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Hello all Freesurfer experts!
Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females.
When plotting the summed verticies of ?h.area for each person on the other hand (albeit after mapping the ?h.area to fsaverage), this main association with sex is not at all present. I am a bit puzzled by this and I am wondering if some sort of global scaling is performed when computing vertex-wise surface area? So that corresponding differences in vertex-wise area are relative sex differences?
I understand that area at a single vertex does not hold biological relevance in the same way that for instance thickness does, but unfortunately I still don't quite understand the differing sex associations between aparcs total surface area and the summed vertex-wise surface area.
Thanks so much in advance! Kind regards Linn
How did you map the area to fsaverage? If you don't do it properly, you can get some funny results because area has to be jacobian corrected.
On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote:
External Email - Use Caution
Hello all Freesurfer experts!
Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females.
When plotting the summed verticies of ?h.area for each person on the other hand (albeit after mapping the ?h.area to fsaverage), this main association with sex is not at all present. I am a bit puzzled by this and I am wondering if some sort of global scaling is performed when computing vertex-wise surface area? So that corresponding differences in vertex-wise area are relative sex differences?
I understand that area at a single vertex does not hold biological relevance in the same way that for instance thickness does, but unfortunately I still don't quite understand the differing sex associations between aparcs total surface area and the summed vertex-wise surface area.
Thanks so much in advance! Kind regards Linn
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks so much for the reply.
I am performing linked-ICA on cortical thickness, grey-/white matter contrast (GWC), and cortical surface area, and I must admit I sampled the surfaces onto fsaverage in an identical way across modalities using surf2surf. I have attached the code for fsaverage re-sampling of area.
While I found a global signal for GWC and thickness in my analyses, I found no global signal for surface area (and also no main effect of sex which was unexpected).
So if I understand correctly: -my results are probably off as I have not performed the Jacobian correction that retains the information of global surface area when mapping onto fsaverage using surf2surf? -Is there a "Jacobian flag" that can be added to the surf2surf code? If else it appeared that the correction is default if running mri_preproc on area,? is that correct?
Thanks so much for helping me out with this, I really appreciate it! Linn
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 07 October 2019 16:50 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area
How did you map the area to fsaverage? If you don't do it properly, you can get some funny results because area has to be jacobian corrected.
On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote:
External Email - Use Caution
Hello all Freesurfer experts!
Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females.
When plotting the summed verticies of ?h.area for each person on the other hand (albeit after mapping the ?h.area to fsaverage), this main association with sex is not at all present. I am a bit puzzled by this and I am wondering if some sort of global scaling is performed when computing vertex-wise surface area? So that corresponding differences in vertex-wise area are relative sex differences?
I understand that area at a single vertex does not hold biological relevance in the same way that for instance thickness does, but unfortunately I still don't quite understand the differing sex associations between aparcs total surface area and the summed vertex-wise surface area.
Thanks so much in advance! Kind regards Linn
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can add --jac to to the mri_surf2surf command to get jacobian correction. If you use mris_preproc with --meas area (or volume), it will automatically do it
On 10/8/19 3:07 PM, Linn Christin Bonaventure Norbom wrote:
External Email - Use Caution
Thanks so much for the reply.
I am performing linked-ICA on cortical thickness, grey-/white matter contrast (GWC), and cortical surface area, and I must admit I sampled the surfaces onto fsaverage in an identical way across modalities using surf2surf. I have attached the code for fsaverage re-sampling of area.
While I found a global signal for GWC and thickness in my analyses, I found no global signal for surface area (and also no main effect of sex which was unexpected).
So if I understand correctly: -my results are probably off as I have not performed the Jacobian correction that retains the information of global surface area when mapping onto fsaverage using surf2surf? -Is there a "Jacobian flag" that can be added to the surf2surf code? If else it appeared that the correction is default if running mri_preproc on area, is that correct?
Thanks so much for helping me out with this, I really appreciate it! Linn
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* 07 October 2019 16:50 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area How did you map the area to fsaverage? If you don't do it properly, you can get some funny results because area has to be jacobian corrected.
On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote:
External Email - Use Caution
Hello all Freesurfer experts!
Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females.
When plotting the summed verticies of ?h.area for each person on the other hand (albeit after mapping the ?h.area to fsaverage), this main association with sex is not at all present. I am a bit puzzled by this and I am wondering if some sort of global scaling is performed when computing vertex-wise surface area? So that corresponding differences in vertex-wise area are relative sex differences?
I understand that area at a single vertex does not hold biological relevance in the same way that for instance thickness does, but unfortunately I still don't quite understand the differing sex associations between aparcs total surface area and the summed vertex-wise surface area.
Thanks so much in advance! Kind regards Linn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Perfect! Thanks so much. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: 08 October 2019 21:30 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area
You can add --jac to to the mri_surf2surf command to get jacobian correction. If you use mris_preproc with --meas area (or volume), it will automatically do it
On 10/8/19 3:07 PM, Linn Christin Bonaventure Norbom wrote:
External Email - Use CautionThanks so much for the reply.
I am performing linked-ICA on cortical thickness, grey-/white matter contrast (GWC), and cortical surface area, and I must admit I sampled the surfaces onto fsaverage in an identical way across modalities using surf2surf. I have attached the code for fsaverage re-sampling of area.
While I found a global signal for GWC and thickness in my analyses, I found no global signal for surface area (and also no main effect of sex which was unexpected).
So if I understand correctly: -my results are probably off as I have not performed the Jacobian correction that retains the information of global surface area when mapping onto fsaverage using surf2surf? -Is there a "Jacobian flag" that can be added to the surf2surf code? If else it appeared that the correction is default if running mri_preproc on area, is that correct?
Thanks so much for helping me out with this, I really appreciate it! Linn
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* 07 October 2019 16:50 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area How did you map the area to fsaverage? If you don't do it properly, you can get some funny results because area has to be jacobian corrected.
On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote:
External Email - Use CautionHello all Freesurfer experts!
Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females.
When plotting the summed verticies of ?h.area for each person on the other hand (albeit after mapping the ?h.area to fsaverage), this main association with sex is not at all present. I am a bit puzzled by this and I am wondering if some sort of global scaling is performed when computing vertex-wise surface area? So that corresponding differences in vertex-wise area are relative sex differences?
I understand that area at a single vertex does not hold biological relevance in the same way that for instance thickness does, but unfortunately I still don't quite understand the differing sex associations between aparcs total surface area and the summed vertex-wise surface area.
Thanks so much in advance! Kind regards Linn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Linn Christin Bonaventure Norbom