fer/outgoing/flat/greve/make_average_surface
doug
Juergen Haenggi wrote:
Re: [Freesurfer] Problem make_average_subject
Hi
Doug
Thanks a lot for the new version of the make_average_subject scripts. I
tried it but the following error occurred:
Reading surface
/Applicati
age_surface
doug
Juergen Haenggi wrote:
Re: [Freesurfer] Problem make_average_subject
Hi
Doug
Thanks a lot for the new version of the make_average_subject scripts. I
tried it but the following error occurred:
Reading surface
/Applications/freesurfer/subjects/average/su
gt; face
>
> doug
>
> Juergen Haenggi wrote:
>> Re: [Freesurfer] Problem make_average_subject Hi Doug
>>
>> Thanks a lot for the new version of the make_average_subject scripts. I tried
>> it but the following error occurred:
>>
>> Reading surface
The problem is that it is calling mris_preproc with --srcsurfreg, and
you do not have the version of mris_preproc that accepts this flag. You
can edit it to make it --surfreg. Or, you can get a new copy of
make_average_surface from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
Title: Re: [Freesurfer] Problem make_average_subject
I've encountered the exact same error.
mris_preproc --out rh.orig.avg.area.mgh --f /tmp/subjlist.8709
--target Avg175 --hemi rh --area orig --mean --srcsurfreg sphere.reg
ERROR: flag --srcsurfreg not recognized
The mris_preproc usage
Hi Doug
Thanks a lot for the new version of the make_average_subject scripts. I
tried it but the following error occurred:
Reading surface
/Applications/freesurfer/subjects/average/surf/rh.white
Loading annotations from
/Applications/freesurfer/subjects/average/label/rh.aparc.a2005s.annot
max i
I think the failure happens when it tries to create the group aseg.mgz.
I changed the code on 1/3/08 so that it would just print a warning and
continue, but I don't think this version is being distributed yet.
I've put new versions of
make_average_subject make_average_surface make_average_v
Hi James, hi Bruce
Thanks a lot for your help. I can confirm that make_average_subject did not
used any swap memory in my case too when I tried to average 92 subjects with
5 GB RAM. Meanwhile I have 8 GB RAM and the process stopped before all 8 GB
RAM are active.
Regards
Juergen
On 2.2.2008 19:
Hi James,
thanks for the careful analysis. Not sure why it's not using swap, but
we'll get back to you soon.
have a good weekend,
Bruce
On Sat, 2 Feb 2008, James N. Porter wrote:
So, I believe I have isolated the problem. The failure happens during the
mri_concat phase of make_average_volum
So, I believe I have isolated the problem. The failure happens during
the mri_concat phase of make_average_volumes. The seg-subj#.mgh temp
files that are being concatenated are 65 MB each and I can successfully
run 59 subjects, but for 60 subjects and up, mri_concat exits
immediately with the e
Juergen--Have you had successful resolution to this problem?
Nick--I'm attempting to average 175 subjects, but make_average_volume
returns the same error as Juergen reports.
> Allocing output
> MRIalloc(256,256,256): could not allocate 262144 bytes for
15547th slice
I'm running frees
Juergen,
Edit the 'make_average_subject' script removing (or commenting-out) the
line 'limit descriptors unlimited'. You may have to do the same for
'make_average_surface' and 'make_average_volume'. Although in v4.0,
these should already be commented-out.
Nick
On Mon, 2008-01-28 at 16:29 +01
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