Thanks Bruce, I read in another post that these coordinates in ascii file are in native space. So if I load the original volume in another visualization tool (e.g. fslview), these coordinates should be right on the border of white/gray matter. Is that correct? I already checked couple of them but wanted to be sure this is the case. Also, if freeview doesn’t get the header information from ascii files, what header info (probably a default one) it uses to plot them? Is there any way we can give those header information separately to freeview?

Best

-- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University

Alt: razlighi@gmail.commailto:razlighi@gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/

On Nov 2, 2015, at 10:02 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Ray

the ascii format is pretty barebones and doesn't have e.g. ras2vox info that freeview uses to display the surfaces properly. It's for ease of conversion and such.

cheers Bruce

On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:

Hi Guys, Why converting a surface to .asc format changes its spatial orientation? Specifically, I have converted lh.while to lh.white.asc (using: mris_convert lh.white lh.white.asc) and plot both of them using freeview but they are not corresponding. In fact, lh.white corresponds to the volume image (e.g orig.mgz) but the lh.white.asc doesn't. See the attached screenshot. The red curve is the lh.white.asc. Any explanation would be greatly appreciated.

Best

_______________________________________________ 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.

Thanks again -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University

Alt: razlighi@gmail.commailto:razlighi@gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/

On Nov 3, 2015, at 9:59 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Ray

I would assume that they are in "tkras" space, which is still "native" but is not voxel coords.

cheers Bruce

On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote:

Thanks Bruce, I read in another post that these coordinates in ascii file are in native space. So if I load the original volume in another visualization tool (e.g. fslview), these coordinates should be right on the border of white/gray matter. Is that correct? I already checked couple of them but wanted to be sure this is the case. Also, if freeview doesn’t get the header information from ascii files, what header info (probably a default one) it uses to plot them? Is there any way we can give those header information separately to freeview? Best -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi@gmail.commailto:razlighi@gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/ On Nov 2, 2015, at 10:02 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Ray

the ascii format is pretty barebones and doesn't have e.g. ras2vox info that freeview uses to display the surfaces properly. It's for ease of conversion and such.

cheers Bruce

On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:

Hi Guys, Why converting a surface to .asc format changes its spatial orientation? Specifically, I have converted lh.while to lh.white.asc (using: mris_convert lh.white lh.white.asc) and plot both of them using freeview but they are not corresponding. In fact, lh.white corresponds to the volume image (e.g orig.mgz) but the lh.white.asc doesn't. See the attached screenshot. The red curve is the lh.white.asc. Any explanation would be greatly appreciated.

Best

_______________________________________________ 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. _______________________________________________ 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.