Hi Sourav Can you explain why you are reslicing? Cheers Bruce
> On Feb 8, 2015, at 7:26 PM, SOURAV RANJAN KOLE <sourav.k...@utah.edu> wrote: > > Thank you, again, Bruce. > > How do I determine the starting coordinates for extraction, so I do not > cutoff relevant info? > > Regards, > > Sourav > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Sunday, February 08, 2015 5:04 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Reduction of image size > > Hi Sourav > > mri_extract > usage: mri_extract <src_dir> x0 y0 z0 dx dy dz <dst_dir> > > (x0, y0, z0) is the starting coordinate of the rectangle to extract *not* > the size. (dx, dy, dz) is the size. Yours should be something like: > > mri_extract input.mgz 0 0 0 256 256 160 output.mgz > > > or maybe you don't want to start at 0, but further into the volume. > > Also, definitely do NOT use .img at any point as you will lose direction > cosine info > > cheers > Bruce > > On Sun, > 8 Feb 2015, SOURAV RANJAN KOLE wrote: > >> Hello Bruce, >> >> Thank you for the prompt reply. >> >> Although, mri_extract is creating new files but it is giving me the >> following error- MRIextractInto: bad src location (256, 256, 160). Also, >> ITK-SNAP cannot read the new image file. >> >> Here is what I am doing: >> 1. Converting from .mgz to .img >> mri_convert brainmask.mgz brainmask.img --conform --out_data_type float >> 2. Reducing size of image >> mri_extract brainmask.img 256 256 160 1 1 1 new_brainmask.img >> >> I would like the new images to be 256x256x160 and voxel size to be 1x1x1. Am >> I not using mri_extract correctly? >> >> Thank you. >> >> Regards, >> >> Sourav >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Sunday, February 08, 2015 4:12 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Reduction of image size >> >> mri_extract should do the trick >> Bruce >> On Sun, 8 Feb 2015, SOURAV RANJAN KOLE >> wrote: >> >>> Dear Freesurfer community, >>> Please let me know of an elegant way to reduce image size from 256x256x256 >>> to 256x256x160 and keeping the voxel size the same. The images are currently >>> in analyze format but I have access to mri_convert and ImageConvert. >>> >>> Thank you. >>> >>> Sourav >> _______________________________________________ >> 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. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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