Open jyeatman opened 8 years ago
jyeatman
commented
8 years ago See t_alignInplaneToVolume
We think that this could be as simple as 2 matrix multiplications, but there may be an additional, hidden matrix multiplication to put things in RAS format.
JWinawer
commented
8 years ago More generally, we should make use of the headers in the nifti files, rather than relying on the voxel-to-voxel transform stored in the mrSESSION files. Will look into this.
Meantime, can you provide an example of t1 anatomy and an inplane nifti that is aligned? And in these cases, are your EPIs aligned to your inplane as well?
JWinawer
commented
8 years ago Hi Jason,
Can you provide a t1 and an inplane file (and maybe an EPI) whose headers are aligned. I'll test it.
-Jon
On Thu, Jul 21, 2016 at 11:38 AM, Jason D. Yeatman <notifications@github.com
wrote:
See t_alignInplaneToVolume
We think that this could be as simple as 2 matrix multiplications, but there may be an additional, hidden matrix multiplication to put things in RAS format.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/175#issuecomment-234292904, or mute the thread https://github.com/notifications/unsubscribe-auth/ACBX3ockNTnY58eX7PdN5RuZ8glpRukgks5qX5JfgaJpZM4JR5SE .
Jonathan Winawer Assistant Professor of Psychology and Neural Science
New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/
jyeatman
commented
8 years ago Oops, just realized I wasn't getting github notifications for vistasoft. Is this still open and should I provide some data? The data I have been working with is HCP fMRI data and I can upload a subject
Jason D. Yeatman, PhD Assistant Professor, Institute for Learning & Brain Sciences (I-LABS) Department of Speech & Hearing Sciences University of Washington http://brainandeducation.com
On Tue, Aug 16, 2016 at 12:54 PM, Jonathan Winawer <notifications@github.com
wrote:
Hi Jason,
Can you provide a t1 and an inplane file (and maybe an EPI) whose headers are aligned. I'll test it.
-Jon
On Thu, Jul 21, 2016 at 11:38 AM, Jason D. Yeatman < notifications@github.com
wrote:
See t_alignInplaneToVolume
We think that this could be as simple as 2 matrix multiplications, but there may be an additional, hidden matrix multiplication to put things in RAS format.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/vistalab/vistasoft/issues/175#issuecomment-234292904 , or mute the thread https://github.com/notifications/unsubscribe-auth/ ACBX3ockNTnY58eX7PdN5RuZ8glpRukgks5qX5JfgaJpZM4JR5SE .
Jonathan Winawer Assistant Professor of Psychology and Neural Science
New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/175#issuecomment-240218143, or mute the thread https://github.com/notifications/unsubscribe-auth/ABsYyrzTPYmH-OJjqbOea3sJA1bWeGf_ks5qghWMgaJpZM4JR5SE .
JWinawer
commented
8 years ago Sure, you could.
I also received your message offline but just didn't have time to address it yet. Will do so soon and answer on this GitHub issue.
Jon
On Thu, Sep 1, 2016 at 11:35 PM, Jason D. Yeatman notifications@github.com wrote:
Oops, just realized I wasn't getting github notifications for vistasoft. Is this still open and should I provide some data? The data I have been working with is HCP fMRI data and I can upload a subject
Jason D. Yeatman, PhD Assistant Professor, Institute for Learning & Brain Sciences (I-LABS) Department of Speech & Hearing Sciences University of Washington http://brainandeducation.com
On Tue, Aug 16, 2016 at 12:54 PM, Jonathan Winawer < notifications@github.com
wrote:
Hi Jason,
Can you provide a t1 and an inplane file (and maybe an EPI) whose headers are aligned. I'll test it.
-Jon
On Thu, Jul 21, 2016 at 11:38 AM, Jason D. Yeatman < notifications@github.com
wrote:
See t_alignInplaneToVolume
We think that this could be as simple as 2 matrix multiplications, but there may be an additional, hidden matrix multiplication to put things in RAS format.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/vistalab/vistasoft/issues/175# issuecomment-234292904 , or mute the thread https://github.com/notifications/unsubscribe-auth/ ACBX3ockNTnY58eX7PdN5RuZ8glpRukgks5qX5JfgaJpZM4JR5SE .
Jonathan Winawer Assistant Professor of Psychology and Neural Science
New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/vistalab/vistasoft/issues/175#issuecomment-240218143 , or mute the thread https://github.com/notifications/unsubscribe-auth/ABsYyrzTPYmH- OJjqbOea3sJA1bWeGf_ks5qghWMgaJpZM4JR5SE .
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/175#issuecomment-244275050, or mute the thread https://github.com/notifications/unsubscribe-auth/ACBX3oDwGk6cE2x5dy3bhlv0nd8xEHtZks5ql5l6gaJpZM4JR5SE .
Jonathan Winawer Assistant Professor of Psychology and Neural Science
New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/
Many times our functional data has already been aligned to the t1 anatomy. We should use nifti headers for alignment between the functionals and the 3D anatomy