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Dear Freesurfers,
I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are obtained in each individual subject. However, it is not possible because my average subject doesn't contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this issue?
Many thanks in advance.
Best regards, Jose
Hi Jose
can you clarify what you mean by "...to get all the labels that are obtained in each individual subject." You almost certainly don't need to recon fsaverage to do this, but I'm not sure exactly what you mean
cheers Bruce
On Tue, 12 Mar 2019, Laboratorio de Neurociencia Funcional wrote:
External Email - Use Caution
Dear Freesurfers,
I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are obtained in each individual subject. However, it is not possible because my average subject doesn't contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this issue?
Many thanks in advance.
Best regards, Jose
External Email - Use Caution
Hi Bruce,
what I really need is to obtain several labels that are only included in the aparc+aseg, not for each subject but for the entire sample. My goal is to use these labels (ROIs) in VBM analysis after they are trasformed to volume and further registered to MNI. To this aim, I though to obtain first the fsaverage subject from my sample, run the recon-all in that fsaverage, and finally obtain the labels of interest. Is there another way to proceed with this?
Thank you in advance.
Best, Jose
El mar., 12 mar. 2019 a las 14:55, Bruce Fischl (fischl@nmr.mgh.harvard.edu) escribió:
Hi Jose
can you clarify what you mean by "...to get all the labels that are obtained in each individual subject." You almost certainly don't need to recon fsaverage to do this, but I'm not sure exactly what you mean
cheers Bruce
On Tue, 12 Mar 2019, Laboratorio de Neurociencia Funcional wrote:
External Email - Use CautionDear Freesurfers,
I would like to apply recon-all to the fsaverage subject of my sample to
get all the labels that are
obtained in each individual subject. However, it is not possible because
my average subject doesn't
contain the file /orig/001.mgz required to run the recon-all. Could you
help me to handle this
issue?
Many thanks in advance.
Best regards, Jose
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm still not sure what you are trying to do. If you are running vbm, you can usually get the T1 sampled in the MNI space for all subjects. You can average them together and run the average through recon-all
On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote:
External Email - Use Caution
Hi Bruce,
what I really need is to obtain several labels that are only included in the aparc+aseg, not for each subject but for the entire sample. My goal is to use these labels (ROIs) in VBM analysis after they are trasformed to volume and further registered to MNI. To this aim, I though to obtain first the fsaverage subject from my sample, run the recon-all in that fsaverage, and finally obtain the labels of interest. Is there another way to proceed with this?
Thank you in advance.
Best, Jose
El mar., 12 mar. 2019 a las 14:55, Bruce Fischl (<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>) escribió:
Hi Jose can you clarify what you mean by "...to get all the labels that are obtained in each individual subject." You almost certainly don't need to recon fsaverage to do this, but I'm not sure exactly what you mean cheers Bruce On Tue, 12 Mar 2019, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Dear Freesurfers, > > I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are > obtained in each individual subject. However, it is not possible because my average subject doesn't > contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this > issue? > > Many thanks in advance. > > Best regards, > Jose > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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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I just want to use some labels contained in the aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files to build an anatomical template that can be used in VBM analysis. To my understanding, these labels should be obtained from the entire sample since they will be used as the anatomical template for VBM analysis. For that reason, I decided to run the recon-all to my fsaverage subject and take the labels of interest. Is it the right way to proceed?
Thank you in advance.
Best, Jose
El mar., 12 mar. 2019 a las 17:58, Greve, Douglas N.,Ph.D. (< DGREVE@mgh.harvard.edu>) escribió:
I'm still not sure what you are trying to do. If you are running vbm, you can usually get the T1 sampled in the MNI space for all subjects. You can average them together and run the average through recon-all
On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote:
External Email - Use CautionHi Bruce,
what I really need is to obtain several labels that are only included in the aparc+aseg, not for each subject but for the entire sample. My goal is to use these labels (ROIs) in VBM analysis after they are trasformed to volume and further registered to MNI. To this aim, I though to obtain first the fsaverage subject from my sample, run the recon-all in that fsaverage, and finally obtain the labels of interest. Is there another way to proceed with this?
Thank you in advance.
Best, Jose
El mar., 12 mar. 2019 a las 14:55, Bruce Fischl (<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>) escribió:
Hi Jose can you clarify what you mean by "...to get all the labels that are obtained in each individual subject." You almost certainly don't need to recon fsaverage to do this, but I'm not sure exactly what you mean cheers Bruce On Tue, 12 Mar 2019, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Dear Freesurfers, > > I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are > obtained in each individual subject. However, it is not possible because my average subject doesn't > contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this > issue? > > Many thanks in advance. > > Best regards, > Jose > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Dear Doug,
please let me know if it is possible to run the recon-all to the fsaverage subject of my sample to obtain specific labels (from the aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files) derived from my analysis sample.
Many thanks in advance.
Best, Jose
El mar., 12 mar. 2019 a las 18:17, Laboratorio de Neurociencia Funcional (< neuroaginglnf@gmail.com>) escribió:
I just want to use some labels contained in the aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files to build an anatomical template that can be used in VBM analysis. To my understanding, these labels should be obtained from the entire sample since they will be used as the anatomical template for VBM analysis. For that reason, I decided to run the recon-all to my fsaverage subject and take the labels of interest. Is it the right way to proceed?
Thank you in advance.
Best, Jose
El mar., 12 mar. 2019 a las 17:58, Greve, Douglas N.,Ph.D. (< DGREVE@mgh.harvard.edu>) escribió:
I'm still not sure what you are trying to do. If you are running vbm, you can usually get the T1 sampled in the MNI space for all subjects. You can average them together and run the average through recon-all
On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote:
External Email - Use CautionHi Bruce,
what I really need is to obtain several labels that are only included in the aparc+aseg, not for each subject but for the entire sample. My goal is to use these labels (ROIs) in VBM analysis after they are trasformed to volume and further registered to MNI. To this aim, I though to obtain first the fsaverage subject from my sample, run the recon-all in that fsaverage, and finally obtain the labels of interest. Is there another way to proceed with this?
Thank you in advance.
Best, Jose
El mar., 12 mar. 2019 a las 14:55, Bruce Fischl (<fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>) escribió:
Hi Jose can you clarify what you mean by "...to get all the labels that are obtained in each individual subject." You almost certainly don't need to recon fsaverage to do this, but I'm not sure exactly what you mean cheers Bruce On Tue, 12 Mar 2019, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Dear Freesurfers, > > I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are > obtained in each individual subject. However, it is not possible because my average subject doesn't > contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this > issue? > > Many thanks in advance. > > Best regards, > Jose > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
As I said before, I would average the T1weighed images that vbm puts in mni152 space, then run recon-all on that
On 3/14/19 6:06 AM, Laboratorio de Neurociencia Funcional wrote:
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Dear Doug,
please let me know if it is possible to run the recon-all to the fsaverage subject of my sample to obtain specific labels (from the aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files) derived from my analysis sample.
Many thanks in advance.
Best, Jose
El mar., 12 mar. 2019 a las 18:17, Laboratorio de Neurociencia Funcional (<neuroaginglnf@gmail.com mailto:neuroaginglnf@gmail.com>) escribió:
I just want to use some labels contained in the aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files to build an anatomical template that can be used in VBM analysis. To my understanding, these labels should be obtained from the entire sample since they will be used as the anatomical template for VBM analysis. For that reason, I decided to run the recon-all to my fsaverage subject and take the labels of interest. Is it the right way to proceed? Thank you in advance. Best, Jose El mar., 12 mar. 2019 a las 17:58, Greve, Douglas N.,Ph.D. (<DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>) escribió: I'm still not sure what you are trying to do. If you are running vbm, you can usually get the T1 sampled in the MNI space for all subjects. You can average them together and run the average through recon-all On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Hi Bruce, > > what I really need is to obtain several labels that are only included > in the aparc+aseg, not for each subject but for the entire sample. My > goal is to use these labels (ROIs) in VBM analysis after they are > trasformed to volume and further registered to MNI. To this aim, I > though to obtain first the fsaverage subject from my sample, run the > recon-all in that fsaverage, and finally obtain the labels of > interest. Is there another way to proceed with this? > > Thank you in advance. > > Best, > Jose > > El mar., 12 mar. 2019 a las 14:55, Bruce Fischl > (<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>) > escribió: > > Hi Jose > > can you clarify what you mean by "...to get all the labels that are > obtained in each individual subject." You almost certainly don't > need to > recon fsaverage to do this, but I'm not sure exactly what you mean > > cheers > Bruce > > > On Tue, 12 > Mar 2019, Laboratorio de Neurociencia Funcional wrote: > > > > > External Email - Use Caution > > > > Dear Freesurfers, > > > > I would like to apply recon-all to the fsaverage subject of my > sample to get all the labels that are > > obtained in each individual subject. However, it is not possible > because my average subject doesn't > > contain the file /orig/001.mgz required to run the recon-all. > Could you help me to handle this > > issue? > > > > Many thanks in advance. > > > > Best regards, > > Jose > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Laboratorio de Neurociencia Funcional