I have scans that are at .8 and .5 resolution as dicoms. Currently I am using to3d to rotate the images to the proper orientation. After that I have tried using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that mri_convert doesn't resample the image, but this is also messing up the statistics for obvious reasons. Is it reasonable to just multiply the statistics by .512 (.8 ^ 3) and .125 (.5 ^ 3)? or how else can I prevent freesurfer from resampling my images to 1.0 resolution?
-Eric
Why are you going thru those afni cmds? If the original data are in dicom, then they should have the correct geometry info, and mri_convert should orient them correctly. As for the resolution, try running recon-all (or mri_convert) with the -cm option.
doug
Faden, Eric (NIH/NIMH) [F] wrote:
I have scans that are at .8 and .5 resolution as dicoms. Currently I am using to3d to rotate the images to the proper orientation. After that I have tried using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that mri_convert doesn't resample the image, but this is also messing up the statistics for obvious reasons. Is it reasonable to just multiply the statistics by .512 (.8 ^ 3) and .125 (.5 ^ 3)? or how else can I prevent freesurfer from resampling my images to 1.0 resolution?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The monkeys are scanned in different orientation than normal. I also can't use recon-all because it doesn't work correctly with monkeys.
-Eric
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 2/7/2006 12:57 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Importing .8 and .5 scans into freesurfer
Why are you going thru those afni cmds? If the original data are in dicom, then they should have the correct geometry info, and mri_convert should orient them correctly. As for the resolution, try running recon-all (or mri_convert) with the -cm option.
doug
Faden, Eric (NIH/NIMH) [F] wrote:
I have scans that are at .8 and .5 resolution as dicoms. Currently I am using to3d to rotate the images to the proper orientation. After that I have tried using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that mri_convert doesn't resample the image, but this is also messing up the statistics for obvious reasons. Is it reasonable to just multiply the statistics by .512 (.8 ^ 3) and .125 (.5 ^ 3)? or how else can I prevent freesurfer from resampling my images to 1.0 resolution?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Faden, Eric (NIH/NIMH) [F]