Re: [Freesurfer] Scalable recon workflow

[Wighton, Paul]

There's a small percentage of subjects that need more than the 8Gb of memory 
(for mris_fix_topology if my memory is correct).

You could increase the memory allocation for all subjects, or you could run 
your entire dataset with 8Gb per subject, then re-run the ones that failed with 
increased memory.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Horn, Mitchell Jacob 

Sent: Tuesday, May 3, 2022 2:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Scalable recon workflow

Hi Paul,

Thanks for your speedy response! In that case, I assume 1GB/core is the memory 
allocation? Is it helpful to increase that?

Best,
Mitch

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Paul Wighton 

Sent: Tuesday, May 3, 2022 1:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Scalable recon workflow


External Email - Use Caution

Hi Mitch,

In our experience, -openmp 8 gives faster recons than -openmp 4, but the gains 
after -openmp 8 diminish quickly and aren't worth it.

-Paul

On Tue, May 3, 2022 at 12:51 PM Horn, Mitchell Jacob 
mailto:mjh...@mgh.harvard.edu>> wrote:

Hi Experts,



If I have 100s of subjects to recon and have access to an HPC with both GPU and 
CPU options what is the recommended flags to maximize speed performance? Is … 
-parallel -openmp 4 … still the best approach? And if so, is 2GB memory/core 
best (keeping it 8GB memory/subject) or is there some better arrangement?



Best,

Mitch









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Re: [Freesurfer] Scalable recon workflow

[Horn, Mitchell Jacob]

Hi Paul,

Thanks for your speedy response! In that case, I assume 1GB/core is the memory 
allocation? Is it helpful to increase that?

Best,
Mitch

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Paul Wighton 

Sent: Tuesday, May 3, 2022 1:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Scalable recon workflow


External Email - Use Caution

Hi Mitch,

In our experience, -openmp 8 gives faster recons than -openmp 4, but the gains 
after -openmp 8 diminish quickly and aren't worth it.

-Paul

On Tue, May 3, 2022 at 12:51 PM Horn, Mitchell Jacob 
mailto:mjh...@mgh.harvard.edu>> wrote:
Hi Experts,

If I have 100s of subjects to recon and have access to an HPC with both GPU and 
CPU options what is the recommended flags to maximize speed performance? Is … 
-parallel -openmp 4 … still the best approach? And if so, is 2GB memory/core 
best (keeping it 8GB memory/subject) or is there some better arrangement?

Best,
Mitch




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Re: [Freesurfer] Scalable recon workflow

[Paul Wighton]

External Email - Use Caution

Hi Mitch,

In our experience, -openmp 8 gives faster recons than -openmp 4, but the
gains after -openmp 8 diminish quickly and aren't worth it.

-Paul

On Tue, May 3, 2022 at 12:51 PM Horn, Mitchell Jacob 
wrote:

> Hi Experts,
>
>
>
> If I have 100s of subjects to recon and have access to an HPC with both
> GPU and CPU options what is the recommended flags to maximize speed
> performance? Is … -parallel -openmp 4 … still the best approach? And if
> so, is 2GB memory/core best (keeping it 8GB memory/subject) or is there
> some better arrangement?
>
>
>
> Best,
>
> Mitch
>
>
>
>
>
>
>
>
> ___
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[Freesurfer] Scalable recon workflow

[Horn, Mitchell Jacob]

Hi Experts,

If I have 100s of subjects to recon and have access to an HPC with both GPU and 
CPU options what is the recommended flags to maximize speed performance? Is … 
-parallel -openmp 4 … still the best approach? And if so, is 2GB memory/core 
best (keeping it 8GB memory/subject) or is there some better arrangement?

Best,
Mitch




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 .
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Re: [Freesurfer] Probabilistic atlas of human thalamic nuclei

[Iglesias Gonzalez, Juan E.]

Dear Asa,

Thank you very much for the interest in our thalamic atlas.

The atlas is defined as a tetrahedral mesh (not voxels) in its own average 
space. So there is no probabilistic map in MNI space. You could try segmenting 
your MNI template with FreeSurfer + the thalamic module and use that. But 
actually: why not simply segmenting the subjects directly? You can always 
register them to MNI (alone with the thalamic segmentations) if you want.

Kind regards,

Juan Eugenio Iglesias
http://www.jeiglesias.com





On 3 May 2022, at 11:23, Asa Borzabadi Farahani 
mailto:asa.borzabadifarah...@mail.mcgill.ca>>
 wrote:


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Dear Experts,

I would really appreciate it if you could help me with this question:

I would like to use the probabilistic atlas of human thalamic nuclei; provided 
by Iglesias et al. (2018); as a prior knowledge to locate the LGN within my 
subjects (prior knowledge would be the Atlas, the functional/structural data of 
subjects would be available and hence, I assume I would be able to get a better 
estimate for the location of LGN within the subjects).

In order to do so, I need this probabilistic map to be available in the MNI or 
the fsaverage space.



May I ask your opinion about this approach? Do you think it is feasible to have 
these probabilistic atlases in the MNI/fsaverage space?



Best Regards,

Asa Farahani


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[Freesurfer] mri_surf2surf error

[Zhang, Fan]

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Hello Everyone,


I am trying to run mri_surf2surf. But I got some errors saying "no such file or 
directory" while in fact there are files in the pathway. I was able to run this 
previously, so I am not sure if this is relevant to the recent upgrade of the 
Mac operation system (12.2.1). My FreeSurfer version is 
(Darwin-OSX-stable-pub-v6.0.0-2beb96c). Does anyone know how to resolve this?


Thank you so much for the help!​


Fan




mri_surf2surf --hemi lh --s fsaverage5 --sval 
lh.CCn_band.Seed1_20220314.V1.13subjs.mgh --fwhm 13 --tval 
lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh


sysname  Darwin

hostname Hans-iMac-Pro.local

machine  x86_64

user fanzhang

srcsubject = fsaverage5

srcval = lh.CCn_band.Seed1_20220314.V1.13subjs.mgh

srctype=

trgsubject = fsaverage5

trgval = lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh

trgtype=

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

srchemi= lh

trghemi= lh

frame  = 0

fwhm-in= 0

fwhm-out   = 13

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder  = 1

UseDualHemi = 0

Reading source surface reg 
/Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere.reg

Loading source data

MRIallocSequence(0, 0, 0, 0): bad parm

No such file or directory

Segmentation fault: 11


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[Freesurfer] Probabilistic atlas of human thalamic nuclei

[Asa Borzabadi Farahani]

External Email - Use Caution

Dear Experts,

I would really appreciate it if you could help me with this question:

I would like to use the probabilistic atlas of human thalamic nuclei; provided 
by Iglesias et al. (2018); as a prior knowledge to locate the LGN within my 
subjects (prior knowledge would be the Atlas, the functional/structural data of 
subjects would be available and hence, I assume I would be able to get a better 
estimate for the location of LGN within the subjects).

In order to do so, I need this probabilistic map to be available in the MNI or 
the fsaverage space.



May I ask your opinion about this approach? Do you think it is feasible to have 
these probabilistic atlases in the MNI/fsaverage space?



Best Regards,

Asa Farahani

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