Error Message

Hello,

When I am using 3dskullstrip, I keep running into the same error. I am not sure what the problem is. Can someone help me figuring what this is and how to prevent this error?

** ERROR: output dataset name ‘skull_strip_out’ conflicts with existing file
** ERROR: dataset NOT written to disk!

Below I am attaching the entire script and the basic command I used for it.

3dskullstrip -input /Users/rahil/Desktop/manifest-1642531598952_COR_T1_SE_CLEAR_20000423034146_1001.nii
+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /Users/rahil/Desktop/manifest-1642531598952_COR_T1_SE_CLEAR_20000423034146_1001.nii,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/Users/rahil/Desktop/manifest-1642531598952_COR_T1_SE_CLEAR_20000423034146_1001.nii is 9.129141 degrees from plumb.
** ERROR: output dataset name ‘skull_strip_out’ conflicts with existing file
** ERROR: dataset NOT written to disk!
The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip’s -orig_vol option
or run the following command:
3dcalc -a /Users/rahil/Desktop/manifest-1642531598952_COR_T1_SE_CLEAR_20000423034146_1001.nii -b ./skull_strip_out+orig -expr 'a
step(b)’
-prefix ./skull_strip_out_orig_vol
to generate a new masked version of the input.

For most AFNI programs you need to provide the name of the output dataset with the “-prefix” option. Add “-prefix myssname.nii.gz” replacing the dataset name with something you prefer. Most AFNI commands will not overwrite existing files, so that’s the source of the error, where 3dSkullstrip will use a default name for the output, and that dataset already exists.