Thanks bruce. It will work out fine if I can just pull out that c_(ras) array in a pipelined way to apply it to the ascii data.
I'm struggling a bit to achieve that though. I think because mris_info outputs the tables of *_(ras) info in a strange way. For example, if I try to cat the output of mris_info to a txt file: 'mris_info lh.pial > lh_info.txt', the text file will contain everything except the *_(ras) info table that you see if you just call the command by itself: volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : (-1.6000, -5.1750, -15.3313) file : ../mri/filled-pretess255.mgz Are there any mris_info experts on the team who might know how to circumvent this? thanks again for your help! -zack On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Zack > > the ascii format I don't think supports the c_ras info, which is why you > see a shift > > cheers > Bruce > > On Wed, 4 Mar 2015, Zachary Greenberg wrote: > > Ok I figured out that this shift corresponds to the c_(RAS) value in the >> header of lh.pial, which you can get with 'mris_info lh.pial' >> Alternatively you can get the first coordinate and subtract it from the >> first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0' >> >> Is there a way I'm not thinking of to output c_(RAS) directly using >> mris_info or a bash command (cat grep)? >> >> Thanks again, >> >> -zack >> >> On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg >> <zacharyigreenb...@gmail.com> wrote: >> Hi all, >> I discovered that converting the mesh data from freesurfer lh.pial >> format to ascii (.asc) causes a shift in the coordinates of the mesh. >> You can see this by overlaying the two surfaces in freeview, and >> looking at the difference between the [0 0 0] surface RAS coordinate >> in lh.pial vs lh.pial.asc. >> >> The shift is not consistent across different subjects. I'm wondering >> if there is a way to fix this, or if there is some regularity in the >> coordinate shift that can be used to correct (that I'm not seeing). >> >> For example the difference coordinates between lh.pial and lh.pial.asc >> in two different subjects are: >> [ 1.6 , 5.18, 15.33] >> [2.02, -15.80, 0.18] >> >> >> Thanks for any help you can offer! >> >> -zack >> >> >> >> >> >> >> >> >> >> > _______________________________________________ > 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. > > -- *Zachary Greenberg* *Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* *Email: *Zachary <zigreen...@gmail.com>*.G*reenb...@ucsf.edu <reenb...@memory.ucsf.edu>
_______________________________________________ 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.
