Dear all,
I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10,-15,-5. Does a command line exists for that ? It is possible without drawing the label ?
Thanks in advance for your help,
Best regards.
And I wish you a Happy New Year 2017 !
Lisa
Dear all,
I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10,-15,-5. Does a command line exists for that ? It is possible without drawing the label ?
Thanks in advance for your help,
Best regards.
And I wish you a Happy New Year 2017 !
Lisa
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Lisa Delalande delalande.lisa@outlook.fr Envoyé : lundi 9 janvier 2017 15:46 À : freesurfer@nmr.mgh.harvard.edu Objet : [Freesurfer] ROI with precise coordinates
Dear all,
I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10,-15,-5. Does a command line exists for that ? It is possible without drawing the label ?
Thanks in advance for your help,
Best regards.
And I wish you a Happy New Year 2017 !
Lisa
Hi,
Yes you can use fslmaths and Ants ImageMath to make an ROI from the given mni coordinates. The command is like fslmaths MNI_T1...gz -mul 0 -add 1 roi xmin xsize ymin ysize zmin zsize tmin tsize ROI_name. For a box of 10mm , you can use fslmaths kernel boxv... or for a sphere you can use ImageMath MD input sphere-radius
Best regards,
-- Shahid.
On Mon, Jan 9, 2017 at 3:46 PM, Lisa Delalande delalande.lisa@outlook.fr wrote:
Dear all,
I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10, -15,- 5. Does a command line exists for that ? It is possible without drawing the label ?
Thanks in advance for your help,
Best regards.
And I wish you a Happy New Year 2017 !
Lisa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
Thank you so much for your answer !
I'm a debutant with FreeSurfer, can you please add some details please ? Or give me a website or something like that a can look at ?
Thank you so much for your help,
Lisa
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Dr. M. Shahid mohammad.shahid@gmail.com Envoyé : mardi 17 janvier 2017 14:44 À : Freesurfer support list Objet : Re: [Freesurfer] ROI with precise coordinates
Hi,
Yes you can use fslmaths and Ants ImageMath to make an ROI from the given mni coordinates. The command is like fslmaths MNI_T1...gz -mul 0 -add 1 roi xmin xsize ymin ysize zmin zsize tmin tsize ROI_name. For a box of 10mm , you can use fslmaths kernel boxv... or for a sphere you can use ImageMath MD input sphere-radius
Best regards,
-- Shahid.
On Mon, Jan 9, 2017 at 3:46 PM, Lisa Delalande <delalande.lisa@outlook.frmailto:delalande.lisa@outlook.fr> wrote:
Dear all,
I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10, -15,- 5. Does a command line exists for that ? It is possible without drawing the label ?
Thanks in advance for your help,
Best regards.
And I wish you a Happy New Year 2017 !
Lisa
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
if you have FSL installed, you can use this script https://montilab.psych.ucla.edu/fmri-wiki/make-spherical-rois-script/
Best regards,
-- Shahid.
On Fri, Jan 20, 2017 at 10:41 AM, Lisa Delalande delalande.lisa@outlook.fr wrote:
Hi,
Thank you so much for your answer !
I'm a debutant with FreeSurfer, can you please add some details please ? Or give me a website or something like that a can look at ?
Thank you so much for your help,
Lisa
*De :* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh. harvard.edu> de la part de Dr. M. Shahid mohammad.shahid@gmail.com *Envoyé :* mardi 17 janvier 2017 14:44 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] ROI with precise coordinates
Hi,
Yes you can use fslmaths and Ants ImageMath to make an ROI from the given mni coordinates. The command is like fslmaths MNI_T1...gz -mul 0 -add 1 roi xmin xsize ymin ysize zmin zsize tmin tsize ROI_name. For a box of 10mm , you can use fslmaths kernel boxv... or for a sphere you can use ImageMath MD input sphere-radius
Best regards,
-- Shahid.
On Mon, Jan 9, 2017 at 3:46 PM, Lisa Delalande delalande.lisa@outlook.fr wrote:
Dear all,
I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10, -15,- 5. Does a command line exists for that ? It is possible without drawing the label ?
Thanks in advance for your help,
Best regards.
And I wish you a Happy New Year 2017 !
Lisa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Dr. M. Shahid -
Lisa Delalande