SPM realign crashes for newer ADNI cases #877
Description
Description
I have some troubles processing newer ADNI cases. This is quite troublesome for me, since I'm trying to process everything using v1.8.0 and I'm really not sure if we can fix this without a bugfix 😢
This example right here is a case from 2018. It only seems to happen for Siemens datasets with 10 control/label pairs. It's a 3D PASL sequence and you get those typical MOSAIC DICOMs. Everything up to the ExploreASL module works perfectly.
3D_GRASE sequence detected
No TopUp scans available, skipping...
Automatic alignment with center of mass: to XYZ:375 434 1
x.modules.asl.SpikeRemovalThreshold was not defined yet, default setting = 0.01 used
SPM motion estimation
SPM12: spm_realign (v7141) 03:43:21 - 11/10/2021
========================================================================
Estimating motion:
* - SPM12: spm_realign --------------------------------------------
There is not enough overlap in the images to obtain a solution.
Offending image:
...\Process_ADNI_3\output\020_S_6358\derivatives\ExploreASL\sub-020S6358\ASL_1\ASL4D.nii
Please check that your header information is OK.
The Check Reg utility will show you the initial
alignment between the images, which must be
within about 4cm and about 15 degrees in order
for SPM to find the optimal solution.
----------------------------------------- 03:43:22 - 11/10/2021
ERROR: ASL module terminated for subject 1: sub-020S6358
ans =
'Error using spm_realign line 525
Insufficient image overlap.
Error in realign_series line 342
I'm running it using the following settings:
{"x":
{
"dataset":
{
"name":"020_S_6358"
},
"Q":
{
"M0":"UseControlAsM0",
"readoutDim":"3D",
"Sequence":"3D_GRASE"
},
"settings":
{
"Quality":1
}
}
}I saw that in 5 different subjects so far, but there are probably more. Am I doing something wrong or is this a bug @jan-petr ?
Edit: problem seems to be in dcm2niix, resulting ASL4D.nii.gz is in MOSAIC data format.
Release notes
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