rfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Bernardoni, Fabio
Gesendet: Donnerstag, 20. Mai 2021 11:17:05
An: Freesurfer support list
Betreff: Re: [Freesurfer] memory allocation error
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dear Andrew,
I was allowing 8, 16, ~36GB of memory in different runs,
5
An: Freesurfer support list
Betreff: Re: [Freesurfer] memory allocation error
Hi Fabio,
How much memory are you allowing for this process? You might want to just try
increasing the limit on the slurm job to see if that works.
Best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behal
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Subject: Re: [Freesurfer] memory allocation error
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Sorry I forgot the attachment.
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjt
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Sorry I forgot the attachment.
Dr. Fabio Bernardoni
wiss. Mitarbeiter
Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2
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Dear Freesurfers,
when running the longitudinal preprocessing on a subject, I get the same error
as described here (see recon-all.log attached):
https://secure-web.cisco.com/1Ip5HtCg9MqyghYHl20NFxCMImoJoShIH1y6ytQEK2tKtD13Oz0AIBueggTl_ahZFc6uNPUz7V5A3
sure. The mris_sphere command line should be in the recon-all.log file
in the subject's scripts dir. Either run that directly, or look at the
recon-all help to figure out how to do it through recon-all
cheers
Bruce
On Mon, 18 Jun
2012, Arno Klein wrote:
aha -- it seems that just the .spher
aha -- it seems that just the .sphere files, not the .pial or .white files,
are corrupted. is there an easy way to generate just the .sphere files
again?
cheers,
@rno
On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl
wrote:
> Hi Arno
>
> can you load that sphere file in tksurfer? And run mris_in
Hi Arno
can you load that sphere file in tksurfer? And run mris_info or
mris_euler_number on it? I'm wondering if it is corrupted.
Bruce
On Mon, 18 Jun
2012, Arno Klein wrote:
hello!
i am able to run mris_register on all of the OASIS brain images that i have
tested except for one: OAS1_0
hello!
i am able to run mris_register on all of the OASIS brain images that i have
tested except for one: OAS1_0061_MR1:
mris_register -curv OASIS-0061_MR1/surf/rh.sphere
templates/freesurfer/rh.OASIS_template.tif
OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg
using smoothwm curvature for
thank you -- this worked!
cheers,
@rno
On Fri, Jan 20, 2012 at 6:43 PM, Bruce Fischl wrote:
> you can just rerun the mris_sphere command that is in the recon-all.log
> (or recon-all.cmd)
>
> cheers
> Bruce
>
> On Fri, 20 Jan 2012, Arno Klein wrote:
>
>
>> dear bruce,
>> you're right -- i am ab
you can just rerun the mris_sphere command that is in the recon-all.log
(or recon-all.cmd)
cheers
Bruce
On Fri, 20 Jan 2012, Arno Klein wrote:
dear bruce,
you're right -- i am able to view the pial surface, but when i try to view
the spherical surface with tksurfer i get the same memory error
dear bruce,
you're right -- i am able to view the pial surface, but when i try to view
the spherical surface with tksurfer i get the same memory error.
is there any way to fix the sphere without affecting anything else?
neuromorphometrics has painstakingly manually edited the freesurfer labels
g
can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file
that is the problem. Maybe your partition filled up and the sphere file
isn't complete?
On Fri, 20 Jan
2012, Arno Klein wrote:
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Grev
Hi Arno,
Please give these matlab commands a shot.
[v,M, mr] = load_mgh('orig.mgz');
save_mgh(v, 'orig.mgz', M, mr);
-Louis
On Fri, 20 Jan 2012, Arno Klein wrote:
> dear doug,
>
> sadly, no dice.
>
> cheers,
> @rno
>
>
>
> On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
> wrote:
>
>> Try doin
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
wrote:
> Try doing it in matlab, so
> a = MRIread('orig.mgz');
> MRIwrite(a,'orig.mgz');
>
> doug
>
> Arno Klein wrote:
>
>>
>> dear doug,
>>
>> i am using FS v5.1 now but ran the 20 oasis subjects throug
Try doing it in matlab, so
a = MRIread('orig.mgz');
MRIwrite(a,'orig.mgz');
doug
Arno Klein wrote:
>
> dear doug,
>
> i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0.
> i am only having this trouble for one of the subjects.
>
> after the mri_convert workaround i am still ge
dear doug,
i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i am
only having this trouble for one of the subjects.
after the mri_convert workaround i am still getting the same memory
allocation error.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
wrote:
This is a strange problem we've been having with some mgz files that
were generated during a short period of time last summer when there was
a bug in the mgz writing code. What version of FS are you using? In the
current dev version, this should not be a problem. A work-around is to
convert the
i get the following memory allocation error for only one out of 20 oasis
subjects that i processed with freesurfer 5.1 on an ubuntu 11.10 machine
with 24gb memory:
mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere
templates_freesurfer/lh.KKI_2.tif
subjects/OAS1_0061_MR1/surf/lh.sphere_to_K
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