Dear Ramesh,

The subfield segmentations requires running recon-all -all first. But you can greatly speed up the execution with the openmp option. Also, you can try running two subjects simultaneously, but only for the recon-all -all part (the subfields use more memory and might crash).

Cheers,

/Eugenio

Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

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

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ramesh Babu <mgrameshbabu2013@gmail.com>
Sent: Saturday, April 29, 2017 9:46:24 AM
To: Freesurfer support list
Subject: [Freesurfer] Hippo-subfiled Need Help

 

Dear Experts,

I ave done hippocampal subfield segmentation by using 1x1x1 t1 scan. Please see the attached image and give your suggestions.

It took nearly 7 hrs 10 min. to complete hippo-subfield segmentation for one scan by using the command

recon-all -i grp205_t1.nii -s grp205 -sd grp205 -all

Started at Wed Apr 26 11:03:34 IST 2017
Ended   at Wed Apr 26 17:17:35 IST 2017
#@#%# recon-all-run-time-hours 6.234
recon-all -s grp205 finished without error at Wed Apr 26 17:17:35 IST 2017
done

Then for hipposubfield,

recon-all -s grp205 -sd grp205 -hippocampal-subfields-T1


I want to run for 40 scans grp-1 20 scans and grp-2 20 scans. How to modify in the command. Since it is taking long time I want to run 10 scans n give rest again 10 scans. Can I do so?

I am15.6 GiB ram, Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor, GeForce GT 610/PCIe/SSE2 graphic card.It is octa core processor. Can I run 8 analysis simultaneously (in 8 separate terminal?).

Your suggestion will be helpful to me to proceed further.

Thanks

RB

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