Hi again!

Thank you so much for the feedback!

The version I was using was indeed old. I must say the latest one is quite cool! I really like the QC ouput and the overlaying function in the GUI!
The 'nmi' cost function did wonders, cheers! I also switched to the second echo as a ref echo as it has much more signal (even though the contrast is tiny bit poorer).

I've pre-processed our entire dataset and the few scans I've checked so far are looking really nice!
There are a few things that are puzzling me though (sorry for getting a bit off-topic):

1. I'm curious as to why the QC html file doesn't get generated for some of the sessions (see part of the ouput bellow).
2. Looking at the Degree of Freedom part, it got me wondering... What is an 'acceptable' post-(?!)pre-processing DoF value?
3. Given the substantial signal loss that is plaguing our data, I wanted to ask you what would be a good way of creating a mask that would include only voxels that have signal. Not sure how to approach this as there are some differences in the extent of signal loss in the different participant sessions.

Thank you!!!
Misho

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apqc_make_html.py -qc_dir QC_SUBJ
/nan/ceph/network/system/el7/AFNI/AFNI_21.1.07/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
print('** uncensor from vec: nt = %d, but nocen len = %d' \
Traceback (most recent call last):
File "/software/system/AFNI/AFNI_21.1.07/apqc_make_html.py", line 193, in <module>
AAII = lah.read_descrip_json(img_json)
File "/nan/ceph/network/system/el7/AFNI/AFNI_21.1.07/afnipy/lib_apqc_html.py", line 1746, in read_descrip_json
ainfo.set_all_from_dict(ddd) # set everything in this obj that we can
File "/nan/ceph/network/system/el7/AFNI/AFNI_21.1.07/afnipy/lib_apqc_html.py", line 642, in set_all_from_dict
self.add_subtext(DICT)
File "/nan/ceph/network/system/el7/AFNI/AFNI_21.1.07/afnipy/lib_apqc_html.py", line 625, in add_subtext
xx = parse_apqc_text_fields(DICT['subtext'])
File "/nan/ceph/network/system/el7/AFNI/AFNI_21.1.07/afnipy/lib_apqc_html.py", line 517, in parse_apqc_text_fields
sspbar = make_inline_pbar_str(ss)
File "/nan/ceph/network/system/el7/AFNI/AFNI_21.1.07/afnipy/lib_apqc_html.py", line 546, in make_inline_pbar_str
with open(fname_json, 'r') as fff:
FileNotFoundError: [Errno 2] No such file or directory: 'media/qc_08_mot_grayplot.pbar.json'