Hello Bruce, Definitely, I am constructing atlases with these images. Based on the number of available and functioning GPUs in our cluster, I am seemingly able to construct atlases of ~70 images with each image size being 256x256x160 and not of image size 256x256x256. Therefore, I am reslicing and I have not done this before. Please guide me to determine the starting coordinates for extraction. 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 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size 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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu<mailto: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<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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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