Good morning, Bruce. Sounds good. Thank you very much.
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: Monday, February 09, 2015 8:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] Reduction of image size Hi Sourav that won't work - particularly if you are trying to crop in the a/s dimension. Many brains might squeeze into 160 l/r but probably not all, and certainly not with skull. And there won't be any consistent starting coord as it will depend on where the head is in the FOV. The only way for it to definitely work would be to downsample one dimension to 256/160=1.6mm. If you skull strip you could get away with something higher res. Or use fewer than 70 images. cheers Bruce On Mon, 9 Feb 2015, SOURAV RANJAN KOLE wrote: > 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> 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 > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
