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Hi FreeSurfer community,
I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution? 2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated? 3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values? Thanks.
Best, Florent
On 2/16/2022 4:12 AM, k3ops@free.fr wrote:
External Email - Use CautionHi FreeSurfer community,
I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution?
The same stats should be in seg.stats
2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated?
No, not easily. There is a sbtiv.stats file with intracranial volume in it.
3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values?
No, you have to have a surface-based analysis for that
Thanks.
Best, Florent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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_-rYaCj4VoBlufgE4KDcCDmct4ekP97q5p4NhEV... 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
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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 siracusanogiulio@gmail.com a écrit :
External Email - Use CautionHi 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_LHxfarwpgU9bmrPe4UoS0CjjeTiU5... 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gy4vF3zlcnMbwDq8EjHp3Ajgtk44__fZSmrsAds9R7GQym... 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 e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1KQ-nWpupEUQz4B9UokcAWkH1AI_p4XRNkGQIExK_JYUy0Y... < https://secure-web.cisco.com/1KQ-nWpupEUQz4B9UokcAWkH1AI_p4XRNkGQIExK_JYUy0Y... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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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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Why you didn't run recon-all directly ?
Le sam. 27 août 2022 à 11:32, Giulio Siracusano siracusanogiulio@gmail.com a écrit :
External Email - Use CautionHello,
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1BaXjhVNrGgKUE0ji0Yu6JwJ0c-v0Yav3FCTn-Pmifu2KBC... 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 e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1v-fNrOTB8umkRyirv-tSwOU32ZLWx2tJa1L9M92K50aC2f... < https://secure-web.cisco.com/1v-fNrOTB8umkRyirv-tSwOU32ZLWx2tJa1L9M92K50aC2f... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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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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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 siracusanogiulio@gmail.com a écrit :
External Email - Use CautionI'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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/10yr5IlCSs8ur1ncghNHOe8GL61IDSXQgqKCPyvPVk1sGN-... 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 e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1ENNIn7iilC2c2zYafoa6IZwY1XnH4yf8dALBYgRZY8V0if... < https://secure-web.cisco.com/1ENNIn7iilC2c2zYafoa6IZwY1XnH4yf8dALBYgRZY8V0if... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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