Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz is uchar. However, I found that the places surrounding the brain which have 0 grayscale values in the a.mgz are having grayscale value 108 in the confored_a.mgz. This makes the conformed_a.mgz very whitish compared to the original one.
Is there a way to make the float 0 to a uchar 0?
Thanks.
Yang
specify -ns 1 (for no scaling)
On Wed, 15 Dec 2010, Yang Liu wrote:
Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz is uchar. However, I found that the places surrounding the brain which have 0 grayscale values in the a.mgz are having grayscale value 108 in the confored_a.mgz. This makes the conformed_a.mgz very whitish compared to the original one.
Is there a way to make the float 0 to a uchar 0?
Thanks.
Yang
Hi Bruce,
Thank you.
I did try
mri_convert -i a.mgz conformed_a.mgz --conform -ns 1
the pixels with 0 grayscale in a.mgz are still turned into pixels with 108 grayscale in conformed_a.mgz.
Yang
On Wed, Dec 15, 2010 at 11:11 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
specify -ns 1 (for no scaling)
On Wed, 15 Dec 2010, Yang Liu wrote:
Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz is uchar. However, I found that the places surrounding the brain which have 0 grayscale values in the a.mgz are having grayscale value 108 in the confored_a.mgz. This makes the conformed_a.mgz very whitish compared to the original one.
Is there a way to make the float 0 to a uchar 0?
Thanks.
Yang
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Hi,
I found that some of the voxels in my original a.mgz are negative. I think that caused some strange behaviors in the float to uchar conversion. Are there methods in Freesurfer to modify the voxel values ?
Yang
On Wed, Dec 15, 2010 at 11:11 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
specify -ns 1 (for no scaling)
On Wed, 15 Dec 2010, Yang Liu wrote:
Hello all,
I am converting one .mgz file to another like this:
mri_convert -i a.mgz -o conformed_a.mgz --conform
The data type of a.mgz is float. After the conversion, The conformed_a.mgz is uchar. However, I found that the places surrounding the brain which have 0 grayscale values in the a.mgz are having grayscale value 108 in the confored_a.mgz. This makes the conformed_a.mgz very whitish compared to the original one.
Is there a way to make the float 0 to a uchar 0?
Thanks.
Yang
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Yang Liu