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Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
Confidential communication - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email.
Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote:
External Email - Use Caution
Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
- Are these version‐to‐version shifts expected, given the changes in v8?
- Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures?
- Are large shifts expected from run-to-run as well?
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
/*Confidential communication* - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email./
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Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
1. roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Monday, 11 August 2025 at 8:36 am To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote: External Email - Use Caution Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
Confidential communication - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email.
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Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote:
External Email - Use Caution
Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
- */roi_proportional_changes/*: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs
- */etiv_differences/*: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer
- */amyg_differences/*: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
*From: *Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Monday, 11 August 2025 at 8:36 am *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important https://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote:
* External Email - Use Caution * Hi, I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure). I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern. I am wondering: * Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? * Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results. Thanks for your time. Kindest, Hana */Confidential communication/*/ - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email./ _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/
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External Email - Use Caution
Hi Douglas,
Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month).
I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences.
Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thank you very much for your response and assistance again, I really appreciate it.
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Thursday, 28 August 2025 at 4:50 am To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
1. roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 11 August 2025 at 8:36 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote: External Email - Use Caution Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
Confidential communication - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email.
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What commands did you use to generate the hippo subfields in v7 and v8? doug
On 9/17/2025 9:38 PM, Hana McMahon wrote:
External Email - Use Caution
Hi Douglas,
Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month).
I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences.
Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thank you very much for your response and assistance again, I really appreciate it.
Kindest, Hana
*Hana McMahon*
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
*From: *Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Thursday, 28 August 2025 at 4:50 am *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote:
* External Email - Use Caution * Hi Douglas, Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison. Regarding some numbers, please see attached (and in the .zip): 1. */roi_proportional_changes/*: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. */etiv_differences/*: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. */amyg_differences/*: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature. Thank you again for your help and response. Kindest, Hana *From: *Douglas N. Greve <dgreve@mgh.harvard.edu> *Date: *Monday, 11 August 2025 at 8:36 am *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> *Subject: *[Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important <https://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification> Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me. On 8/7/2025 1:40 AM, Hana McMahon wrote: * External Email - Use Caution * Hi, I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure). I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern. I am wondering: * Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? * Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results. Thanks for your time. Kindest, Hana */Confidential communication/*/ - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email./ _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/
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Hi Douglas,
In my scripts for v7.2.0 and v8.0.0 I use the exact same code for segmentation:
# run FreeSurfer recon-all and hip/amyg segmentation cd "$SUBJECTS_DIR" img=/$BASE/nii_converted/sub-${s}_T1w.nii.gz "$FREESURFER_HOME"/bin/recon-all \ -s "${s}" \ -i "$img" \ -all -qcache -parallel -openmp 10 "$FREESURFER_HOME"/bin/segmentHA_T1.sh "${s}”
The only difference in the two scripts is the output folder, and for version 7.2.0 I have a few additional lines that run it inside a container as the version was not installed directly on the Supercomputer I use:
apptainer exec --no-home \ --pwd /tmp \ -B /apps/rhel7:/usr/local \ -B /data/projects:/data/projects \ -B /data/scratch:/data/scratch \ -B $SLURM_TMPDIR:$SLURM_TMPDIR \ /apps/singularity_images/RHEL7_Spartan/rhel7_spartan.img \
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Monday, 22 September 2025 at 7:51 am To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
What commands did you use to generate the hippo subfields in v7 and v8? doug
On 9/17/2025 9:38 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month).
I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences.
Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thank you very much for your response and assistance again, I really appreciate it.
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Thursday, 28 August 2025 at 4:50 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
1. roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 11 August 2025 at 8:36 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote: External Email - Use Caution Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
Confidential communication - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email.
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OK, so you are using /segmentHA_T1.sh for both? If that case, I would think that the only difference is the hippo in the aseg; this probably indicates a little instability in the subfield segmentation due to the difficulty of the task/
On 9/21/2025 8:42 PM, Hana McMahon wrote:
External Email - Use Caution
Hi Douglas,
In my scripts for v7.2.0 and v8.0.0 I use the exact same code for segmentation: / / /# run FreeSurfer recon-all and hip/amyg segmentation/ /cd "$SUBJECTS_DIR"/ /img=//$BASE//nii_converted/sub-${s}_T1w.nii.gz/ /"$FREESURFER_HOME"/bin/recon-all / / -s "${s}" / / -i "$img" / / -all -qcache -parallel -openmp 10/ /"$FREESURFER_HOME"/bin/segmentHA_T1.sh "${s}//”/ / / The only difference in the two scripts is the output folder, and for version 7.2.0 I have a few additional lines that run it inside a container as the version was not installed directly on the Supercomputer I use: / / apptainer exec --no-home \ --pwd /tmp \ -B /apps/rhel7:/usr/local \ -B /data/projects:/data/projects \ -B /data/scratch:/data/scratch \ -B $SLURM_TMPDIR:$SLURM_TMPDIR \ /apps/singularity_images/RHEL7_Spartan/rhel7_spartan.img \
Kindest, Hana
*Hana McMahon*
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
*From: *Douglas N. Greve dgreve@mgh.harvard.edu *Date: *Monday, 22 September 2025 at 7:51 am *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
What commands did you use to generate the hippo subfields in v7 and v8? doug
On 9/17/2025 9:38 PM, Hana McMahon wrote:
* External Email - Use Caution * Hi Douglas, Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month). I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences. Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to? Thank you very much for your response and assistance again, I really appreciate it. Kindest, Hana *Hana McMahon* PhD/MPsych (Clinical) Candidate School of Psychology UNSW Sydney *From: *Douglas N. Greve <dgreve@mgh.harvard.edu> *Date: *Thursday, 28 August 2025 at 4:50 am *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> *Subject: *[Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok? For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes. On 8/10/2025 11:47 PM, Hana McMahon wrote: * External Email - Use Caution * Hi Douglas, Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison. Regarding some numbers, please see attached (and in the .zip): 1. */roi_proportional_changes/*: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. */etiv_differences/*: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. */amyg_differences/*: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature. Thank you again for your help and response. Kindest, Hana *From: *Douglas N. Greve <dgreve@mgh.harvard.edu> *Date: *Monday, 11 August 2025 at 8:36 am *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> *Subject: *[Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs You don't often get email from dgreve@mgh.harvard.edu. Learn why this is important <https://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification> Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me. On 8/7/2025 1:40 AM, Hana McMahon wrote: * External Email - Use Caution * Hi, I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure). I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern. I am wondering: * Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? * Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results. Thanks for your time. Kindest, Hana */Confidential communication/*/ - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email./ _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/
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Sorry for being late to the party! Yeah the atlas deformation is initialized with ASEG, so the differences between the method in the Neuron paper and SynthSeg will certainly have an impact. Cheers, /Eugenio
--
Juan Eugenio Iglesias
From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Tuesday, September 23, 2025 at 1:05 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
OK, so you are using segmentHA_T1.sh for both? If that case, I would think that the only difference is the hippo in the aseg; this probably indicates a little instability in the subfield segmentation due to the difficulty of the task
On 9/21/2025 8:42 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
In my scripts for v7.2.0 and v8.0.0 I use the exact same code for segmentation:
# run FreeSurfer recon-all and hip/amyg segmentation cd "$SUBJECTS_DIR" img=/$BASE/nii_converted/sub-${s}_T1w.nii.gz "$FREESURFER_HOME"/bin/recon-all \ -s "${s}" \ -i "$img" \ -all -qcache -parallel -openmp 10 "$FREESURFER_HOME"/bin/segmentHA_T1.sh "${s}”
The only difference in the two scripts is the output folder, and for version 7.2.0 I have a few additional lines that run it inside a container as the version was not installed directly on the Supercomputer I use:
apptainer exec --no-home \ --pwd /tmp \ -B /apps/rhel7:/usr/local \ -B /data/projects:/data/projects \ -B /data/scratch:/data/scratch \ -B $SLURM_TMPDIR:$SLURM_TMPDIR \ /apps/singularity_images/RHEL7_Spartan/rhel7_spartan.img \
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 22 September 2025 at 7:51 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
What commands did you use to generate the hippo subfields in v7 and v8? doug
On 9/17/2025 9:38 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month).
I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences.
Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thank you very much for your response and assistance again, I really appreciate it.
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Thursday, 28 August 2025 at 4:50 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
1. roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 11 August 2025 at 8:36 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote: External Email - Use Caution Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
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External Email - Use Caution
Hi Douglas and Eugenio,
Thanks for your replies and for clarifying. In terms of my analysis moving forward, I am wondering whether you think it is best to proceed with the outputs from version 8 as the hippocampal and amygdala segmentation uses synthseg? Or would it be best to move forward with the version 7 outputs as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thanks again for your help.
Best, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Tuesday, 23 September 2025 at 9:50 am To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from jiglesiasgonzalez@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1ktjU9IltnSGN7Hvu50EwvIHXrJXx6uS9qQXs20hEE0-LTJQxFtXh_HhlGQ1T78lQKDD5qXbfI1UGUpj1UXpmrSwLNXpmLs26OYhOzEE8RHJlapvbh_GQeOlupbadpbxSJ32EHthFr8yfcL6uNql3D0upE6TNvCz0NqDRGghpmm03sqXGp8J957-EQ0VNlupraGXhoFJbPpStEmD-MAB_5wTB4DVSHKDEKz3AjVva8p1Q3XnLYCeIsQ89kvkBajsu5vV-H_QYJAng_s-1ezEsNhOl0LSyPwTGJb9_NT3dmoqZ6lLrSNAXxeQqBTbGIl6PZskT1AQ0wLjpMCHtb_KbXw/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Sorry for being late to the party! Yeah the atlas deformation is initialized with ASEG, so the differences between the method in the Neuron paper and SynthSeg will certainly have an impact. Cheers, /Eugenio
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1sppXbO1KdFwY9jnJlwsOUzJgcJG4aqXe9ysdnWfOe7ICrLu...
From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Tuesday, September 23, 2025 at 1:05 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
OK, so you are using segmentHA_T1.sh for both? If that case, I would think that the only difference is the hippo in the aseg; this probably indicates a little instability in the subfield segmentation due to the difficulty of the task
On 9/21/2025 8:42 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
In my scripts for v7.2.0 and v8.0.0 I use the exact same code for segmentation:
# run FreeSurfer recon-all and hip/amyg segmentation cd "$SUBJECTS_DIR" img=/$BASE/nii_converted/sub-${s}_T1w.nii.gz "$FREESURFER_HOME"/bin/recon-all \ -s "${s}" \ -i "$img" \ -all -qcache -parallel -openmp 10 "$FREESURFER_HOME"/bin/segmentHA_T1.sh "${s}”
The only difference in the two scripts is the output folder, and for version 7.2.0 I have a few additional lines that run it inside a container as the version was not installed directly on the Supercomputer I use:
apptainer exec --no-home \ --pwd /tmp \ -B /apps/rhel7:/usr/local \ -B /data/projects:/data/projects \ -B /data/scratch:/data/scratch \ -B $SLURM_TMPDIR:$SLURM_TMPDIR \ /apps/singularity_images/RHEL7_Spartan/rhel7_spartan.img \
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 22 September 2025 at 7:51 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
What commands did you use to generate the hippo subfields in v7 and v8? doug
On 9/17/2025 9:38 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month).
I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences.
Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thank you very much for your response and assistance again, I really appreciate it.
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Thursday, 28 August 2025 at 4:50 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
1. roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 11 August 2025 at 8:36 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1MqnwtIXwk_y2mtTMDDJngSoVHxOaArm8wMLgHSKFQJqE6AwfTEzuCx8uOhK2cTrNEViLUDcNxVREqEI3-utWhU6Nl8lS-CRRxz76aQdd4H1Eg22F8tHY_RAxhlhPOEAwEenCVeyRapP0EZqiwy3KR4DGXsxqJuHebzG1VDF5iTCRg3RhjG0NdVugSFhKMNAB-pVahZhPtbjw9LWzIGggWFb3nmuXoDrSPXxUrCstC_N0xOR6XkKg1h_LA-cBmIa_wsQ70opeOVkf_5WNZ3HMlHLzcGAy5Z43VOZghF6bkM4blZm_1JwtOmBTozBrdUm_BRy57rL-WCbB-xtmGAIiew/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote: External Email - Use Caution Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
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I would go for 7.x. But it is true that it will be significantly slower :-S
--
Juan Eugenio Iglesias
From: Hana McMahon hana.mcmahon@unsw.edu.au Date: Friday, September 26, 2025 at 11:48 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
External Email - Use Caution Hi Douglas and Eugenio,
Thanks for your replies and for clarifying. In terms of my analysis moving forward, I am wondering whether you think it is best to proceed with the outputs from version 8 as the hippocampal and amygdala segmentation uses synthseg? Or would it be best to move forward with the version 7 outputs as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thanks again for your help.
Best, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Tuesday, 23 September 2025 at 9:50 am To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
You don't often get email from jiglesiasgonzalez@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1ktjU9IltnSGN7Hvu50EwvIHXrJXx6uS9qQXs20hEE0-LTJQxFtXh_HhlGQ1T78lQKDD5qXbfI1UGUpj1UXpmrSwLNXpmLs26OYhOzEE8RHJlapvbh_GQeOlupbadpbxSJ32EHthFr8yfcL6uNql3D0upE6TNvCz0NqDRGghpmm03sqXGp8J957-EQ0VNlupraGXhoFJbPpStEmD-MAB_5wTB4DVSHKDEKz3AjVva8p1Q3XnLYCeIsQ89kvkBajsu5vV-H_QYJAng_s-1ezEsNhOl0LSyPwTGJb9_NT3dmoqZ6lLrSNAXxeQqBTbGIl6PZskT1AQ0wLjpMCHtb_KbXw/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Sorry for being late to the party! Yeah the atlas deformation is initialized with ASEG, so the differences between the method in the Neuron paper and SynthSeg will certainly have an impact. Cheers, /Eugenio
--
Juan Eugenio Iglesias
From: Douglas N. Greve dgreve@mgh.harvard.edu Date: Tuesday, September 23, 2025 at 1:05 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
OK, so you are using segmentHA_T1.sh for both? If that case, I would think that the only difference is the hippo in the aseg; this probably indicates a little instability in the subfield segmentation due to the difficulty of the task
On 9/21/2025 8:42 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
In my scripts for v7.2.0 and v8.0.0 I use the exact same code for segmentation:
# run FreeSurfer recon-all and hip/amyg segmentation cd "$SUBJECTS_DIR" img=/$BASE/nii_converted/sub-${s}_T1w.nii.gz "$FREESURFER_HOME"/bin/recon-all \ -s "${s}" \ -i "$img" \ -all -qcache -parallel -openmp 10 "$FREESURFER_HOME"/bin/segmentHA_T1.sh "${s}”
The only difference in the two scripts is the output folder, and for version 7.2.0 I have a few additional lines that run it inside a container as the version was not installed directly on the Supercomputer I use:
apptainer exec --no-home \ --pwd /tmp \ -B /apps/rhel7:/usr/local \ -B /data/projects:/data/projects \ -B /data/scratch:/data/scratch \ -B $SLURM_TMPDIR:$SLURM_TMPDIR \ /apps/singularity_images/RHEL7_Spartan/rhel7_spartan.img \
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 22 September 2025 at 7:51 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
What commands did you use to generate the hippo subfields in v7 and v8? doug
On 9/17/2025 9:38 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you very much for your reply (and apologies for taking so long to repsond to it - I have been on annual leave for a month).
I have checked the registrations and they look okay. Regarding the software, both were run on Python on a supercomputer using a very similar script, so I don’t think that is the cause of the differences.
Thanks for explaining how the segmentation works, it makes sense that the ROIs are very small and therefore the changes seen could be very large. I am wondering whether you have any recommendations of which version to use moving forward, as my results (between groups) are different depending on which version of FreeSurfer I use. Do you believe version 8 is better for this hippocampal and amygdala segmentation as it uses synthseg? Or would it be best to move forward with the version 7 results as this version has been used and published innumerable times and therefore is the most validated? Alternatively, would you suggest running it through a different version altogether, such as 7.4.1 and determining which these results are most similar to?
Thank you very much for your response and assistance again, I really appreciate it.
Kindest, Hana
Hana McMahon
PhD/MPsych (Clinical) Candidate
School of Psychology
UNSW Sydney
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Thursday, 28 August 2025 at 4:50 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
Hi, sorry for the delay. For etiv, the algorithm depends on the linear registration of the brain to the mni305 (ie, it is not based on a segmentation to compute the TIV -- that is what the stiv and it is probably better than the etiv). With v8, we changed algorithms for this computation, and so it is not surprising that there are differences. In my evaluation, the difference was typically about 5%. It looks like you are seeing a much larger difference. Have you checked the registrations to see if they look ok?
For the others, what command did you use? We actually have two versions of this software (one matlab-based and one python), so I want to make sure you are not comparing against those two versions. The underlying software for the hippo/amyg subfields did not change from 7 to 8. However, those segmentation make use of the hippo and amyg segmentations in the aseg, which is now performed by synthseg instead of the gca. My guess is that this is the source of the change. Why is the change so big? Not sure, but these segmentations are very difficult as there is not really any contrast at the edge of the subfield ROIs and the ROIs are very small. Because the ROIs are so small, it does not take much of a change to get big volume changes.
On 8/10/2025 11:47 PM, Hana McMahon wrote: External Email - Use Caution Hi Douglas,
Thank you for your reply. The regions I am primarily interested in are the segmentations of the Hippocampus and Amygdala, as well as eTIV as a covariate. However, I will also run exploratory analyses on the whole brain, as the study is a clinical group comparison.
Regarding some numbers, please see attached (and in the .zip):
1. roi_proportional_changes: for each ROI (whole brain) I ran the formula mean(abs((v8 - v7) / v7) to determine the average absolute proportional difference between the versions, which is where I got the ~ 1-200% differences between versions in different ROIs 2. etiv_differences: this is the eTIV (estimated total intracranial volume) for each participant in my study directly taken from the output of each version of FreeSurfer 3. amyg_differences: this is an example of an amygdala subfield (Medial Nucleus LH) for each participant in my study directly taken from the output of each version of FreeSurfer
If you could please kindly explain a bit more about why there are big differences between v7 and v8 that would be very helpful, as I am currently not sure which version to move forward with, as the findings are completely different. I was under the impression that v8 is meant to be better, particularly for segmentation, however I am worried about publishing and reviewers, particularly if the outcomes cannot be compared to earlier versions and therefore the current literature.
Thank you again for your help and response.
Kindest, Hana
From: Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Monday, 11 August 2025 at 8:36 am To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
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Please be (much) more specific. What are the regions that you are finding changes in? Can you provide some numbers? There are big differences between v8 and v7 so it does not totally surprise me.
On 8/7/2025 1:40 AM, Hana McMahon wrote: External Email - Use Caution Hi,
I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure).
I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern.
I am wondering:
* Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? *
Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results.
Thanks for your time.
Kindest, Hana
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Douglas N. Greve -
Hana McMahon -
Iglesias Gonzalez, Juan E.