Re: [Freesurfer] mri_ca_label with high resolution data

Hi Falk

the dev version of mri_ca_label does use openmp, so should be faster.

cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote:

Hi Bruce,

I started the process again with openmp set to 12 using the dev build from 12th July. However, mri_ca_label uses only 1 thread at that point. So I don't assume any faster processing.

Best, Falk

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 19. Juli 2016 15:37 An: Freesurfer support list Betreff: Re: [Freesurfer] mri_ca_label with high resolution data

Hi Falk

I think openmp will help with this in V6, but probably not before Bruce

On Tue, 19 Jul 2016, Falk Lüsebrink wrote:

...

Hi all,

I’m currently processing a 250 µm MPRAGE with a dev build from mid of May. Running recon-all with default parameters ran flawlessly. Afterwards I added the -hires flag to process the data without conformation. However, since Saturday morning it is kind of stuck at mri_ca_label stating:

saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt

while  consuming around 30 GB of memory. I ran something similar before and processing works, it’s just terribly slow. Maybe this particular stage is just not very efficient as it does take a few minutes on 1 mm data only? Would it help to add the openmp flag in that case?

Best,

Falk

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Falk Lüsebrink, M. Sc.

Otto-von-Guericke-Universität Magdeburg

Forschungscampus STIMULATE

http://www.forschungscampus-stimulate.de/

Universitätsplatz 2

39106 Magdeburg

Raum:    ExFa - 4.06

Telefon: 0391-67-19366

Fax:       0391-67-19347