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Thanks! I am fairly confident it's a memory issue, then. Do you have access to
a machine with more RAM you can test the code on?
Sent from my phone, please excuse brevity and typos
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of ???? <530337...@qq.com>
Sent: Thursday, July 19, 2018 5:27:46 AM
To: Freesurfer support list
Subject: [Freesurfer] Re?? Re?? Re??segmentHA_T2.sh
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I tried to run"segmentHA_T2.sh subject001 T2.nii T2 0" and "segmentHA_T1.sh
subject003", it's well done! When run
Thanks,
Fiona
------------------ ???????? ------------------
??????: "Iglesias Gonzalez, Eugenio"<e.igles...@ucl.ac.uk>;
????????: 2018??7??18??(??????) ????8:35
??????: "Freesurfer support
list"<freesurfer@nmr.mgh.harvard.edu>;"Freesurfersupport
list"<freesurfer@nmr.mgh.harvard.edu>;
????: Re: [Freesurfer] Re?? Re??segmentHA_T2.sh
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Thanks!
Do you have the same problem if you use the T2 alone? For instance
segmentHA_T2.sh subject001 T2.nii T2 0
Sent from my phone, please excuse brevity and typos
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of ???? <530337...@qq.com>
Sent: Wednesday, July 18, 2018 1:21:25 PM
To: Freesurfer support list
Subject: [Freesurfer] Re?? Re??segmentHA_T2.sh
External Email - Use Caution
Dear Eugenio,
I tried 3 subjects ,it dies at the same step ,and it stops there all the time
even 3 days. No error reported here.
Thanks ,
Fiona Ding.
------------------ ???????? ------------------
??????: "Iglesias Gonzalez, Eugenio"<e.igles...@ucl.ac.uk>;
????????: 2018??7??18??(??????) ????7:29
??????: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
????: Re: [Freesurfer] Re??segmentHA_T2.sh
External Email - Use Caution
Thanks, Fiona.
Is the error reproducible? Does it always die at the same step? Do you get the
same problem with other subjects?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of ????
<530337...@qq.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 18 July 2018 at 10:15
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re??segmentHA_T2.sh
External Email - Use Caution
hello??
I think RAM is enough??my computer is imac pro.There is 16G DDDR3. This process
takes up about 1-2G. The total RAM occupied is 5G. Thanks Fiona Ding.
---------------- External Email - Use Caution Weird! Maybe you ran out of RAM
memory?
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/
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Subject: [Freesurfer] segmentHA_T2.sh
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Dear freesurfer experts,
when i run the command??segmentHA_T2.sh subject001 T2.nii T2 1?? ,it runs as
following:
--------------
Making Left-Thalamus-Proper map to reduced label 10
--------------
Making Left-choroid-plexus map to reduced label 11
--------------
Making Left-VentralDC map to reduced label 12
--------------
Making Left-Accumbens-area map to reduced label 13
--------------
Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians parameters
znzreadInt: znzread failed
No such file or directory
Estimating typical intensities of molecular layer and alveus
numberOfLabels: 2
Rasterizing mesh...here: 2
here2: 2
done
Smoothing mesh collection with kernel size 1.500000 ...Smoothing class: 0
Smoothing class: 1
Smoothing class: 2
Smoothing class: 3
Smoothing class: 4
Smoothing class: 5
Smoothing class: 6
Smoothing class: 7
Smoothing class: 8
Smoothing class: 9
Smoothing class: 10
Smoothing class: 11
Smoothing class: 12
Smoothing class: 13
done
numberOfImages = 2
Image: 0
Image: 2
Iteration 1 of 7
1 0.00035804
2 0.089592
fianally,it stop here and can't run anymore,no error reported??I didn't know
what??s wrong??
What can i do??
Thanks very much
Fiona Ding
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