External Email - Use Caution
Dear All,
I am a master student in Turkey. For my thesis; I have to do exactly this;
Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
This is a mail dated 2014, freesurfer maillist, and I find this via internet.
Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file?
And what is your opinion, is it good idea?
(To transform Desikan atlas to mni space for visualization VBM results?)
Thanks in advance
E. Ece Uluğ
It depends on exactly what you mean. Transforming it into MNI space is fine if you keep it on the surface. If you try to sample it to a voxel mesh you will lose effective resolution. I believe we distribute lh.aparc.annot and rh.aparc.annot files for the fsaverage subject (in the label dir). These are annotation overlays on the surface, which is already in MNI space.
cheers Bruce
On Wed, 10 Oct 2018, ece ulug wrote:
External Email - Use Caution
Dear All, I am a master student in Turkey. For my thesis; I have to do exactly this;Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
This is a mail dated 2014, freesurfer maillist, and I find this via internet.
Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file?
And what is your opinion, is it good idea?
(To transform Desikan atlas to mni space for visualization VBM results?)
Thanks in advance
E. Ece Uluğ
External Email - Use Caution
Hi,
May be i cannot tell well,
I would like to use the Desikan atlas, which is a surface-based atlas normally, as a volume template.
Generally Desikan_surface.gii file is accesible. Can I visualize VBM results correctly in for instances SPMglass brain using Desikan Atlas.nii?
Ece
________________________________ Gönderen: ece ulug eceulug77@hotmail.com Gönderildi: 10 Ekim 2018 Çarşamba 12:27 Kime: freesurfer@nmr.mgh.harvard.edu Konu: Desikan Atlas in MNI Space
Dear All,
I am a master student in Turkey. For my thesis; I have to do exactly this;
Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
This is a mail dated 2014, freesurfer maillist, and I find this via internet.
Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file?
And what is your opinion, is it good idea?
(To transform Desikan atlas to mni space for visualization VBM results?)
Thanks in advance
E. Ece Uluğ
I'm not sure what you are trying to do. Do you want to map the vbm results to the surface and visualize the aparc (desikan atlas) or do you want to map the aparc into the vbm volume?
On 10/11/2018 09:59 AM, ece ulug wrote:
External Email - Use Caution
Hi,
May be i cannot tell well,
I would like to use the Desikan atlas, which is a surface-based atlas normally, as a volume template.
Generally Desikan_surface.gii file is accesible. Can I visualize VBM results correctly in for instances SPMglass brain using Desikan Atlas.nii?
Ece
*Gönderen:* ece ulug eceulug77@hotmail.com *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27 *Kime:* freesurfer@nmr.mgh.harvard.edu *Konu:* Desikan Atlas in MNI Space
/Dear All,/ / I am a master student in Turkey. For my thesis; I have to do exactly this;
/ /*Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work? */ /This is a mail dated 2014, freesurfer maillist, and I find this via internet./ /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file? / /And what is your opinion, is it good idea? / /(To transform Desikan atlas to mni space for visualization VBM results?) / /Thanks in advance/ /E. Ece Uluğ/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for your response;
I had already mapped normalized volume to template surface, so now I want to map the desikan atlas into the vbm volume.
________________________________ Gönderen: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 11 Ekim 2018 Perşembe 18:26 Kime: freesurfer@nmr.mgh.harvard.edu Konu: Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space
I'm not sure what you are trying to do. Do you want to map the vbm results to the surface and visualize the aparc (desikan atlas) or do you want to map the aparc into the vbm volume?
On 10/11/2018 09:59 AM, ece ulug wrote:
External Email - Use CautionHi,
May be i cannot tell well,
I would like to use the Desikan atlas, which is a surface-based atlas normally, as a volume template.
Generally Desikan_surface.gii file is accesible. Can I visualize VBM results correctly in for instances SPMglass brain using Desikan Atlas.nii?
Ece
*Gönderen:* ece ulug eceulug77@hotmail.com *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27 *Kime:* freesurfer@nmr.mgh.harvard.edu *Konu:* Desikan Atlas in MNI Space
/Dear All,/ / I am a master student in Turkey. For my thesis; I have to do exactly this;
/ /*Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work? */ /This is a mail dated 2014, freesurfer maillist, and I find this via internet./ /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file? / /And what is your opinion, is it good idea? / /(To transform Desikan atlas to mni space for visualization VBM results?) / /Thanks in advance/ /E. Ece Uluğ/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using Freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Which template surface? fsaverage? Are you using the 2mm MNI template for VBM? If so, then you can use mri_label2vol specifying the desikan annotation as the --annot and using $FREESURFER_HOME/average/mni152.register.dat as the registration file.
On 10/11/2018 11:42 AM, ece ulug wrote:
External Email - Use Caution
Thanks for your response;
I had already mapped normalized volume to template surface, so now I want to map the desikan atlas into the vbm volume.
*Gönderen:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Gönderildi:* 11 Ekim 2018 Perşembe 18:26 *Kime:* freesurfer@nmr.mgh.harvard.edu *Konu:* Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space I'm not sure what you are trying to do. Do you want to map the vbm results to the surface and visualize the aparc (desikan atlas) or do you want to map the aparc into the vbm volume?
On 10/11/2018 09:59 AM, ece ulug wrote:
External Email - Use Caution
Hi,
May be i cannot tell well,
I would like to use the Desikan atlas, which is a surface-based atlas normally, as a volume template.
Generally Desikan_surface.gii file is accesible. Can I visualize VBM results correctly in for instances SPMglass brain using Desikan
Atlas.nii?
Ece
*Gönderen:* ece ulug eceulug77@hotmail.com *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27 *Kime:* freesurfer@nmr.mgh.harvard.edu *Konu:* Desikan Atlas in MNI Space
/Dear All,/ / I am a master student in Turkey. For my thesis; I have to do exactly this;
/ /*Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work? */ /This is a mail dated 2014, freesurfer maillist, and I find this via internet./ /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file? / /And what is your opinion, is it good idea? / /(To transform Desikan atlas to mni space for visualization VBM results?) / /Thanks in advance/ /E. Ece Uluğ/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using 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
External Email - Use Caution
I tried to confirm VBM analysis lots of platform i study in CAT, these days. Thanks for your reply.
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu şunları yazdı (11 Eki 2018 18:47):
Which template surface? fsaverage? Are you using the 2mm MNI template for VBM? If so, then you can use mri_label2vol specifying the desikan annotation as the --annot and using $FREESURFER_HOME/average/mni152.register.dat as the registration file.
On 10/11/2018 11:42 AM, ece ulug wrote:
External Email - Use CautionThanks for your response;
I had already mapped normalized volume to template surface, so now I want to map the desikan atlas into the vbm volume.
*Gönderen:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *Gönderildi:* 11 Ekim 2018 Perşembe 18:26 *Kime:* freesurfer@nmr.mgh.harvard.edu *Konu:* Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space I'm not sure what you are trying to do. Do you want to map the vbm results to the surface and visualize the aparc (desikan atlas) or do you want to map the aparc into the vbm volume?
On 10/11/2018 09:59 AM, ece ulug wrote:
External Email - Use CautionHi,
May be i cannot tell well,
I would like to use the Desikan atlas, which is a surface-based atlas normally, as a volume template.
Generally Desikan_surface.gii file is accesible. Can I visualize VBM results correctly in for instances SPMglass brain using Desikan
Atlas.nii?
Ece
*Gönderen:* ece ulug eceulug77@hotmail.com *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27 *Kime:* freesurfer@nmr.mgh.harvard.edu *Konu:* Desikan Atlas in MNI Space
/Dear All,/ / I am a master student in Turkey. For my thesis; I have to do exactly this;
/ /*Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations.
Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz in fsaverage is in mni305 space. will that work? */ /This is a mail dated 2014, freesurfer maillist, and I find this via internet./ /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these file? / /And what is your opinion, is it good idea? / /(To transform Desikan atlas to mni space for visualization VBM results?) / /Thanks in advance/ /E. Ece Uluğ/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
ece ulug -
Greve, Douglas N.,Ph.D.