[Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)

[randrews]

Hello FreeSurfer Experts/Community,

I am currently working with NITRC (as a novice user) to build and investigate the operability of FreeSurfer v6.0 in their Computational Environment (NITRC-CE).

We have been able to get a "recon-all" run to work, but we are failing to get the sub-calls

-hippocampal-subfields-T1
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

-brainstem-structures
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures 

... to run correctly / run to completion.  We are aware that Matlab Runtime needed to be installed, and a partial completion is a testament to that.

However, they seem to choke near the end, and it would be good to get some insight as to why.  To wit, I am pasting the last dozen or so lines from each (see below) in the hopes we might get a tip or a comment from this forum.

For this exercise, we used an ADNI subject (N3-corrected, downloaded from ADNI/LONI as *.nii)

The syntax/command I used was:

recon-all -s ADNI_003_S_2374_m00 \
-i $SUBJECTS_DIR/ADNI_003_S_2374__MRI_m00__EMCI-EMCI__20110506__S108554_I235638.nii \
-all -hippocampal-subfields-T1 -brainstem-structures

I'm simply not sure if there's something wrong with my syntax or if there is something else we're missing.  Any help would be greatly appreciated, and I can pass on what is shared to my developer (and so that eventually everyone might begin to have a vetted version of v6.0 using NITRC-CE if they wish in the future)

-Randy

From:

/scripts/brainstem-structures

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<<<start excerpt>>>

Resolution level 3 iteration 3 deformation iterations 8
Did one deformation step of max. 1.6685e-05 voxels in 8.485 seconds

minLogLikelihoodTimesPrior =

7.5772e+06

Resolution level 3 iteration 3 deformation iterations 9
Did one deformation step of max. 5.3959e-05 voxels in 3.4185 seconds

minLogLikelihoodTimesPrior =

7.5772e+06

Resolution level 3 iteration 3 deformation iterations 10
Did one deformation step of max. 0 voxels in 6.782 seconds

minLogLikelihoodTimesPrior =

7.5772e+06

maximalDeformation is too small; stopping
Fitting mesh to image data mask took 919.7675 seconds
numberOfLabels: 21
Rasterizing mesh...here: 21
here2: 21
done
Error using kvlGEMSMatlab
std::bad_alloc

Error in kvlRasterizeAtlasMesh (line 11)



Error in segmentSubject (line 1151)

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<<<end of logfile>>>

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From:

/scripts/hippocampal-subfields-T1

_______________________________________________________________

<<<start excerpt>>>

 

Making alveus map to reduced label 3
--------------
Making Left-Lateral-Ventricle map to reduced label 4
--------------
Making hippocampal-fissure map to reduced label 5
--------------
Making Left-Pallidum map to reduced label 6
--------------

Making Left-Putamen map to reduced label 7
--------------
Making Left-Caudate map to reduced label 8
--------------
Making Left-Thalamus-Proper map to reduced label 9
--------------
Making Left-choroid-plexus map to reduced label 10
--------------
Making Left-VentralDC map to reduced label 11
--------------
Making Left-Accumbens-area map to reduced label 12
--------------
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
numberOfLabels: 13
Rasterizing mesh...here: 13
here2: 13
done
Error using double
Out of memory. Type HELP MEMORY for your options.

Error in segmentSubjectT1_autoEstimateAlveusML (line 834)



MATLAB:nomem

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<<<end of logfile>>>

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