Hello All,
I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all.
I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies?
I really appreciate your time and assistant with this issue.
Thank you in advance for your help!
Tamara
Hello Tamara,
It IS expected to see differences in volumetric data calculated when using versions if freesurfer compiled for different platforms. That is why we make the claim of "When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform".
You dont specify the % differences in your email below, but we have found that the differences observed in Mac vs. Linux will typically have deltas of less than 5%. Sometimes larger percent differences are observed in smaller structures, only because the delta of a single voxel can carry a larger percentage weight for smaller structures.
-Zeke
On 05/12/2016 10:20 AM, Tamara Tavares wrote:
Hello All,
I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all.
I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies?
I really appreciate your time and assistant with this issue.
Thank you in advance for your help!
Tamara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and just to chime in, before anyone flames us on this topic (as has happened in the past), we would *love* to have the resources to track down and eliminate this kind of thing, but it is very, very difficult to get NIH funding to do so.
cheers Bruce
On Thu, 12 May 2016, Z K wrote:
Hello Tamara,
It IS expected to see differences in volumetric data calculated when using versions if freesurfer compiled for different platforms. That is why we make the claim of "When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform".
You dont specify the % differences in your email below, but we have found that the differences observed in Mac vs. Linux will typically have deltas of less than 5%. Sometimes larger percent differences are observed in smaller structures, only because the delta of a single voxel can carry a larger percentage weight for smaller structures.
-Zeke
On 05/12/2016 10:20 AM, Tamara Tavares wrote:
Hello All,
I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all.
I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies?
I really appreciate your time and assistant with this issue.
Thank you in advance for your help!
Tamara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Zeke,
Thank you for your quick reply.
I am specifically interested in examining the ventricles and calculated the percent differences for these segmented areas:
Left lateral ventricle = 2.08%
Left inferior lateral ventricle = 6.81%
3rd ventricle= 6.31%
4th ventricle =2.68%
Right lateral ventricle = 0.40%
5th ventricle =200%
I am a bit concerned of the 5th ventricle as it is well greater than the expected 5% difference you suggested. However, I assume the other percent differences are within normal range? This is the first time I am using Freesurfer so I just want to confirm that my results are correct.
Thank you in advance for your help. It is very much appreciated!
Tamara
On Thu, May 12, 2016 at 1:36 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Hello Tamara,
It IS expected to see differences in volumetric data calculated when using versions if freesurfer compiled for different platforms. That is why we make the claim of "When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform".
You dont specify the % differences in your email below, but we have found that the differences observed in Mac vs. Linux will typically have deltas of less than 5%. Sometimes larger percent differences are observed in smaller structures, only because the delta of a single voxel can carry a larger percentage weight for smaller structures.
-Zeke
On 05/12/2016 10:20 AM, Tamara Tavares wrote:
Hello All,
I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all.
I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies?
I really appreciate your time and assistant with this issue.
Thank you in advance for your help!
Tamara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The 5th ventricle is a very small structure, so larger deltas are to be expected (due to a few missagned voxels). Otherwise I would categorize those differences as normal.
However, I must specify, if you are doing cross subject comparisons, please stick with the same version of freesurfer (i.e same platform).
-Zele
On 05/12/2016 03:02 PM, Tamara Tavares wrote:
Hi Zeke,
Thank you for your quick reply.
I am specifically interested in examining the ventricles and calculated the percent differences for these segmented areas:
Left lateral ventricle = 2.08%
Left inferior lateral ventricle = 6.81%
3^rd ventricle= 6.31%
4^th ventricle =2.68%
Right lateral ventricle = 0.40%
5^th ventricle =200%
I am a bit concerned of the 5^th ventricle as it is well greater than the expected 5% difference you suggested. However, I assume the other percent differences are within normal range? This is the first time I am using Freesurfer so I just want to confirm that my results are correct.
Thank you in advance for your help. It is very much appreciated!
Tamara
On Thu, May 12, 2016 at 1:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
Hello Tamara, It IS expected to see differences in volumetric data calculated when using versions if freesurfer compiled for different platforms. That is why we make the claim of "When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform". You dont specify the % differences in your email below, but we have found that the differences observed in Mac vs. Linux will typically have deltas of less than 5%. Sometimes larger percent differences are observed in smaller structures, only because the delta of a single voxel can carry a larger percentage weight for smaller structures. -Zeke On 05/12/2016 10:20 AM, Tamara Tavares wrote: Hello All, I was hoping someone would be able to shed some light on an issue I have been having concerning the volumetric data calculated by FreeSurfer (version 5.3) using the asegstats output file. For information purposes, I am currently using the following command line: recon-all –I [path] –s –sd [Path] –segmentation –all. I have noticed some differences in the volumetric outputs from a scan I ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran on a Mac OS version 10.10.5. These differences in volume range from 5.2-639.4. I have been having difficulty in finding the source of this discrepancy. Are discrepancies commonly found? Could the different computers and operating systems be the reason for these discrepancies? I really appreciate your time and assistant with this issue. Thank you in advance for your help! Tamara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Tamara Tavares -
Z K