Ciftify_fmri_subject on fMRIPrep's MNI152NLin2009cAsym_desc-smoothAROMAnonaggr output


I’m trying to run ciftify_fmri_subject on fMRIPrep’s AROMA output (MNI152NLin2009cAsym_desc-smoothAROMAnonaggr output_bold).

We know that we need first to transform from LAS to RAS so I first applied
wb_command -volume-reorient $FUNC RPI $FUNC_FLIPPED when $FUNC is the MNI152NLin2009cAsym_desc-smoothAROMAnonaggr output_bold.nii.gz created by fMRIPrep.

run ciftify with the following command
ciftify_subject_fmri --already-in-MNI --ciftify-work-dir $CIFTIDIR $FUNC_FLIPPED $SBJ $TASK_DIR
and crashes with
ERROR: label volume has a different volume space than data volume

when checking the header stuff (>> fslhd file | grep xyz) I get (omitting many irrelevant zeros):

(base) xxxx:~$ fslhd $FUNC_FLIPPED | grep xyz
qto_xyz:1       -2.0 0.0 -0.0  89.5
qto_xyz:2        0.0 2.0 -0.0 -126.5
qto_xyz:3        0.0 0.0  2.0 -72.5
qto_xyz:4       0.0  0.0  0.0  1.0
<same in sform>


(base) vr@shaharar_labpc:~$ fslhd /mnt/d/Repositories/Places_I_Remember/ciftify/sub-AdKl/MNINonLinear/ROIs/ROIs.2.nii.gz | grep xyz
qto_xyz:1       -2.0  0.0  -0.0  90.0
qto_xyz:2        0.0  2.0  -0.0  -126.0
qto_xyz:3        0.0  0.0   2.0  -72.0
qto_xyz:4       0.0  0.0  0.0  1.0
<same in sform>

Clearly the 4th column is larger by 0.5 in the template than in the bold.
1- is this the reason for the error?
2- what can I do with that?

Thank you

Hi there, yes the main problem is that the AROMA outputs are in space-MNI152NLin2009cAsym whereas ciftify’s --already-in-MNI assumes that the data is in space-MNI152NLin6ASym, as you noticed. The most obvious difference between those two templates is the number of slices.

For a solution - I’ve had some luck with resampling the data from one space to another. But be careful. Make sure to look carefully at the QA pages to make sure that the MNI space EPI data overlaps with the MNI space surfaces in the ciftify outputs.