presumably you mean GB, not MB? That's not enough - a single
distance transform of a 256^3 volumes at 0.25 mm is 1GB of 4-8 byte voxels
and we have to hold a few in memory
On Thu, 10 Sep 2015, Sebastien Proulx wrote:
11.9 MB on a virtual Ubuntu 14.04.3 with VMware Player.
-----Original Message-----
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 10, 2015 10:06 AM
To: Sebastien Proulx
Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
how much ram do you have in the machine? You probably need more. Also, can you
please cc the list on this type of email so others can answer and learn?
thanks
Bruce
On Thu, 10 Sep 2015, Sebastien Proulx wrote:
Hello Bruce !
Thanks for the tip. I tried it but it did not run through, it was killed
without much error message:
----------------------------------------------------------------------
-------------------------------
-------------------------------------------------------
bass@ubuntu:/mnt/hgfs/workOnDropbox/projects/150422_decodingHRF/HRphen
omenology$ mri_compute_volume_fractions -r 0.25
$curSubj"_registerIdentity.dat" $curSubj_FS/mri/brain.mgz
$outVol"_PLUS_r"
setting resolution = 0.250
arg = 4
reading registration file
ha/ha_run3_tissueFractionMasks__tmp/ha_registerIdentity.dat
reading surface
/mnt/hgfs/workOnDropbox/projects/150422_decodingHRF/HRphenomenology/s2
5_HA_freesurfer/surf/lh.white
reading surface
/mnt/hgfs/workOnDropbox/projects/150422_decodingHRF/HRphenomenology/s2
5_HA_freesurfer/surf/rh.white
reading surface
/mnt/hgfs/workOnDropbox/projects/150422_decodingHRF/HRphenomenology/s2
5_HA_freesurfer/surf/lh.pial
reading surface
/mnt/hgfs/workOnDropbox/projects/150422_decodingHRF/HRphenomenology/s2
5_HA_freesurfer/surf/rh.pial
reading volume
/mnt/hgfs/workOnDropbox/projects/150422_decodingHRF/HRphenomenology/s2
5_HA_freesurfer/mri/aseg.mgz
reading movable volume s25_HA_freesurfer/mri/brain.mgz
filling interior of lh pial surface...
filling interior of rh pial surface...
filling interior of lh white matter surface...
Killed
----------------------------------------------------------------------
-------------------------------
-------------------------------------------------------
Could it have exceeded memory? I’ll rerun it, but in the meanwhile,
any tip to get more information for debugging?
Also, here attached is a sample script, and you can get a compressed
version of the FS folder for one subject here
https://www.dropbox.com/s/s0h8flnxonskzbu/s25_HA_freesurfer.tar.gz?dl=0.
Thanks a lot again and
Have a very good day!
Sébastien
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