External Email - Use Caution        

Thanks,

I am very sorry for the late reply.
I didn't have a machine with more RAM at present,but i ran the code on another 
machine(mac mini,4G or 8G LPDDR3 SDRAM ,500GB) several month ago. it ran 
well.so i didn't  certain it.  I will try to test the code on a machine with 
more RAM if I get the opportunity.
Thanks for your help .
Fiona Ding.




------------------ ???????? ------------------
??????: "Iglesias Gonzalez, Eugenio"<e.igles...@ucl.ac.uk>;
????????: 2018??7??19??(??????) ????3:54
??????: "Freesurfer support 
list"<freesurfer@nmr.mgh.harvard.edu>;"Freesurfersupport 
list"<freesurfer@nmr.mgh.harvard.edu>;

????: Re: [Freesurfer]Re??  Re??  Re??segmentHA_T2.sh



 
        External Email - Use Caution        


  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  
 
  
        External Email - Use Caution        
 

 
 
  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
 
 
 
 
        External Email - Use Caution        
 

  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://cmictig.cs.ucl.ac.uk/
 
 
 

 
 
 

 
 
 
From: <freesurfer-bounces
 
at nmr.mgh.harvard.edu>
 
on behalf of ???? <530337973
 
at qq.com>
 
 
 
Reply-To: Freesurfer support list <freesurfer
 
at nmr.mgh.harvard.edu>
 
 
 
Date: Tuesday, 17 July 2018 at 13:40
 
 
 
To: freesurfer <freesurfer
 
at nmr.mgh.harvard.edu>
 
 
 
Subject: [Freesurfer] segmentHA_T2.sh
 
 
 

 
 
 

 
 
 
        External Email - Use Caution
 
 
 
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
_______________________________________________
Freesurfer mailing list
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.

Reply via email to