Chauffeur_afni

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1

Hello,

I’m utilizing the following script to do quality checks for EPI/ANAT alignments.

@chauffeur_afni -ulay ANAT.${subj}_SS_alREST.MNI.ICA.nii \
-olay RESTING.${subj}.ICA.tdrp.MotReg.sf+tlrc \
-prefix $DataOutPath/pic.${subj}.ca.tdrp.MotReg \
-set_xhairs OFF \
-opacity 5 \
-save_ftype PNM \
-do_clean

The error message I keep getting is:

** FATAL ERROR: -percentile can only be used on one sub-brick only.
Use sub-brick selectors ‘[.]’ to specify sub-brick of interest.

Any help appreciated :slight_smile:

2

Hi, L-

In AFNI-speak, we refer to a full, 3D volume of data as a “brick”. Basically, “brick” is the same as a 3D “volume”. Datasets can also have several bricks together in a 4D fashion (often called 3D+time), which would be useful for EPI/FMRI data because a set of 3D volumes are acquired; in this case, we often refer to the i-th volume as a “sub-brick” (starting with 0). Typically, however, we can just display one volume (=brick) at a time.

The message is complaining that your overlay (“-olay …”) dataset has more than one brick, and it doesn’t know which one to pick. You can specify this using brick selectors at the end of the file name-- but note that they must be in single quotes (because of shell syntax).

So, let’s say you wanted to overlay the first brick in your overlaid EPI dtaset-- the [0]th one. Then, this should work:


@chauffeur_afni -ulay ANAT.${subj}_SS_alREST.MNI.ICA.nii \
-olay RESTING.${subj}.ICA.tdrp.MotReg.sf+tlrc'[0]' \
-prefix $DataOutPath/pic.${subj}.ca.tdrp.MotReg \
-set_xhairs OFF \
-opacity 5 \
-save_ftype PNM \
-do_clean

On another note, are you processing your resting state data with afni_proc.py, and if so, are you using the “-volreg_align_to MIN_OUTLIER” option, in order to specify your volume with fewest outliers as a reference? (I would highly recommend using both that program and then that option-- they are good for making your life relatively easier whilst processing FMRI data…) If you did, then you should likely look at the “vr_base_min_outlier*” volume as the olay volume, since that would be the one used a reference for alignment to the anatomical.

–pt