awesome! thanks a bunch Don.
-zack On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N. <krieg...@upmc.edu> wrote: > Hi Zack, > > > > It looks like mris_info send that matrix out on the error output rather > than the standard output. > > I just tried it and you can get it by redirecting both to your file like > this: > > Try mris_info lh.pial >& lh_info.txt > > > > Regards, > > > > Don > > > > [image: Signature0001] > > Don Krieger, Ph.D. > > Department of Neurological Surgery > > University of Pittsburgh > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Zachary Greenberg > *Sent:* Wednesday, March 04, 2015 7:05 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc > coordinate shift > > > > 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. > > -- *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>
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