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Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu)https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs).
Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice?
Thankyou, Marianna Pope
did you draw the labels on each subject separately? In that case there is no need to go through fsaverage. Projfrac is the fractional distance between the white and pial surfaces (0.5 is half way) projdist is the absolute distance (eg, 1.5 is 1.5mm) Generally projfrac is preferred as it adapts to changes in thickness In your case, you might want to use --projfrac-max where it will look over a range of projfrac values for the maximum. This might make your maps look better because it will be sampling the label or nothing.
On 5/10/2021 12:25 PM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu) https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs).
Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice?
Thankyou,
Marianna Pope
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EtPv_nAVWK64cSK36g2w70t5Ms8Ox2zKrCf40ENIjKJs5y...
External Email - Use Caution
The labels are derived from ASHS- but yes they are registered to each subject seperately. Could I ask then what the tutorial refers to- for future reference? When is it best to go through fsaverage?
Thank you for the information
BW, Marianna
________________________________ Από: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu εκ μέρους του Douglas N. Greve dgreve@mgh.harvard.edu Στάλθηκε: Δευτέρα, 10 Μαΐου 2021 4:30 μμ Προς: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Θέμα: Re: [Freesurfer] volume ROI to surface for cortical thickness
did you draw the labels on each subject separately? In that case there is no need to go through fsaverage. Projfrac is the fractional distance between the white and pial surfaces (0.5 is half way) projdist is the absolute distance (eg, 1.5 is 1.5mm) Generally projfrac is preferred as it adapts to changes in thickness In your case, you might want to use --projfrac-max where it will look over a range of projfrac values for the maximum. This might make your maps look better because it will be sampling the label or nothing.
On 5/10/2021 12:25 PM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu)https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs).
Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice?
Thankyou,
Marianna Pope
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EtPv_nAVWK64cSK36g2w70t5Ms8Ox2zKrCf40ENIjKJs5y...
For when your ROI is in fsaverage (or MNI152) space.
On 5/10/2021 12:34 PM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
The labels are derived from ASHS- but yes they are registered to each subject seperately. Could I ask then what the tutorial refers to- for future reference? When is it best to go through fsaverage?
Thank you for the information
BW, Marianna
*Από:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu εκ μέρους του Douglas N. Greve dgreve@mgh.harvard.edu *Στάλθηκε:* Δευτέρα, 10 Μαΐου 2021 4:30 μμ *Προς:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Θέμα:* Re: [Freesurfer] volume ROI to surface for cortical thickness did you draw the labels on each subject separately? In that case there is no need to go through fsaverage. Projfrac is the fractional distance between the white and pial surfaces (0.5 is half way) projdist is the absolute distance (eg, 1.5 is 1.5mm) Generally projfrac is preferred as it adapts to changes in thickness In your case, you might want to use --projfrac-max where it will look over a range of projfrac values for the maximum. This might make your maps look better because it will be sampling the label or nothing.
On 5/10/2021 12:25 PM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu) https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs).
Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice?
Thankyou,
Marianna Pope
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EtPv_nAVWK64cSK36g2w70t5Ms8Ox2zKrCf40ENIjKJs5y... https://secure-web.cisco.com/1EtPv_nAVWK64cSK36g2w70t5Ms8Ox2zKrCf40ENIjKJs5yJk5oM7eVbJvbJmmybMMtlX_emdEpmjx7PsJoMKm5AR2_sbLzIkea-Dj9X8yNFkLZDRIvWTS3QUEp2yOM_jqGN5zdEdx-L02P48pgjPNyKgW0TxUujlxsbdByAmqmiXGM-KhnFsgXDh_USmsLfOChDS2_RQ_GeI5TWoFKEyxxUuqORfr5C1It17h_BeIrNACBgTyyAfF1fLfZCee_eQrmfL5C5B47JWuDxLtbFqOw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aHyhdnrg4B1uTG2ggjx-fgISHxeu7Fahod6C42dby6phIU...
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Hi Douglas,
I have a follow-up question regarding vol2surf. What is the best practice for quality control and checking the surface rendering of the ROI? Are there any protocols or suggestions? As slight changes in projfrac change the output by a large degree, it's difficult to assess what is the closest to the orginal volume ROI.
Thanks Marianna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: 10 May 2021 4:36 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Απ: volume ROI to surface for cortical thickness
For when your ROI is in fsaverage (or MNI152) space.
On 5/10/2021 12:34 PM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
The labels are derived from ASHS- but yes they are registered to each subject seperately. Could I ask then what the tutorial refers to- for future reference? When is it best to go through fsaverage?
Thank you for the information
BW, Marianna
________________________________ Από: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu εκ μέρους του Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Στάλθηκε: Δευτέρα, 10 Μαΐου 2021 4:30 μμ Προς: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Θέμα: Re: [Freesurfer] volume ROI to surface for cortical thickness
did you draw the labels on each subject separately? In that case there is no need to go through fsaverage. Projfrac is the fractional distance between the white and pial surfaces (0.5 is half way) projdist is the absolute distance (eg, 1.5 is 1.5mm) Generally projfrac is preferred as it adapts to changes in thickness In your case, you might want to use --projfrac-max where it will look over a range of projfrac values for the maximum. This might make your maps look better because it will be sampling the label or nothing.
On 5/10/2021 12:25 PM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu)https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs).
Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice?
Thankyou,
Marianna Pope
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EtPv_nAVWK64cSK36g2w70t5Ms8Ox2zKrCf40ENIjKJs5y...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aHyhdnrg4B1uTG2ggjx-fgISHxeu7Fahod6C42dby6phIU...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
M Pope