I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested and the process took off but has been running for more than 6 hours and seems to be not doing anything after the step which reads MRISunfold() max_passes = 1 ----------- it has a few steps after that, but doesn't say that it completed. The last line reads - randomSeed 1234. Is it hung? Should I exit the program?
Thank you for your help! Ankita
nope, keep waiting. Depending on your hardware and how different the anatomy is from normal it can take up to a day.
as for LGI, check recon-all -help cheers Bruce On Sun, 24 Jan 2016, Ankita Chatterjee wrote:
I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested and the process took off but has been running for more than 6 hours and seems to be not doing anything after the step which reads MRISunfold() max_passes = 1 -----------it has a few steps after that, but doesn't say that it completed. The last line reads - randomSeed 1234. Is it hung? Should I exit the program?
Thank you for your help! Ankita
Thank you for your help! The process took 22 hours, but it completed without errors! Now I will start looking at the output to analyze.
I was wondering if it is possible to run 3-4 of the freesurfer processes like recon-all simultaneously? I will be running these on a Mac with 8 Ghz of Memory and a 2.66 GHz processor - is that sufficient hardware capability to run several simultaneous processes?
Thanks again! Ankita
On Sun, Jan 24, 2016 at 6:41 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
nope, keep waiting. Depending on your hardware and how different the anatomy is from normal it can take up to a day.
as for LGI, check recon-all -help cheers Bruce On Sun, 24 Jan 2016, Ankita Chatterjee wrote:
I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested
and
the process took off but has been running for more than 6 hours and
seems to
be not doing anything after the step which reads MRISunfold() max_passes
= 1
-----------it has a few steps after that, but doesn't say that it
completed.
The last line reads - randomSeed 1234. Is it hung? Should I exit the program?
Thank you for your help! Ankita
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Hi Ankita
Glad it worked :) How many cores do you have? If only 1 there is nothing to be gained by running them in parallel. If more than 1 I think you should be able to fit at least two in that much ram, but perhaps someone else can comment? Maybe 3?
Cheers Bruce
On Jan 24, 2016, at 10:55 PM, Ankita Chatterjee achat04@gmail.com wrote:
Thank you for your help! The process took 22 hours, but it completed without errors! Now I will start looking at the output to analyze.
I was wondering if it is possible to run 3-4 of the freesurfer processes like recon-all simultaneously? I will be running these on a Mac with 8 Ghz of Memory and a 2.66 GHz processor - is that sufficient hardware capability to run several simultaneous processes?
Thanks again! Ankita
On Sun, Jan 24, 2016 at 6:41 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: nope, keep waiting. Depending on your hardware and how different the anatomy is from normal it can take up to a day.
as for LGI, check recon-all -help cheers Bruce On Sun, 24 Jan 2016, Ankita Chatterjee wrote:
I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested and the process took off but has been running for more than 6 hours and seems to be not doing anything after the step which reads MRISunfold() max_passes = 1 -----------it has a few steps after that, but doesn't say that it completed. The last line reads - randomSeed 1234. Is it hung? Should I exit the program?
Thank you for your help! Ankita
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Ankita Chatterjee -
Bruce Fischl