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
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