Hi Antonella,
If you are applying the morph to a mask file, then yes, the nearest neighbor interpolation shoudl be used.
The masking option that you ask about below depends on whether you want to use wmparc to guide your masking (option 1) or whether you want to do the masking based upon intensity values found in the fa image (option 2).
--Lilla
On Tue, 17 Jan 2012, Antonella Kis wrote:
Dear Lilla,
Many thanks for your reply and for your help.
Regarding the way I resampled my fa data to the CVS space I was reading on the FSTutorial/Diffusion that if you wanted to resample a segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option.The fa mask was calculated using the wmparc2diff as you can see below so I thought because I am using the wmparc which is a segmentation volume I should use for resampling the nearst interp. Please let me know if I am wrong.
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz Is this the right way to calculate my fa-masked or I should use all my fa data only:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz Thank you very much! Antonella
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 16, 2012 5:39 PM Subject: Re: [Freesurfer] Converting mgz to nii.gz
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
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