You can also get the cras from mri_info --cras orig.mgz
On 03/04/2015 07:35 PM, Bruce Fischl wrote: > hmmm, not sure why. If this is a problem we can certainly change it, > just let us know > On Thu, 5 Mar 2015, Krieger, Donald N. 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 >> >> >> >> 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.greenb...@ucsf.edu >> >> >> >> >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
