| T O P I C R E V I E W |
| crozier |
Posted - Jun 12 2007 : 09:16:41 AM
Hi,
I would like to create a mask that is a 27 voxel cube around a given coordinate (45, 86, 64) (coordinates in voxels not mm). From the FSL documentation on the web it seems that I would use avwroi to do this.
The syntax is the following:
avwroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
The mask.nii.gz file is a 3-D with a "1" for all voxels in the brain so I thought this should be the input file.
I tried variations of the following without success thus far:
avwroi mask.nii.gz mask1.nii.gz [44, 2] [85, 2] [63, 2] [0, 0]
Anyone know the right syntax for this?
Joe
|
| 4 L A T E S T R E P L I E S (Newest First) |
| crozier |
Posted - Jun 12 2007 : 10:41:07 AM
Thanks, Syam! |
| syam.gadde |
Posted - Jun 12 2007 : 10:32:27 AM
Sorry try:
avwmaths mask -roi 44 2 85 2 63 2 0 1 mask1
(previously it said 0 0 for t, which means a size of 0) |
| crozier |
Posted - Jun 12 2007 : 10:26:45 AM
Hey Syam,
Thanks. I tried avwmaths with the following:
avwmaths mask.nii.gz -roi 39 2 56 2 63 2 0 0 mask2.nii.gz
However, when I check mask2 all of the voxels in the ROI are zero (as is the rest of the brain) even though mask.nii.gz has 1's for the whole brain.
Did I do something wrong here?
Joe
Joe |
| syam.gadde |
Posted - Jun 12 2007 : 10:00:14 AM
I think avwroi will create a 2x2x2 image as the output, which seems like it is not what you want. Perhaps you want to use avwmaths with the -roi option:
avwmaths mask -roi 44 2 85 2 63 2 0 0 mask1 |
