Error when processing Freesurfer Longitudinal stream results

[donghm]

Hi mindboggle experts,
I am now processing longitudinal data with mindboggle. I’ve tried to set the FreeSurfer longitudinal results as the input to mindboggle, however, it failed since no 001.mgz in mri/orig directory. So I try to use FreeSurfer base results this time and a surface mismatch error occurs, any advice for dealing with longitudinal data?

Attached are the crash files.
Thanks very much for your help!
Best
Dong Haoming

error.zip

[binarybottle]

@akeshavan -- How do you process FreeSurfer longitudinal data with Mindboggle?

[donghm]

Thanks very much for your reply.

Fowllowing are the commands I used:
DOCK=/home/jovyan/work
ID=CCSSUB
FREESURFER_SUBJECT=$DOCK/FreeSurfer60_long/$ID
FREESURFER_OUT=$DOCK/output/MindBoggled_FS_output
ANTS_OUT=$DOCK/output/MindBoggled_ants_output
ANTS_SUBJECT=$ANTS_OUT/$ID
OUT=$DOCK/output/MindBoggled_output
TEMPLATE=/opt/data/OASIS-30_Atropos_template
IMAGE=${FREESURFER_SUBJECT}/mri/T1.mgz
antsCorticalThickness.sh -d 3 -a $IMAGE -o $ANTS_OUT/$ID/ants
-e $TEMPLATE/T_template0.nii.gz
-t $TEMPLATE/T_template0_BrainCerebellum.nii.gz
-m $TEMPLATE/T_template0_BrainCerebellumProbabilityMask.nii.gz
-f $TEMPLATE/T_template0_BrainCerebellumExtractionMask.nii.gz
-p $TEMPLATE/Priors2/priors%d.nii.gz

mindboggle $FREESURFER_SUBJECT --out $OUT --roygbiv
--ants $ANTS_SUBJECT/antsBrainSegmentation.nii.gz

I have tried to use FS longitudinal runs for feature extraction at first, but it fails, fowllowing is what I got from the crash file:
OSError: Output key: MRI_mgh_format Template: /home/jovyan/work/colornest_001_1.long.colornest_001/mri/orig/001.mgz returned no files
Interface DataGrabber failed to run.

So I tried FS base runs for the second time and another error occurs, it seems that something wrong with my surface files :
180104-07:14:55,346 workflow ERROR:
['Node Combine_freesurfer_ants_cerebrum_graywhite failed to run on host 960a7b328fb3.']
180104-07:14:55,354 workflow INFO:
Saving crash info to /home/jovyan/work/crash-20180104-071455-jovyan-Combine_freesurfer_ants_cerebrum_graywhite-0fe4b2fe-e7ac-402f-903d-a5fef8427770.pklz
180104-07:14:55,354 workflow INFO:
Traceback (most recent call last):
File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py", line 43, in run
node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py", line 372, in run
self._run_interface()
File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py", line 482, in _run_interface
self._result = self._run_command(execute)
File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py", line 613, in _run_command
result = self._interface.run()
File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 1081, in run
runtime = self._run_wrapper(runtime)
File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 1029, in _run_wrapper
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/utility/wrappers.py", line 194, in _run_interface
out = function_handle(**args)
File "", line 98, in combine_2labels_in_2volumes
IndexError: index 8940857 is out of bounds for axis 1 with size 8940800
Interface Function failed to run.

Any advice for this?
Many thanks
Best
Dong Haoming

[akeshavan]

Hi @donghm - does mindboggle work on the longitudinal run when you input only freesurfer, and you don't use ANTS?

[akeshavan]

I wonder if its because there is a mismatch between the ants input (is that from a single timepoint?) and freesurfer long's base (which is the average of all the timepoints) . If it works with Freesurfer only, then this might be why.

[binarybottle]

@donghm -- Has @akeshavan helped elucidate/resolve your error? Please respond, as this will help others who run into a similar issue in the future.