Dear all,
I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation.
I used for converting this .mgz image to .nii.gz the mri_convert as you can see below:
mri_convert --in_type mgz --out_type nii --out_orientation RAS /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz \ /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz
I understood that --out orientation RAS states that I am flipping the image. Do I need to use this option? Even if I am using or not I see my image is having different direction than the .mgz image. Also while running with the option --out orientation RAS I saw that the program is doing a triliniar interp and I don't want to resample anymore my iamge just to converte this from mgz to nii.
What is the best way I should do it?
Thank you. Antonella
Hi Antonella,
You should be able to just do
mri_convert /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz
BTW, when resampling your FA data to CVS space, I think you should be using trilinear interpolation. We only suggest the nearest neigbour option for segmentation and parcellation files.
--Lilla
On Mon, 16 Jan 2012, Antonella Kis wrote:
Dear all,
I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation.
I used for converting this .mgz image to .nii.gz the mri_convert as you can see below:
mri_convert --in_type mgz --out_type nii --out_orientation RAS /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz \ /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz
I understood that --out orientation RAS states that I am flipping the image. Do I need to use this option? Even if I am using or not I see my image is having different direction than the .mgz image. Also while running with the option --out orientation RAS I saw that the program is doing a triliniar interp and I don't want to resample anymore my iamge just to converte this from mgz to nii.
What is the best way I should do it?
Thank you. Antonella
Dear all,
I wonder why when I am using the mri_convert to convert my mgz image which is very little tilted to the left into a nii.gz image which appears very little tilted to the right instead to keep the same direction to the left.
I was using:
mri_convert /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz
and while this was done ion the command window it shows:
mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz...
Thank you. Antonella
Are you using the same viewer?
On Tue, Jan 17, 2012 at 11:34 AM, Antonella Kis atorok9@yahoo.com wrote:
Dear all,
I wonder why when I am using the mri_convert to convert my mgz image which is very little tilted to the left into a nii.gz image which appears very little tilted to the right instead to keep the same direction to the left.
I was using:
mri_convert /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz
and while this was done ion the command window it shows:
mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz...
Thank you. Antonella
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Antonella Kis -
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Lilla Zollei