Re: [Freesurfer] SAMSEG estimation error

2022-08-27 Thread giulio siracusano 
External Email - Use Caution

Hi Stefano,

I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2
version of Freesurfer and I've realized that I get different results using
the same data but when I run the SAMSEG multiple times.

Differently from using ASEG, SAMSEG provides also the chance to execute the
code using multiple threads.

In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using
the MP-RAGE series having ID I18211 (the link below provides the NIFTI
version of the series which has been used for the processing).

https://secure-web.cisco.com/1iXLPU1Pah9fJGAnXTC3r119YX5fn9IazKSNeP15n5H0EkfhUuqjLEyVd217sla87VuARJY9yP5bznF73e2Y5xluUmJ0ZwnWfRzixJ5i62tZMQCZlAUyJtUiLOpkmLkpyfQHm-PPsC-1HIb1SY-t9erhrXS0Mpoh_2twrlpw9mCWhAKEJpfCrnPtneLfrszq5j3Epq-rFSun73djFlQsXgJp7MRd2I2j-nESHQ6eEWiQLPBW4AWvhu2v-5JbO-XsojdqugwMRYo3zKQsrDBqz9qf9TF-RftjVozbCLGNBkYoWb2wN5959FRHgFhhKUJM9yO1MS6kz8fHQmAVtU5TSYg/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F15oghna17Qz-OSuo9E3-rldOt935AEEuO%3Fusp%3Dsharing

The first execution of SAMSEG was with default settings (1 thread) and
results are attached, the second was using --threads 6.

These results from the SAME series are similar but they are NOT the same.

How can we explain that?

Regards

Giulio


samseg_1.stats
Description: Binary data


samseg_2.stats
Description: Binary data
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Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Giulio Siracusano 
   External Email - Use Caution


Hi Douglas,
I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 
7.2 version of Freesurfer and I've realized that I get different results 
using the same data but when I run the SAMSEG multiple times (on the 
same patient).


Differently from using ASEG, SAMSEG provides also the chance to execute 
the code using multiple threads.


In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 
using the MP-RAGE series having ID I18211 (the link below provides the 
NIFTI version of the series which has been used for the processing). 
This patients is part of ADNI dataset.


https://secure-web.cisco.com/1fi2W1V4_-rYaCj4VoBlufgE4KDcCDmct4ekP97q5p4NhEV8GTeeMTUUAEhXL8MHNWtVbBoyd2-9Wb7uoqiyWHs1A00hpFn4_hXix06Wic82VWju3KJRxrCvVNxgrY04ituYHERUX7lg1eMaxcyxPAuAog3Vocj6FwM34M2dg56JzEFeYRM-UDN8XjqmULiSKhUpSLPx2RgQ2QsjYYnq1ZwzwI_Z3RxuJAC5LaAEIoTA-YEmW0r0E3zapUsXCeyz-u8zlXOZDDMF53MJt0G07k90wH4CH3GPEs7NzrE2uZ0FtZ_sjrAELB37rB2Z2X7ErpBj9TsIHBarvypTq_Rc7BQ/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F15oghna17Qz-OSuo9E3-rldOt935AEEuO%3Fusp%3Dsharing 



The first execution of SAMSEG was with default settings (1 thread) and 
results are attached, the second was using --threads 6.


These results from the SAME series are similar but they are NOT the same.

How can we explain that?

Regards
# Measure Unknown, 938678.804563, mm^3
# Measure Skull, 70514.097706, mm^3
# Measure Soft_Nonbrain_Tissue, 1117216.914116, mm^3
# Measure Brain-Stem, 19382.400237, mm^3
# Measure CSF, 510336.929212, mm^3
# Measure Left-Cerebellum-Cortex, 46227.404805, mm^3
# Measure Right-Cerebellum-Cortex, 46954.827348, mm^3
# Measure 4th-Ventricle, 1927.249860, mm^3
# Measure Fluid_Inside_Eyes, 10681.567722, mm^3
# Measure Left-Cerebral-Cortex, 194854.703127, mm^3
# Measure Right-Cerebral-Cortex, 198395.911108, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.296942, mm^3
# Measure Right-Cerebellum-White-Matter, 13442.628195, mm^3
# Measure Right-Cerebral-White-Matter, 200768.332902, mm^3
# Measure Left-Cerebral-White-Matter, 199392.351036, mm^3
# Measure Right-choroid-plexus, 2202.554448, mm^3
# Measure Right-Amygdala, 1483.776188, mm^3
# Measure Left-Amygdala, 1543.083787, mm^3
# Measure Right-Hippocampus, 3889.943347, mm^3
# Measure Right-Inf-Lat-Vent, 773.181432, mm^3
# Measure Left-Hippocampus, 3957.909089, mm^3
# Measure Left-choroid-plexus, 1732.272325, mm^3
# Measure Left-Inf-Lat-Vent, 374.679073, mm^3
# Measure Optic-Chiasm, 194.020527, mm^3
# Measure Right-VentralDC, 3517.897243, mm^3
# Measure Left-VentralDC, 3616.708619, mm^3
# Measure 3rd-Ventricle, 2767.856042, mm^3
# Measure Left-Accumbens-area, 582.221221, mm^3
# Measure Left-Putamen, 4786.334982, mm^3
# Measure Right-Putamen, 4722.605242, mm^3
# Measure Right-vessel, 80.863621, mm^3
# Measure Right-Accumbens-area, 461.768868, mm^3
# Measure WM-hypointensities, 20335.889722, mm^3
# Measure Left-Lateral-Ventricle, 20190.963456, mm^3
# Measure Left-vessel, 61.352892, mm^3
# Measure Right-Lateral-Ventricle, 18727.913621, mm^3
# Measure Right-Pallidum, 1703.159618, mm^3
# Measure Left-Caudate, 3777.300280, mm^3
# Measure Right-Thalamus, 5636.150208, mm^3
# Measure Left-Pallidum, 1656.295530, mm^3
# Measure Right-Caudate, 3583.231471, mm^3
# Measure Left-Thalamus, 6017.696659, mm^3
# Measure non-WM-hypointensities, 89.673417, mm^3
# Measure 5th-Ventricle, 15.867564, mm^3
# Measure Unknown, 939056.015091, mm^3
# Measure Skull, 71767.719764, mm^3
# Measure Soft_Nonbrain_Tissue, 1112717.212711, mm^3
# Measure Brain-Stem, 19396.749933, mm^3
# Measure CSF, 511873.576213, mm^3
# Measure Left-Cerebellum-Cortex, 46226.557363, mm^3
# Measure Right-Cerebellum-Cortex, 46977.164462, mm^3
# Measure 4th-Ventricle, 1932.334854, mm^3
# Measure Fluid_Inside_Eyes, 10678.846479, mm^3
# Measure Left-Cerebral-Cortex, 195097.957627, mm^3
# Measure Right-Cerebral-Cortex, 198722.232809, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.963053, mm^3
# Measure Right-Cerebellum-White-Matter, 13448.109331, mm^3
# Measure Right-Cerebral-White-Matter, 201145.753968, mm^3
# Measure Left-Cerebral-White-Matter, 199725.946038, mm^3
# Measure Right-choroid-plexus, 2196.836003, mm^3
# Measure Right-Amygdala, 1483.180736, mm^3
# Measure Left-Amygdala, 1541.752663, mm^3
# Measure Right-Hippocampus, 3885.522213, mm^3
# Measure Right-Inf-Lat-Vent, 774.735928, mm^3
# Measure Left-Hippocampus, 3954.921244, mm^3
# Measure Left-choroid-plexus, 1727.665580, mm^3
# Measure Left-Inf-Lat-Vent, 375

[Freesurfer] Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG

2022-08-27 Thread Giulio Siracusano 
   External Email - Use Caution


Hi Donatas,

I've read your full paper and it is very interesting. During my 
investigation on the use of SAMSEG and ASEG for AD/MCI patients, I've 
found some unexpected behaviors.
I'm using the 7.2 version of Freesurfer and I've realized that I get 
different results using the same data but when I run the SAMSEG multiple 
times (on the same patient). This doesn't happen with ASEG.



Differently from using ASEG, SAMSEG provides also the chance to execute 
the code using multiple threads.


In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 
using the MP-RAGE series having ID I18211 (the link below provides the 
NIFTI version of the series which has been used for the processing). 
This patient is part of ADNI dataset.


https://secure-web.cisco.com/1KGFjZ54FVizRaBAYNTLAcv85dT0_beezGbs4UoaUZ1cTiAMhZAR-GM0mZREUuyafaa4hndgos5M4uRnTMs6hkKM7klAHWb_uqxvnO8aQCcrZGGS0D49MR9NL-iDHp-G3_IZ7pC6PscN4A9gcIE2LoSyzVTao33yqp37uZ1qw0sL-YPTllLWayJ4cZvm-IkMJ-cYT-lsmmbkKopS2kdx0iCMB1oWDsE3JXqNiZmM-Xu-8uMmhpg3V0lvtbrZENBuUEWcI1ZVgVVGwTt7duMprlxkKZ8lT6gZKF2bU6BMELkMdmGU_AWZZGfmsdYpa3AHwcYgi7jCW4vK8mO7otukXlg/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F15oghna17Qz-OSuo9E3-rldOt935AEEuO%3Fusp%3Dsharing 



The first execution of SAMSEG was with default settings (1 thread) and 
results are attached, the second was using --threads 6.


These results from the SAME series are similar but they are NOT the same.

Do you have an explanation for that?

Regards
# Measure Unknown, 938678.804563, mm^3
# Measure Skull, 70514.097706, mm^3
# Measure Soft_Nonbrain_Tissue, 1117216.914116, mm^3
# Measure Brain-Stem, 19382.400237, mm^3
# Measure CSF, 510336.929212, mm^3
# Measure Left-Cerebellum-Cortex, 46227.404805, mm^3
# Measure Right-Cerebellum-Cortex, 46954.827348, mm^3
# Measure 4th-Ventricle, 1927.249860, mm^3
# Measure Fluid_Inside_Eyes, 10681.567722, mm^3
# Measure Left-Cerebral-Cortex, 194854.703127, mm^3
# Measure Right-Cerebral-Cortex, 198395.911108, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.296942, mm^3
# Measure Right-Cerebellum-White-Matter, 13442.628195, mm^3
# Measure Right-Cerebral-White-Matter, 200768.332902, mm^3
# Measure Left-Cerebral-White-Matter, 199392.351036, mm^3
# Measure Right-choroid-plexus, 2202.554448, mm^3
# Measure Right-Amygdala, 1483.776188, mm^3
# Measure Left-Amygdala, 1543.083787, mm^3
# Measure Right-Hippocampus, 3889.943347, mm^3
# Measure Right-Inf-Lat-Vent, 773.181432, mm^3
# Measure Left-Hippocampus, 3957.909089, mm^3
# Measure Left-choroid-plexus, 1732.272325, mm^3
# Measure Left-Inf-Lat-Vent, 374.679073, mm^3
# Measure Optic-Chiasm, 194.020527, mm^3
# Measure Right-VentralDC, 3517.897243, mm^3
# Measure Left-VentralDC, 3616.708619, mm^3
# Measure 3rd-Ventricle, 2767.856042, mm^3
# Measure Left-Accumbens-area, 582.221221, mm^3
# Measure Left-Putamen, 4786.334982, mm^3
# Measure Right-Putamen, 4722.605242, mm^3
# Measure Right-vessel, 80.863621, mm^3
# Measure Right-Accumbens-area, 461.768868, mm^3
# Measure WM-hypointensities, 20335.889722, mm^3
# Measure Left-Lateral-Ventricle, 20190.963456, mm^3
# Measure Left-vessel, 61.352892, mm^3
# Measure Right-Lateral-Ventricle, 18727.913621, mm^3
# Measure Right-Pallidum, 1703.159618, mm^3
# Measure Left-Caudate, 3777.300280, mm^3
# Measure Right-Thalamus, 5636.150208, mm^3
# Measure Left-Pallidum, 1656.295530, mm^3
# Measure Right-Caudate, 3583.231471, mm^3
# Measure Left-Thalamus, 6017.696659, mm^3
# Measure non-WM-hypointensities, 89.673417, mm^3
# Measure 5th-Ventricle, 15.867564, mm^3
# Measure Unknown, 939056.015091, mm^3
# Measure Skull, 71767.719764, mm^3
# Measure Soft_Nonbrain_Tissue, 1112717.212711, mm^3
# Measure Brain-Stem, 19396.749933, mm^3
# Measure CSF, 511873.576213, mm^3
# Measure Left-Cerebellum-Cortex, 46226.557363, mm^3
# Measure Right-Cerebellum-Cortex, 46977.164462, mm^3
# Measure 4th-Ventricle, 1932.334854, mm^3
# Measure Fluid_Inside_Eyes, 10678.846479, mm^3
# Measure Left-Cerebral-Cortex, 195097.957627, mm^3
# Measure Right-Cerebral-Cortex, 198722.232809, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.963053, mm^3
# Measure Right-Cerebellum-White-Matter, 13448.109331, mm^3
# Measure Right-Cerebral-White-Matter, 201145.753968, mm^3
# Measure Left-Cerebral-White-Matter, 199725.946038, mm^3
# Measure Right-choroid-plexus, 2196.836003, mm^3
# Measure Right-Amygdala, 1483.180736, mm^3
# Measure Left-Amygdala, 1541.752663, mm^3
# Measure Right-Hippocampus, 3885.522213, mm^3
# Measure Right-Inf

Re: [Freesurfer] Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG

2022-08-27 Thread Giulio Siracusano 
   External Email - Use Caution


Hi Donatas,

I've read your full paper and it is very interesting. During my 
investigation on the use of SAMSEG and ASEG for AD/MCI patients, I've 
found some unexpected behaviors.
I'm using the 7.2 version of Freesurfer and I've realized that I get 
different results using the same data but when I run the SAMSEG multiple 
times (on the same patient). This doesn't happen with ASEG.



Differently from using ASEG, SAMSEG provides also the chance to execute 
the code using multiple threads.


In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 
using the MP-RAGE series having ID I18211 (the link below provides the 
NIFTI version of the series which has been used for the processing). 
This patient is part of ADNI dataset.


https://secure-web.cisco.com/17-NqRPTAKNaVCf_i6zhkdra4uObi5n9QwHlBaAsfxUilF3YlRCCMnG3JWzp7vK6jLC93IssuFIawxv6AiuG07kkilM8R6uINFjkrDH88uafjcSNKfZaf_hh3l_JWeYzYT9UKCPn3mtP3yzw4fWfPczuXqpfclCm4vKIRu6oJlFJwsNo_YAP_QoAagY3LZU4UoxJnSOkZs5tP-eRBVqkzLf8Kn7_GD0OE2tUggJ9bOM6yjRATNqC6aA9Ndb_9z7uzxZOMAFfPZC2WaXdAT_aZA4bubzLI5D1JFQagC9J2VCxatC0tfvTleHPMUxuaxvon4MdteS5Mp2YWlz7RmWP7Mg/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F15oghna17Qz-OSuo9E3-rldOt935AEEuO%3Fusp%3Dsharing 



The first execution of SAMSEG was with default settings (1 thread) and 
results are attached, the second was using --threads 6.


These results from the SAME series are similar but they are NOT the same.

Do you have an explanation for that?

Regards
# Measure Unknown, 938678.804563, mm^3
# Measure Skull, 70514.097706, mm^3
# Measure Soft_Nonbrain_Tissue, 1117216.914116, mm^3
# Measure Brain-Stem, 19382.400237, mm^3
# Measure CSF, 510336.929212, mm^3
# Measure Left-Cerebellum-Cortex, 46227.404805, mm^3
# Measure Right-Cerebellum-Cortex, 46954.827348, mm^3
# Measure 4th-Ventricle, 1927.249860, mm^3
# Measure Fluid_Inside_Eyes, 10681.567722, mm^3
# Measure Left-Cerebral-Cortex, 194854.703127, mm^3
# Measure Right-Cerebral-Cortex, 198395.911108, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.296942, mm^3
# Measure Right-Cerebellum-White-Matter, 13442.628195, mm^3
# Measure Right-Cerebral-White-Matter, 200768.332902, mm^3
# Measure Left-Cerebral-White-Matter, 199392.351036, mm^3
# Measure Right-choroid-plexus, 2202.554448, mm^3
# Measure Right-Amygdala, 1483.776188, mm^3
# Measure Left-Amygdala, 1543.083787, mm^3
# Measure Right-Hippocampus, 3889.943347, mm^3
# Measure Right-Inf-Lat-Vent, 773.181432, mm^3
# Measure Left-Hippocampus, 3957.909089, mm^3
# Measure Left-choroid-plexus, 1732.272325, mm^3
# Measure Left-Inf-Lat-Vent, 374.679073, mm^3
# Measure Optic-Chiasm, 194.020527, mm^3
# Measure Right-VentralDC, 3517.897243, mm^3
# Measure Left-VentralDC, 3616.708619, mm^3
# Measure 3rd-Ventricle, 2767.856042, mm^3
# Measure Left-Accumbens-area, 582.221221, mm^3
# Measure Left-Putamen, 4786.334982, mm^3
# Measure Right-Putamen, 4722.605242, mm^3
# Measure Right-vessel, 80.863621, mm^3
# Measure Right-Accumbens-area, 461.768868, mm^3
# Measure WM-hypointensities, 20335.889722, mm^3
# Measure Left-Lateral-Ventricle, 20190.963456, mm^3
# Measure Left-vessel, 61.352892, mm^3
# Measure Right-Lateral-Ventricle, 18727.913621, mm^3
# Measure Right-Pallidum, 1703.159618, mm^3
# Measure Left-Caudate, 3777.300280, mm^3
# Measure Right-Thalamus, 5636.150208, mm^3
# Measure Left-Pallidum, 1656.295530, mm^3
# Measure Right-Caudate, 3583.231471, mm^3
# Measure Left-Thalamus, 6017.696659, mm^3
# Measure non-WM-hypointensities, 89.673417, mm^3
# Measure 5th-Ventricle, 15.867564, mm^3
# Measure Unknown, 939056.015091, mm^3
# Measure Skull, 71767.719764, mm^3
# Measure Soft_Nonbrain_Tissue, 1112717.212711, mm^3
# Measure Brain-Stem, 19396.749933, mm^3
# Measure CSF, 511873.576213, mm^3
# Measure Left-Cerebellum-Cortex, 46226.557363, mm^3
# Measure Right-Cerebellum-Cortex, 46977.164462, mm^3
# Measure 4th-Ventricle, 1932.334854, mm^3
# Measure Fluid_Inside_Eyes, 10678.846479, mm^3
# Measure Left-Cerebral-Cortex, 195097.957627, mm^3
# Measure Right-Cerebral-Cortex, 198722.232809, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.963053, mm^3
# Measure Right-Cerebellum-White-Matter, 13448.109331, mm^3
# Measure Right-Cerebral-White-Matter, 201145.753968, mm^3
# Measure Left-Cerebral-White-Matter, 199725.946038, mm^3
# Measure Right-choroid-plexus, 2196.836003, mm^3
# Measure Right-Amygdala, 1483.180736, mm^3
# Measure Left-Amygdala, 1541.752663, mm^3
# Measure Right-Hippocampus, 3885.522213, mm^3
# Measure Right-Inf

Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Bouchra Guelib 
External Email - Use Caution

I used freesurfer for ADNI data, specifically MRI for AD/CN.  Even I run
segmentation many times , I always  having the same statistics. Would you
share with us the commend line you used !

Le sam. 27 août 2022 à 09:32, Giulio Siracusano 
a écrit :

> External Email - Use Caution
>
> Hi Douglas,
> I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2
> version of Freesurfer and I've realized that I get different results using
> the same data but when I run the SAMSEG multiple times (on the same
> patient).
>
> Differently from using ASEG, SAMSEG provides also the chance to execute
> the code using multiple threads.
>
> In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using
> the MP-RAGE series having ID I18211 (the link below provides the NIFTI
> version of the series which has been used for the processing). This
> patients is part of ADNI dataset.
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1-84Hdwis5Bbu4zAZ_LHxfarwpgU9bmrPe4UoS0CjjeTiU58RBTpBpPhdNcPat1aZuY4JU_Z6YtYVSoUvkPxCvVPGY4lN4veEw1ACAwZpxQZ1FVglxHDg6lPEirWxIdtfOf4gs1lNO-llsdTRvgylLQUYOmNblsdDBGot5k4aiwW04ngM7Uazj4YbpblX1Nn1RF9oxQOpwL7WbBkpCit7UZjoS0UjHeb4bGt2aFx9YcLdwPgvHs3OlDu9bpy0_RcZGkyThvnAoN_alXJnKCbk7d_n68dEUNIdb0MVKzb4Eo4TTgfIKufMg57lCCAMD930/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F15oghna17Qz-OSuo9E3-rldOt935AEEuO%3Fusp%3Dsharing
> 
>
> The first execution of SAMSEG was with default settings (1 thread) and
> results are attached, the second was using --threads 6.
>
> These results from the SAME series are similar but they are NOT the same.
>
> How can we explain that?
>
> Regards
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1gy4vF3zlcnMbwDq8EjHp3Ajgtk44__fZSmrsAds9R7GQymiOLtDzKqXFl_sq-rWQUaE0BGO7A5gSJM6VIe9Rn0b734pymR-xavqSOYdwZADemZ_ZcOgoq04Es74QyqiaNTGRZBw7ncLrkaY15WCcGfzx9oPAMIRdxGo5jDiOG3-7fwwBtFcTTUz-aQs3PregsVXFCSAUDwsOims6wCA_BoxW_YKYDJVPMOxZVzuL6cJa9VRWaWT6yaScVrAiOJQtS8ELpX95rtXUZX4eZ3isT89u_DDQ1laaDT-ZMvrSVgxY4UXaUNfPUEwEzkQkjijL/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Giulio Siracusano 
External Email - Use Caution

Hello,

this is true (i.e. reproducibility) for ASEG (when running recon-all -all).

But, if you use SAMSEG (i.e. running run_samseg instead) you get 
slightly different results everytime. This is regardless you use 
-threads flag or not.

My command line is (using the file I've provided in the link in my 
previous email):

run_samseg --input ./I18211_ADNI_12M4_TS_2_20060706103342_2.nii --output 
/usr/local/freesurfer/7.2.0/subjects/002_S_0685-I18211/SAMSEG_NIF

either using this version (1-thread) or a multi-thread

run_samseg --input ./I18211_ADNI_12M4_TS_2_20060706103342_2.nii --output 
/usr/local/freesurfer/7.2.0/subjects/002_S_0685-I18211/SAMSEG_NIF -threads 6


You get always slightly different results.


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Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Bouchra Guelib 
External Email - Use Caution

Why you didn't run recon-all directly ?

Le sam. 27 août 2022 à 11:32, Giulio Siracusano 
a écrit :

> External Email - Use Caution
>
> Hello,
>
> this is true (i.e. reproducibility) for ASEG (when running recon-all -all).
>
> But, if you use SAMSEG (i.e. running run_samseg instead) you get
> slightly different results everytime. This is regardless you use
> -threads flag or not.
>
> My command line is (using the file I've provided in the link in my
> previous email):
>
> run_samseg --input ./I18211_ADNI_12M4_TS_2_20060706103342_2.nii --output
> /usr/local/freesurfer/7.2.0/subjects/002_S_0685-I18211/SAMSEG_NIF
>
> either using this version (1-thread) or a multi-thread
>
> run_samseg --input ./I18211_ADNI_12M4_TS_2_20060706103342_2.nii --output
> /usr/local/freesurfer/7.2.0/subjects/002_S_0685-I18211/SAMSEG_NIF -threads
> 6
>
>
> You get always slightly different results.
>
>
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Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Giulio Siracusano 
   External Email - Use Caution

I've tested reproducibility of the results either using ASEG (therefore 
via recon-all -all) and also SAMSEG (via run_samseg).


The methods are different either in terms of reproducibility of results.

Multiple runs of ASEG (recon-all -all) provide the same result but it 
requires 8+ hours to be executed (each). By comparing the results of 
multiple runs using the file from a single patient, such results are 
exactly the same, no changes at all.


If I use SAMSEG (which is a lot faster, execution time is less than 1h 
using multi-thread execution), I get overall slightly similar results 
(when compared to ASEG) except for the CSF which is very different.


The problem I've found is that if I run SAMSEG on the same patient data 
and evaluate the results, these results (which I would expect they 
should be exactly the same), are slightly different. I've done multiple 
test, whether using single-thread or multi-thread execution. Every time 
I execute run_samseg the results express variability. I think this is 
because multiple calls to numpy.random in the python code of samseg. 
This problem should be fixed to ensure reproducibility of the data.


I hope to be clear now.

I just wanted to understand is the results from ASEG and SAMSEG (which 
is again, a lot faster) could be compared in terms of reproducibility, 
even if these results are not equivalent per se.



Regards

# Measure Unknown, 938678.804563, mm^3
# Measure Skull, 70514.097706, mm^3
# Measure Soft_Nonbrain_Tissue, 1117216.914116, mm^3
# Measure Brain-Stem, 19382.400237, mm^3
# Measure CSF, 510336.929212, mm^3
# Measure Left-Cerebellum-Cortex, 46227.404805, mm^3
# Measure Right-Cerebellum-Cortex, 46954.827348, mm^3
# Measure 4th-Ventricle, 1927.249860, mm^3
# Measure Fluid_Inside_Eyes, 10681.567722, mm^3
# Measure Left-Cerebral-Cortex, 194854.703127, mm^3
# Measure Right-Cerebral-Cortex, 198395.911108, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.296942, mm^3
# Measure Right-Cerebellum-White-Matter, 13442.628195, mm^3
# Measure Right-Cerebral-White-Matter, 200768.332902, mm^3
# Measure Left-Cerebral-White-Matter, 199392.351036, mm^3
# Measure Right-choroid-plexus, 2202.554448, mm^3
# Measure Right-Amygdala, 1483.776188, mm^3
# Measure Left-Amygdala, 1543.083787, mm^3
# Measure Right-Hippocampus, 3889.943347, mm^3
# Measure Right-Inf-Lat-Vent, 773.181432, mm^3
# Measure Left-Hippocampus, 3957.909089, mm^3
# Measure Left-choroid-plexus, 1732.272325, mm^3
# Measure Left-Inf-Lat-Vent, 374.679073, mm^3
# Measure Optic-Chiasm, 194.020527, mm^3
# Measure Right-VentralDC, 3517.897243, mm^3
# Measure Left-VentralDC, 3616.708619, mm^3
# Measure 3rd-Ventricle, 2767.856042, mm^3
# Measure Left-Accumbens-area, 582.221221, mm^3
# Measure Left-Putamen, 4786.334982, mm^3
# Measure Right-Putamen, 4722.605242, mm^3
# Measure Right-vessel, 80.863621, mm^3
# Measure Right-Accumbens-area, 461.768868, mm^3
# Measure WM-hypointensities, 20335.889722, mm^3
# Measure Left-Lateral-Ventricle, 20190.963456, mm^3
# Measure Left-vessel, 61.352892, mm^3
# Measure Right-Lateral-Ventricle, 18727.913621, mm^3
# Measure Right-Pallidum, 1703.159618, mm^3
# Measure Left-Caudate, 3777.300280, mm^3
# Measure Right-Thalamus, 5636.150208, mm^3
# Measure Left-Pallidum, 1656.295530, mm^3
# Measure Right-Caudate, 3583.231471, mm^3
# Measure Left-Thalamus, 6017.696659, mm^3
# Measure non-WM-hypointensities, 89.673417, mm^3
# Measure 5th-Ventricle, 15.867564, mm^3
# Measure Unknown, 939056.015091, mm^3
# Measure Skull, 71767.719764, mm^3
# Measure Soft_Nonbrain_Tissue, 1112717.212711, mm^3
# Measure Brain-Stem, 19396.749933, mm^3
# Measure CSF, 511873.576213, mm^3
# Measure Left-Cerebellum-Cortex, 46226.557363, mm^3
# Measure Right-Cerebellum-Cortex, 46977.164462, mm^3
# Measure 4th-Ventricle, 1932.334854, mm^3
# Measure Fluid_Inside_Eyes, 10678.846479, mm^3
# Measure Left-Cerebral-Cortex, 195097.957627, mm^3
# Measure Right-Cerebral-Cortex, 198722.232809, mm^3
# Measure Left-Cerebellum-White-Matter, 13367.963053, mm^3
# Measure Right-Cerebellum-White-Matter, 13448.109331, mm^3
# Measure Right-Cerebral-White-Matter, 201145.753968, mm^3
# Measure Left-Cerebral-White-Matter, 199725.946038, mm^3
# Measure Right-choroid-plexus, 2196.836003, mm^3
# Measure Right-Amygdala, 1483.180736, mm^3
# Measure Left-Amygdala, 1541.752663, mm^3
# Measure Right-Hippocampus, 3885.522213, mm^3
# Measure Right-Inf-Lat-Vent, 774.735928, mm^3
# Measure Left-Hippocampus, 3954.921244, mm^3
# Measure Left-choroid-plexus, 1727.665580, mm^3
# Measure Left-Inf-Lat-Vent, 375.969644, mm^3
# Measure Optic-Chiasm, 194.100725, mm^3
# Measure Right-VentralDC, 3514.663768, mm^3
# Measure Left-VentralDC, 3624.351918, mm^3
# Measure 3rd-Ventricle, 2772.144481, mm^3
# Measure Left-Accumbens-area, 583.409147, mm^3
# Measure Left-Putamen, 4795.974528, mm^3
# Measure Right-Putamen, 4727.161970, mm^3
# Measure Right-vessel, 81.049494, mm^3
# Measure Right-Accumbens-area, 460.463919,

Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Bouchra Guelib 
External Email - Use Caution

Firstly, thanks for your explanation, I didn't know that it would take less
than hours since I used recon-all to run 202 samples, I used parallel to
run 8 images at once and it took almost 13 hours, but at the end , you can
be sure of the results you have. Also it gives you a variety of  aseg
statistics for subcortical and cortex regions, which would be useful if you
want to use them as features for machine learning frameworks, so since you
don't have the same results each time recon-all would be better solution.

Le sam. 27 août 2022 à 12:47, Giulio Siracusano 
a écrit :

> External Email - Use Caution
>
> I've tested reproducibility of the results either using ASEG (therefore
> via recon-all -all) and also SAMSEG (via run_samseg).
>
> The methods are different either in terms of reproducibility of results.
>
> Multiple runs of ASEG (recon-all -all) provide the same result but it
> requires 8+ hours to be executed (each). By comparing the results of
> multiple runs using the file from a single patient, such results are
> exactly the same, no changes at all.
>
> If I use SAMSEG (which is a lot faster, execution time is less than 1h
> using multi-thread execution), I get overall slightly similar results
> (when compared to ASEG) except for the CSF which is very different.
>
> The problem I've found is that if I run SAMSEG on the same patient data
> and evaluate the results, these results (which I would expect they
> should be exactly the same), are slightly different. I've done multiple
> test, whether using single-thread or multi-thread execution. Every time
> I execute run_samseg the results express variability. I think this is
> because multiple calls to numpy.random in the python code of samseg.
> This problem should be fixed to ensure reproducibility of the data.
>
> I hope to be clear now.
>
> I just wanted to understand is the results from ASEG and SAMSEG (which
> is again, a lot faster) could be compared in terms of reproducibility,
> even if these results are not equivalent per se.
>
>
> Regards
>
> ___
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[Freesurfer] R: SAMSEG estimation error

2022-08-27 Thread Cerri, Stefano 
Hi Giulio,

Although SAMSEG is a deterministic algorithm the default version might give you 
different results when executed with a different number of threads. These are 
small differences when looking at seg.mgz (a few voxels with swapped labels), 
but they are more visible when looking at volumes computed from soft 
segmentations like the stats files.

Note that you will obtain the same exact results when running SAMSEG with the 
same number of threads.

If you want to have cross-thread reproducible results with SAMSEG you can 
download the source files of FS 7.2 and build FS with the flag 
(GEMS_CROSS_THREAD_REPRODUCIBLE ON when doing cmake). Note that this version of 
SAMSEG will run slower than the original version.

Source files can be downloaded here: 
https://github.com/freesurfer/freesurfer/tags?after=v7.3.1

and instructions on how to build FS are here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide

Hope it helps,
Stefano


Da: giulio siracusano 
Inviato: sabato 27 agosto 2022 04:22
A: freesurfer@nmr.mgh.harvard.edu 
Cc: Cerri, Stefano 
Oggetto: Re: [Freesurfer] SAMSEG estimation error


External Email - Use Caution

Hi Stefano,

I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2 
version of Freesurfer and I've realized that I get different results using the 
same data but when I run the SAMSEG multiple times.

Differently from using ASEG, SAMSEG provides also the chance to execute the 
code using multiple threads.

In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using the 
MP-RAGE series having ID I18211 (the link below provides the NIFTI version of 
the series which has been used for the processing).

https://drive.google.com/drive/folders/15oghna17Qz-OSuo9E3-rldOt935AEEuO?usp=sharing

The first execution of SAMSEG was with default settings (1 thread) and results 
are attached, the second was using --threads 6.

These results from the SAME series are similar but they are NOT the same.

How can we explain that?

Regards

Giulio
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