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Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best, Leo
External Email - Use Caution
Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva < leonardo.saraiva@usp.br> escreveu:
Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best, Leo
External Email - Use Caution
Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right.
On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva leonardo.saraiva@usp.br escreveu:
Dear Freesurfer Experts, I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’. In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below: mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong? Thank you for your time and attention. Best, Leo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KSZYX614qEx8hfwcMoajkL8do58-clrjyyKjwomQIwZord...
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Actually there is a whole Bayesian segmentation on the surface procedure that generates the individual subject parcellation so it definitely won’t be the same as just mapping fsaverage
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Sunday, September 10, 2023 1:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right. On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva <leonardo.saraiva@usp.brmailto:leonardo.saraiva@usp.br> escreveu: Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best, Leo
_______________________________________________
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Many thanks for reaching out and providing such clear information, Douglas and Bruce! I really appreciate it.
I was indeed comparing the ?h.aparc.annot files produced by recon-all to those produced by mri_surf2surf.
The aim of my analyses is to compare groups in morphometric features, using parcellations initially generated in fsaverage and then resampled to each subject's native surface. Based on the information you provided, it sounds like my approach is valid as long as I consistently use the mri_surf2surf command with identical arguments for all subjects within each group. Is that correct?
Thanks again for your time and attention!
Best, Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use CautionActually there is a whole Bayesian segmentation on the surface procedure that generates the individual subject parcellation so it definitely won’t be the same as just mapping fsaverage
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Sunday, September 10, 2023 1:35 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution *Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right.
On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution *Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva < leonardo.saraiva@usp.br> escreveu:
Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best,
Leo
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Yes, although I expect the individual subject parcellations to be a bit more accurate than the ones mapped from fsaverage. Probably not enough to make a significant difference though Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Leonardo Cardoso Saraiva Sent: Sunday, September 10, 2023 3:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution Many thanks for reaching out and providing such clear information, Douglas and Bruce! I really appreciate it.
I was indeed comparing the ?h.aparc.annot files produced by recon-all to those produced by mri_surf2surf.
The aim of my analyses is to compare groups in morphometric features, using parcellations initially generated in fsaverage and then resampled to each subject's native surface. Based on the information you provided, it sounds like my approach is valid as long as I consistently use the mri_surf2surf command with identical arguments for all subjects within each group. Is that correct?
Thanks again for your time and attention!
Best, Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution Actually there is a whole Bayesian segmentation on the surface procedure that generates the individual subject parcellation so it definitely won’t be the same as just mapping fsaverage
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Sunday, September 10, 2023 1:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right. On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva <leonardo.saraiva@usp.brmailto:leonardo.saraiva@usp.br> escreveu: Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best, Leo
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1xKVWnw14AJPAWEjfHoTP2z53fIHfnqXyDzlGEeFZMJJjo2...https://secure-web.cisco.com/1KSZYX614qEx8hfwcMoajkL8do58-clrjyyKjwomQIwZordqlVUH_j9GvZhrYerbuYDuIH3jFfhKBtkUoV1nvJ9hEKX1Sg7rM4wZQZPGPPSU81wPwxt7aU17Wu378Tq__w1zreh76384bvc5AAWF1bXfhdCuw4XmOem-N1Kzax2E4MTsdsH49OKjuOc3V5OY70Gph6QPaBHDlBqK0hse-7g7mHxv_p1KUR2lD8Fn1g87i7UsAiiwukjJ7Iz-LB-j0NYseCuA2LRtmtFBesglG0g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Thank you once more for your response, Bruce!
I intend to only use the parcellations that were initially mapped onto fsaverage and subsequently resampled to the subjects' native surfaces. This should ensure that the parcellations for all subjects are generated in the same way, right?
Many thanks again!
Best, Leo
Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use CautionYes, although I expect the individual subject parcellations to be a bit more accurate than the ones mapped from fsaverage. Probably not enough to make a significant difference though
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Leonardo Cardoso Saraiva *Sent:* Sunday, September 10, 2023 3:53 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution *Many thanks for reaching out and providing such clear information, Douglas and Bruce! I really appreciate it.
I was indeed comparing the ?h.aparc.annot files produced by recon-all to those produced by mri_surf2surf.
The aim of my analyses is to compare groups in morphometric features, using parcellations initially generated in fsaverage and then resampled to each subject's native surface. Based on the information you provided, it sounds like my approach is valid as long as I consistently use the mri_surf2surf command with identical arguments for all subjects within each group. Is that correct?
Thanks again for your time and attention!
Best, Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution *Actually there is a whole Bayesian segmentation on the surface procedure that generates the individual subject parcellation so it definitely won’t be the same as just mapping fsaverage
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Sunday, September 10, 2023 1:35 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution *Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right.
On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution *Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva < leonardo.saraiva@usp.br> escreveu:
Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best,
Leo
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Yes, although they would be generated in the same way across subjects with either method
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Leonardo Cardoso Saraiva Sent: Sunday, September 10, 2023 4:07 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution Thank you once more for your response, Bruce!
I intend to only use the parcellations that were initially mapped onto fsaverage and subsequently resampled to the subjects' native surfaces. This should ensure that the parcellations for all subjects are generated in the same way, right?
Many thanks again!
Best, Leo
Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution Yes, although I expect the individual subject parcellations to be a bit more accurate than the ones mapped from fsaverage. Probably not enough to make a significant difference though Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Leonardo Cardoso Saraiva Sent: Sunday, September 10, 2023 3:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution Many thanks for reaching out and providing such clear information, Douglas and Bruce! I really appreciate it.
I was indeed comparing the ?h.aparc.annot files produced by recon-all to those produced by mri_surf2surf.
The aim of my analyses is to compare groups in morphometric features, using parcellations initially generated in fsaverage and then resampled to each subject's native surface. Based on the information you provided, it sounds like my approach is valid as long as I consistently use the mri_surf2surf command with identical arguments for all subjects within each group. Is that correct?
Thanks again for your time and attention!
Best, Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution Actually there is a whole Bayesian segmentation on the surface procedure that generates the individual subject parcellation so it definitely won’t be the same as just mapping fsaverage
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Sunday, September 10, 2023 1:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right. On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva <leonardo.saraiva@usp.brmailto:leonardo.saraiva@usp.br> escreveu: Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best, Leo
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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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1e0UaB_jbadXfes95oWzVIlC5rVOH93V7knffEj8UrhJi-B...https://secure-web.cisco.com/1vFGUhLCrnBe_bNYtBBOzGQKLFJ8uxAa5gChepvrp9D7eR_mSTg5IL5O4-lPg--0uY6tEMM7q7ViLs4CrfilQZf4tK9hkiVBfe8ECXkNSxYrJKSqt3L6NrKjCUrglUe3OhsX3yQAwOuDvuUlWEgbtpss0OYJVfvoF_wc54M9v7mLlUsFxg83p76osf5SYJQm0yi6NfjjK7sl7c4ppirp4D0-GB7B2Jw7IiFOjV5daKON-OpucYcxyoxMsBpcxmTsp_EifLoQjZR4tVDmY2FGMez_HXHyBBTg93soJ87IlsQUA_QkABMviRvLmK9hJ2b8-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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Got it. Thank you very much for your replies and attention, Bruce! It helped me a lot.
Em dom., 10 de set. de 2023 às 17:07, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use CautionYes, although they would be generated in the same way across subjects with either method
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Leonardo Cardoso Saraiva *Sent:* Sunday, September 10, 2023 4:07 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution *Thank you once more for your response, Bruce!
I intend to only use the parcellations that were initially mapped onto fsaverage and subsequently resampled to the subjects' native surfaces. This should ensure that the parcellations for all subjects are generated in the same way, right?
Many thanks again!
Best, Leo
Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution *Yes, although I expect the individual subject parcellations to be a bit more accurate than the ones mapped from fsaverage. Probably not enough to make a significant difference though
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Leonardo Cardoso Saraiva *Sent:* Sunday, September 10, 2023 3:53 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution *Many thanks for reaching out and providing such clear information, Douglas and Bruce! I really appreciate it.
I was indeed comparing the ?h.aparc.annot files produced by recon-all to those produced by mri_surf2surf.
The aim of my analyses is to compare groups in morphometric features, using parcellations initially generated in fsaverage and then resampled to each subject's native surface. Based on the information you provided, it sounds like my approach is valid as long as I consistently use the mri_surf2surf command with identical arguments for all subjects within each group. Is that correct?
Thanks again for your time and attention!
Best, Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> escreveu:
External Email - Use Caution *Actually there is a whole Bayesian segmentation on the surface procedure that generates the individual subject parcellation so it definitely won’t be the same as just mapping fsaverage
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Sunday, September 10, 2023 1:35 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between resampled and recon-all generated annot files
External Email - Use Caution *Which annot files are you comparing? Some of them (eg, aparc) have an extra procedure where the labels boundaries are fine-tuned, so that could cause the difference. Your command looks right.
On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
External Email - Use Caution *Dear Freesurfer Experts,
I would like to follow up on my last email and ask if you had a chance to take a look at it.
Any guidance or feedback would be greatly appreciated!
Thank you for your time!
Best, Leo
Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva < leonardo.saraiva@usp.br> escreveu:
Dear Freesurfer Experts,
I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’.
In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below:
mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh
As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong?
Thank you for your time and attention.
Best,
Leo
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Freesurfer@nmr.mgh.harvard.edu
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ODNWJL85zFsUfXj2zKfI7QsKTKNrY3mzJjAreFma9_GNWr... https://secure-web.cisco.com/1IAq-5SGA-W0qw5aaHaPMvuU_Fvw8foFkdrdco39XswlsTxWTrONRTRbkyRsEqH7YLQLsfDcst5tV3ztMKKTe_ZlPDAj3fFxAYFsIFYhuKGeLq10tmoTa2sn-JU5zPKng1K3ne2fcStYyYRI-7VENoiH_bBKYckRl8tiwfqROy47PGKGp668YrqI2Nix4jgsEUdFYyAsrsOlq1IXi991o5_9r85uF0H7ncj0wBvtvDGMfSWaKzB8vYvouCnBWdn6eDZTdXhX1Q4NrEV7ePx4bNr1e6XT-rUYFPR8g52inoOyZ_GZCYihm5tEQ47UFUkLQla7PjUR6YEA8suVRBlt6OQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EpHraHnvwU2EaiAnYcTsAnTANKRtxIFN6kIDT59lkgDv5W... https://secure-web.cisco.com/1CA9K3JfPpK3GXgggqc2FeT4lpDWCHVYCjSa8cCcz-uZ_9rW7p7AdWJ0BSvJhFIur8AChWCWqN1SVTNg4_w8L3pD_ZmA42vsefxx7zg_9PXiaT63vaGVbklL3glbKL5zsgcbAUkhpSXmlWuMFoVJEfDvrHiy_N6OhaOdi6e7FkPgQl1m25ADLCUgS7GNL5XSNUwwfJZUtAB62xAaK9NonLNKXQDgM9XX0skyetRdOFvS62_rY6rjIybIMiOitVFQ9YWoQDi6uNFNLavXPqW1211HlfdIyHwLDSlWMwmV_UOuk8Ay1-tgRlkTFhw4f7RXiOpfk2OAJtzz6UMcE8kWBuQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EpHraHnvwU2EaiAnYcTsAnTANKRtxIFN6kIDT59lkgDv5W... https://secure-web.cisco.com/1CA9K3JfPpK3GXgggqc2FeT4lpDWCHVYCjSa8cCcz-uZ_9rW7p7AdWJ0BSvJhFIur8AChWCWqN1SVTNg4_w8L3pD_ZmA42vsefxx7zg_9PXiaT63vaGVbklL3glbKL5zsgcbAUkhpSXmlWuMFoVJEfDvrHiy_N6OhaOdi6e7FkPgQl1m25ADLCUgS7GNL5XSNUwwfJZUtAB62xAaK9NonLNKXQDgM9XX0skyetRdOFvS62_rY6rjIybIMiOitVFQ9YWoQDi6uNFNLavXPqW1211HlfdIyHwLDSlWMwmV_UOuk8Ay1-tgRlkTFhw4f7RXiOpfk2OAJtzz6UMcE8kWBuQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ODNWJL85zFsUfXj2zKfI7QsKTKNrY3mzJjAreFma9_GNWr... https://secure-web.cisco.com/1vFGUhLCrnBe_bNYtBBOzGQKLFJ8uxAa5gChepvrp9D7eR_mSTg5IL5O4-lPg--0uY6tEMM7q7ViLs4CrfilQZf4tK9hkiVBfe8ECXkNSxYrJKSqt3L6NrKjCUrglUe3OhsX3yQAwOuDvuUlWEgbtpss0OYJVfvoF_wc54M9v7mLlUsFxg83p76osf5SYJQm0yi6NfjjK7sl7c4ppirp4D0-GB7B2Jw7IiFOjV5daKON-OpucYcxyoxMsBpcxmTsp_EifLoQjZR4tVDmY2FGMez_HXHyBBTg93soJ87IlsQUA_QkABMviRvLmK9hJ2b8-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EpHraHnvwU2EaiAnYcTsAnTANKRtxIFN6kIDT59lkgDv5W... https://secure-web.cisco.com/1ftf5nbrfIoTVgDUlkwd_lSe13urxvTnVDeO7pQoUEkNSrdeiZ2IR1jWKc9f2f8s-3EbeRWrS27DZZFiNWYuJx_AORj4u4KAGYab8_QCt6MpCCVaH35WxT3qIs-QR_A3oZg6j_Jw8clEQpfsJOtJHUw8wrP4VRjXmzpOS2eBaMyLIOPQ16u9YQqDhPdeq3nQDnp4WyD-i2FVthk7jAO3mjEhQUDrKLZbVHw5KC9XPRvEGNICSrPhG4RdjkJ2vmunAPPjXP9iqZ8rfzb-LdQwDW8XBvt0snyDPyWehHFrsQIlB5NReVnYrVlQ2-K_uzJpJ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EpHraHnvwU2EaiAnYcTsAnTANKRtxIFN6kIDT59lkgDv5W... https://secure-web.cisco.com/1ftf5nbrfIoTVgDUlkwd_lSe13urxvTnVDeO7pQoUEkNSrdeiZ2IR1jWKc9f2f8s-3EbeRWrS27DZZFiNWYuJx_AORj4u4KAGYab8_QCt6MpCCVaH35WxT3qIs-QR_A3oZg6j_Jw8clEQpfsJOtJHUw8wrP4VRjXmzpOS2eBaMyLIOPQ16u9YQqDhPdeq3nQDnp4WyD-i2FVthk7jAO3mjEhQUDrKLZbVHw5KC9XPRvEGNICSrPhG4RdjkJ2vmunAPPjXP9iqZ8rfzb-LdQwDW8XBvt0snyDPyWehHFrsQIlB5NReVnYrVlQ2-K_uzJpJ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ODNWJL85zFsUfXj2zKfI7QsKTKNrY3mzJjAreFma9_GNWr... 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/1EpHraHnvwU2EaiAnYcTsAnTANKRtxIFN6kIDT59lkgDv5W... < https://secure-web.cisco.com/1EpHraHnvwU2EaiAnYcTsAnTANKRtxIFN6kIDT59lkgDv5W... . 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.
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fischl, Bruce R.,PHD -
Leonardo Cardoso Saraiva