, as expected. When I tried to run the step 
manually, it produced the correct output, but the next step gave me the similar 
error: command not found. I looked into 
/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other 
binaries were there, as well. The binaries are correctly exported on my PATH. I 
also made sure to download the Matlab compiler runtime and made sure they were 
on my PATH.

Any help is greatly appreciated.

Thanks,
Ryan



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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 Partners Compliance 
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in 
error
but does not contain patient information, please contact the sender and 
properly
dispose of the e-mail.




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[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer users,

I am trying to run hippocampal subfield segmentation on our subjects on 
FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an 
error relatively early:

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: 
kvlAutoCrop.bin: command not found

When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, 
kvlAutoCrop.bin was located there, as expected. When I tried to run the step 
manually, it produced the correct output, but the next step gave me the similar 
error: command not found. I looked into 
/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other 
binaries were there, as well. The binaries are correctly exported on my PATH. I 
also made sure to download the Matlab compiler runtime and made sure they were 
on my PATH.

Any help is greatly appreciated.

Thanks,
Ryan



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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.