I'm currently running niak fmri preprocessing using niak-boss-0.12.15 to analyze a set of public RS fMRI data from NYU (http://www.nitrc.org/projects/nyu_trt/). They provide three T1-images and three EPI images for each subject, obtained from three different sessions respectively. I converted the NIFTI files to MINC files by using nii2mnc.

When I run the script for 25 subjects from this dataset,
from some of the subjects I found that there's a resampling error, while it is not for other subjects. so I take a look at one of the subjects.
When I check the intermediate files generated in the folder /intermediate/,
the slice-timing corrected functional image was normal,
motion_target_subject2_session1_run1.mnc was normal, (the target for coregistration)
however,

fmri_subject2_session1_run1_a_res.mnc was failed in /intermediate/resample/ (file attached),
fmri_subject2_session1_run1_cor.mnc was failed in /intermediate/regress_confounds/, 

indicating that resampling in stereotaxic space was failed.

When I take a look at the folder /anat/subject2/, the images in the following files are not normal, just like as shown in the resampling failure.

anat_subject2_nativefunc_hires. mnc
anat_subject2_nativefunc_lowres.mnc
func_subject2_mask_stereonl.mnc
func_subject2_mean_stereonl.mnc
func_subject2_std_stereonl.mnc

Also looking at the quality control directory, for example I can see that the relative overlap of individual brain functional masks with the group mask in those subjects are extremely low (ex 0.22, 0.04, etc), shown from the file func_tab_qc_coregister_stereonl.csv.

what can I check now to solve this problem?

Thank you,
Kangjoo