Hi Bruce,
I used following command:
recon-all -subject 8 -i /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8.nii.gz -sd /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8 -all -cw256
I had to use -cw256 option due to the fact that in third dimension my volume has more than 256 slices (256x256x268), so without that option I was getting error.
I got aseg.mgz orig.mgz and norm.mgz files in mri folder.
I checked the segmentation using following command:
tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
(please find the attached screenshot named tkmedit.png)
Now, I wanted to convert this into nifti format so I ran following command:
mri_convert --in_type mgz --out_type nii *.mgz *.niiI
where, * = {aseg,orig,norm}
it converted mgz volumes into nii volumes.
Now I opened the volume and segmentation in ITKSNAP. But I am getting totally different output in ITKSNAP. (see attached ITKSNAP.png) also there are some lables numbered 255, 253 etc when I open segmentation in ITKSNAP, which doesn't make any sense. Also it looks like due to the use of -cw256 option in recon-all command my images are cropped to 256x256x256.
Now, there are two questions:
1) How can I convert this 256x256x256 into original image size 256x256x268
2) Am I using proper syntax for mri_convert ?? as I am getting totally different output in both of them. ( screenshots are for slice 128 in norm.nii)
Thanks for your help.
Regards,