I am attempting to use the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”, but keep getting a flawed output.
My dataset consists of images from a longitudinal study with some dropouts. First, I ran the reconall longitudinal pipeline in fs60 for all subjects. I got no errors. Then, I tried
1. Running the longitudinal pipeline of the hippocampal module, loading Matlab 8.2 to run
I got an error in most of these jobs (mostly for templates of subjects with multiple visits) that read
"ERROR: MatlabObjectArray(0x7fd7ce84cea0): Trying to access non-existing object (25)
Error in kvlGetOptimizer (line 11)
Error in SegmentSubfieldsT1Longitudinal (line 1155)”
2. I then tried running the cross sectional pipeline for each one of the timepoints in subjects already processed by the
reconall longitudinal pipeline (i. e. segmentations in the .long. directories)
segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate
segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_basetemplate
segmentHA_T1.sh SUBJ2_timepoint1.long.SUBJ2_basetemplate
segmentHA_T1.sh SUBJ3_timepoint1.long.SUBJ3_basetemplate
etc
Most of them ran without errors, but some still did.
3. I then tried to run the cross sectional hippocampal module for all subjects/timepoints without using the reconall longitudinal pipeline
segmentHA_T1.sh SUBJ1_timepoint1
segmentHA_T1.sh SUBJ1_timepoint2
segmentHA_T1.sh SUBJ2_timepoint1
segmentHA_T1.sh SUBJ3_timepoint1
etc
They were processed without errors. But when inspecting the processing log, there was a message that appeared 4 times in the file
"WARNING: Registration did not converge in 5 steps!
* Problem might be ill posed.
* Please inspect output manually!
………
……..
…...
Everything done!
It took 766.0135 seconds “
With manual inspection, subfield segmentations output by fs60 seemed fine in all the directories of the reconall cross sectional and longitudinal outputs (hippoSfLabels-T1). For the
Hippocampal Module outputs (hippoAmygLabels-T1), the hippocampus was abbruptly cut, sometimes laterally, sometimes dorsally. This was the case for all three analyses.
I wonder what is the problem and what I can do to fix it so I can successfully run the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”