Glad it helped, Zack. It’s such a pleasure to come across something I understand.
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 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift awesome! thanks a bunch Don. -zack On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N. <krieg...@upmc.edu<mailto: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 [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> [mailto: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<mailto: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<mailto: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<mailto: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<mailto:zigreen...@gmail.com>.greenb...@ucsf.edu<mailto:reenb...@memory.ucsf.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:zigreen...@gmail.com>.greenb...@ucsf.edu<mailto: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.
