Hi Prof. Yeo,
I have problems utilizing yeo 7/17 cortical network parcellation maps as templates in MRIcron (I aim to use your cortical parcellation maps to underlay my findings in order to derive the implications based on iFC networks). To be specific, there is an orientation problem in the current version of parcellation maps in MNI space.
Thank you for your help in advance.
Best, Hsiang-Yuan
Hi Hsiang-Yuan,
That's because the header information is different. You can do the following:
mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz
The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation compatible with mricron. Can you let me know if this works.
Thanks, Thomas
On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin louislin28@gmail.com wrote:
Hi Prof. Yeo,
I have problems utilizing yeo 7/17 cortical network parcellation maps as templates in MRIcron (I aim to use your cortical parcellation maps to underlay my findings in order to derive the implications based on iFC networks). To be specific, there is an orientation problem in the current version of parcellation maps in MNI space.
Thank you for your help in advance.
Best, Hsiang-Yuan
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin... https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin... https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
Hi Thomas,
Thanks for swift instruction. It works well. However, I have further question: could I write the color lut into header? Because I used your suggested Colorlut information to create a new .lut file and put them into MRIcron templates folder with the correctely oriented Yeo2011_7network template. But it failed to present the designated color in MRIcron.
Thank you!
Best, Hsiang-Yuan
On Mon, Jul 4, 2016 at 4:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Hsiang-Yuan,
That's because the header information is different. You can do the following:
mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ
FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz
The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation compatible with mricron. Can you let me know if this works.
Thanks, Thomas
On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin louislin28@gmail.com wrote:
Hi Prof. Yeo,
I have problems utilizing yeo 7/17 cortical network parcellation maps as templates in MRIcron (I aim to use your cortical parcellation maps to underlay my findings in order to derive the implications based on iFC networks). To be specific, there is an orientation problem in the current version of parcellation maps in MNI space.
Thank you for your help in advance.
Best, Hsiang-Yuan
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV:
https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin...
https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV:
https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin...
Hi Hsiang-Yuan,
I do not know how color file works for MRIcron, so I am unable to help.
Regards, Thomas
On Tue, Jul 5, 2016 at 2:41 AM, Hsiang-Yuan Lin louislin28@gmail.com wrote:
Hi Thomas,
Thanks for swift instruction. It works well. However, I have further question: could I write the color lut into header? Because I used your suggested Colorlut information to create a new .lut file and put them into MRIcron templates folder with the correctely oriented Yeo2011_7network template. But it failed to present the designated color in MRIcron.
Thank you!
Best, Hsiang-Yuan
On Mon, Jul 4, 2016 at 4:37 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Hsiang-Yuan,
That's because the header information is different. You can do the following:
mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz
The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation compatible with mricron. Can you let me know if this works.
Thanks, Thomas
On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin louislin28@gmail.com wrote:
Hi Prof. Yeo,
I have problems utilizing yeo 7/17 cortical network parcellation maps as templates in MRIcron (I aim to use your cortical parcellation maps to underlay my findings in order to derive the implications based on iFC networks). To be specific, there is an orientation problem in the current version of parcellation maps in MNI space.
Thank you for your help in advance.
Best, Hsiang-Yuan
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV:
https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin... https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV:
https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin... https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
-- Hsiang-Yuan Lin, M.D. Attending Psychiatrist & Adjunct Lecturer Department of Psychiatry & Child Mental Health Center National Taiwan University Hospital and College of Medicine email: louislin28@gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharin... https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
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