Hi, Bit-warrior-

OK, I see what is happening. So, this program is meant for taking a set of DWI volumes and corresponding gradient file(s) and outputting a new set of those where bad volumes (and corresponding bad gradients) have been removed from each of those types of files. One specifies which are the "good" volumes+grads to keep by using the "-select ..." option, using the AFNI index selection notation to specify *good* indices. For example, from the help of the program:

fat_proc_filter_dwis  \
        -in_dwi       UNFILT_AP/AP.nii.gz       \
        -in_col_matT  UNFILT_AP/AP_bmatT.dat    \
        -select       '0..5,8,20..$'           \
        -prefix       FILT_AP/AP

... this example would produce a new set of filtered data, having removed volumes with index [6] and [9-19] from both the DWI nifti file and the bmatrix file.

In your first example, you are not including any indices to keep using "-select ...", and so the program is unhappy (in truth, this is probably a minor bug, that if the user doesn't specify any volumes the program could keep all of them). If you really want to keep all volumes, you could specify this in the following edited version of your command above:

fat_proc_filter_dwis -in_dwi /home/ahoxha/Desktop/dti_fatproc/dwi_nii.nii.gz -in_col_matT /home/ahoxha/Desktop/dti_fatproc/dwi_nii_matT.dat -prefix /home/ahoxha/Desktop/dti_fatproc/filt -select '0..$'

In general, if you aren't filtering out any volumes, you probably don't *need* to use this program, because the input and outputs will just be the same; however, I could guess that you might be using this in a general pipeline, and it is just the case that some subjects having nothing to filter. Therefore, using the above should sort things out.

Please let me know how that works for you.

And you may be aware of this already, but the string that comes after '-select ...' can be built using the fat_proc_select_vols program, which uses some nice AFNI driving functionality (courtesy of J. Rajendra) to have the user click on a montage view of the DWIs to point out bad volumes, building a selection string. But one can also specify the selection string based on other approaches, as well.

--pt [borrowing g. chen's login]

Gang