ERROR: There was an error in the harmonisation of $ID

[0rC0]

# MELD Version 2.2 native installation
# OS Ubuntu 22.04

Hello everybody,

I'm experiencing an issue with harmonization in my dataset and would like to ask for help in finding a solution. After preprocessing with FreeSurfer, I initially ran the pipeline with the --harmo_only option on about 40 subjects, and then ran it again without --harmo_only for segmentation after preprocessing all subjects. However, I'm encountering the following error (complete log below) for all my subjects:

[neuroCombatFromTraining] In development ...

ERROR: There was an error in the harmonisation of ['sub-FCD000420241031']

It seems that the dict_combat['data'] from the neuroCombatFromTraining function returns an array with NAs. I'm unsure why this is happening. My dataset consists of about 40 3 Tesla images (T1w + FLAIR), which appear to be of good quality.

My MELD invocation:

./meldgraph.sh new_pt_pipeline.py -id sub-FCD000420241031 -demos ../../derivatives/meld_data/demo_sidses2.csv --harmo_code H250

The subject ID is present in the demographic file and all the subjects are correctly segmented without harmonization.

Thanks in advance for any assistance.

Log:

./meldgraph.sh new_pt_pipeline.py -id sub-FCD0
00420241031 -demos ../../derivatives/meld_data/demo_sidses2.csv --harmo_code H250                          
Setting MELD_DATA_PATH to /home/orco/data/FCD/derivatives/meld_data                                        
Setting BASE_PATH to /home/orco/data/FCD/derivatives/meld_data/output/preprocessed_surf_data               
Setting EXPERIMENT_PATH to /home/orco/data/FCD/derivatives/meld_data/models                                
Setting FS_SUBJECTS_PATH to /home/orco/data/FCD/derivatives/meld_data/output/fs_outputs                    
Setting BASE_PATH to /home/orco/data/FCD/derivatives/meld_data/meld_params                                 
setting license/home/orco/data/FCD/code/meld_graph_fork/license.txt                                        
Namespace(id='sub-FCD000420241031', list_ids=None, harmo_code='H250', fastsurfer=False, parallelise=False, 
demographic_file='../../derivatives/meld_data/demo_sidses2.csv', harmo_only=False, skip_feature_extraction=
False, no_nifti=False, no_report=False, debug_mode=False)                                                  
SCRIPT 1: Call script segmentation                                                                         
FCD000420241031                                                                                            
BIDS Layout: ...CD/derivatives/meld_data/input | Subjects: 115 | Sessions: 0 | Runs: 0                     
INFO - sub-FCD000420241031: T1 file used : /home/orco/data/FCD/derivatives/meld_data/input/sub-FCD000420241
031/anat/sub-FCD000420241031_T1w.nii.gz                                                                    
INFO - sub-FCD000420241031: FLAIR file used : /home/orco/data/FCD/derivatives/meld_data/input/sub-FCD000420
241031/anat/sub-FCD000420241031_FLAIR.nii.gz                                                               
STEP 1 - sub-FCD000420241031: Freesurfer outputs already exists for subject sub-FCD000420241031. Freesurfer
 will be skipped                                                                                           
STEP 2 - sub-FCD000420241031: Extract surface-based features                                               
INFO - sub-FCD000420241031: Creating registration to template surface                                      
INFO - sub-FCD000420241031: Sampling features in native space                                              
INFO - sub-FCD000420241031: Sample FLAIR features : []                                                     
INFO - sub-FCD000420241031: Sample FLAIR features : []                                                     
INFO - sub-FCD000420241031: Calculate curvatures                                                           
INFO - sub-FCD000420241031: Compute gaussian curvature                                                     
INFO - sub-FCD000420241031: Get thickness and white-grey matter contrast                                   
INFO - sub-FCD000420241031: Calculate curvatures                                                           
INFO - sub-FCD000420241031: Compute gaussian curvature
INFO - sub-FCD000420241031: Get thickness and white-grey matter contrast
INFO - sub-FCD000420241031: Moving features to template surface
INFO - sub-FCD000420241031: Move feature to xhemi flip
INFO - sub-FCD000420241031: Moving lesion masks to template surface
INFO - sub-FCD000420241031: Creating final training data matrix
scanner for subject sub-FCD000420241031is set as default XT
INFO - sub-FCD000420241031: All features have been extracted and saved in /home/orco/data/FCD/derivatives/meld_data/output/preprocessed_surf_data/MELD_H250
SCRIPT 2: Call script preprocessing
INFO: Use combat parameters from site
STEP: Smoothing feature .on_lh.curv.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
WARNING - sub-FCD000420241031: 15 extremes vertices
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.gm_FLAIR_0.25.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.gm_FLAIR_0.5.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.gm_FLAIR_0.75.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.gm_FLAIR_0.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.pial.K_filtered.sm20.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : no smoothing for this feature
INFO - all : saving data
STEP: Smoothing feature .on_lh.sulc.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.thickness.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.w-g.pct.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
WARNING - sub-FCD000420241031: 10 extremes vertices
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.wm_FLAIR_0.5.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP: Smoothing feature .on_lh.wm_FLAIR_1.mgh
INFO - all: Clip data to remove very extreme values using clip_params_MELD.json
INFO - all : Smoothing with 6 iterations ...
INFO - all : saving data
STEP - sub-FCD000420241031: Regress thickness with curvature
Add feature .on_lh.thickness_regression.sm3.mgh in features
STEP - sub-FCD000420241031: Combat harmonise subjects 
STEP: Combat feature .on_lh.thickness.sm3.mgh
[neuroCombatFromTraining] In development ...

ERROR: There was an error in the harmonisation of ['sub-FCD000420241031']

[0rC0]

UPDATE.1.: It seems that the issue is only related to the native installation. Using the same meld_data directory and Docker does not produce the same error message.