Make all params and models lower-case (#90)

* Make all params lower-case.

* Make models lower-case too.

* Fix things up.

* Fix underscores in entities.

* fix

* Revert some changes.

* Update pyafq_recon_external_trk_outputs.txt

qsirecon/data/scalars/brainsuite_3dshore.yaml

@@ -6,44 +6,44 @@ cnr_image:
         Description: Contrast to noise ratio for 3dSHORE fit
 lapnorm_file:
     bids:
-        model: 3dSHORE
+        model: 3dshore
         param: lapnorm
     metadata:
         Description: Laplacian norm from regularized MAPMRI (MAPL)
 mapcoeffs_file:
     bids:
-        model: 3dSHORE
+        model: 3dshore
         param: mapcoeffs
     metadata:
         Description: MAPMRI coefficients
 msd_file:
     bids:
-        model: 3dSHORE
-        param: MSD
+        model: 3dshore
+        param: msd
     metadata:
         Description: mean square displacement from MAPMRI
 ng_file:
     bids:
-        model: 3dSHORE
-        param: NG
+        model: 3dshore
+        param: ng
     metadata:
         Description: Non-Gaussianity from MAPMRI
 ngpar_file:
     bids:
-        model: 3dSHORE
-        param: NGpar
+        model: 3dshore
+        param: ngpar
     metadata:
         Description: Non-Gaussianity parallel from MAPMRI
 ngperp_file:
     bids:
-        model: 3dSHORE
-        param: NGperp
+        model: 3dshore
+        param: ngperp
     metadata:
         Description: Non-Gaussianity perpendicular from MAPMRI
 qiv_file:
     bids:
-        model: 3dSHORE
-        param: QIV
+        model: 3dshore
+        param: qiv
     metadata:
         Description: q-space inverse variance from MAPMRI
 r2_image:
@@ -54,19 +54,19 @@ regularization_image:
         Description: regularization of the 3dSHORE fit
 rtap_file:
     bids:
-        model: 3dSHORE
-        param: RTAP
+        model: 3dshore
+        param: rtap
     metadata:
         Description: Return to axis probability from MAPMRI
 rtop_file:
     bids:
-        model: 3dSHORE
-        param: RTOP
+        model: 3dshore
+        param: rtop
     metadata:
         Description: Return to origin probability from MAPMRI
 rtpp_file:
     bids:
-        model: 3dSHORE
-        param: RTPP
+        model: 3dshore
+        param: rtpp
     metadata:
         Description: Return to plane probability from MAPMRI

qsirecon/data/scalars/dipy_dki.yaml

@@ -1,54 +1,54 @@
 dki_ad:
     bids:
         model: dki
-        param: AD
+        param: ad
     metadata:
         Description: DKI AD
 dki_ak:
     bids:
         model: dki
-        param: AK
+        param: ak
     metadata:
         Description: DKI AK
 dki_fa:
     bids:
         model: tensor
-        param: FA
+        param: fa
     metadata:
         Description: DKI FA
 dki_kfa:
     bids:
         model: dki
-        param: KFA
+        param: kfa
     metadata:
         Description: DKI KFA
 dki_md:
     bids:
         model: dki
-        param: MD
+        param: md
     metadata:
         Description: DKI MD
 dki_mk:
     bids:
         model: dki
-        param: MK
+        param: mk
     metadata:
         Description: DKI MK
 dki_mkt:
     bids:
         model: dki
-        param: MKT
+        param: mkt
     metadata:
         Description: DKI MKT
 dki_rd:
     bids:
         model: dki
-        param: RD
+        param: rd
     metadata:
         Description: DKI RD
 dki_rk:
     bids:
         model: dki
-        param: RK
+        param: rk
     metadata:
         Description: DKI RK

qsirecon/data/scalars/dipy_mapmri.yaml

@@ -13,48 +13,48 @@ mapcoeffs_file:
 msd_file:
     bids:
         model: mapmri
-        param: MSD
+        param: msd
     metadata:
         Description: mean square displacement from MAPMRI
 ng_file:
     bids:
         model: mapmri
-        param: NG
+        param: ng
     metadata:
         Description: Non-Gaussianity from MAPMRI
 ngpar_file:
     bids:
         model: mapmri
-        param: NGpar
+        param: ngpar
     metadata:
         Description: Non-Gaussianity parallel from MAPMRI
 ngperp_file:
     bids:
         model: mapmri
-        param: NGperp
+        param: ngperp
     metadata:
         Description: Non-Gaussianity perpendicular from MAPMRI
 qiv_file:
     bids:
         model: mapmri
-        param: QIV
+        param: qiv
     metadata:
         Description: q-space inverse variance from MAPMRI
 rtap_file:
     bids:
         model: mapmri
-        param: RTAP
+        param: rtap
     metadata:
         Description: Return to axis probability from MAPMRI
 rtop_file:
     bids:
         model: mapmri
-        param: RTOP
+        param: rtop
     metadata:
         Description: Return to origin probability from MAPMRI
 rtpp_file:
     bids:
         model: mapmri
-        param: RTPP
+        param: rtpp
     metadata:
         Description: Return to plane probability from MAPMRI

qsirecon/data/scalars/dsistudio_gqi.yaml

@@ -12,7 +12,7 @@ dti_fa_file:
         Description: Radial Diffusivity from a tensor fit
 gfa_file:
     bids:
-        model: GQI
+        model: gqi
         param: gfa
     metadata:
         Description: Generalized Fractional Anisotropy
@@ -24,7 +24,7 @@ ha_file:
         Description: HA
 iso_file:
     bids:
-        model: GQI
+        model: gqi
         param: iso
     metadata:
         Description: Isotropic Diffusion
@@ -36,19 +36,19 @@ md_file:
         Description: Mean Diffusivity
 qa_file:
     bids:
-        model: GQI
+        model: gqi
         param: qa
     metadata:
         Description: Fractional Anisotropy from a tensor fit
 rd1_file:
     bids:
-        model: RDI
+        model: rdi
         param: rd1
     metadata:
         Description: RD1
 rd2_file:
     bids:
-        model: RDI
+        model: rdi
         param: rd2
     metadata:
         Description: RD2

qsirecon/data/scalars/tortoise.yaml

@@ -7,7 +7,7 @@ ad_file:
 am_file:
     bids:
         model: tensor
-        param: AM
+        param: am
     metadata:
         Description: A0 from a tensor fit
 fa_file:
@@ -25,31 +25,31 @@ li_file:
 ng_file:
     bids:
         model: mapmri
-        param: NG
+        param: ng
     metadata:
         Description: Non-Gaussianity from MAPMRI
 ngpar_file:
     bids:
         model: mapmri
-        param: NGpar
+        param: ngpar
     metadata:
         Description: Non-Gaussianity parallel from MAPMRI
 ngperp_file:
     bids:
         model: mapmri
-        param: NGperp
+        param: ngperp
     metadata:
         Description: Non-Gaussianity perpendicular from MAPMRI
 pa_file:
     bids:
         model: mapmri
-        param: PA
+        param: pa
     metadata:
         Description: PA from MAPMRI
 path_file:
     bids:
         model: mapmri
-        param: PAth
+        param: path
     metadata:
         Description: PAth from MAPMRI
 rd_file:
@@ -61,18 +61,18 @@ rd_file:
 rtap_file:
     bids:
         model: mapmri
-        param: RTAP
+        param: rtap
     metadata:
         Description: Return to axis probability from MAPMRI
 rtop_file:
     bids:
         model: mapmri
-        param: RTOP
+        param: rtop
     metadata:
         Description: Return to origin probability from MAPMRI
 rtpp_file:
     bids:
         model: mapmri
-        param: RTPP
+        param: rtpp
     metadata:
         Description: Return to plane probability from MAPMRI

qsirecon/tests/data/amico_noddi_outputs.txt

@@ -11,7 +11,7 @@ derivatives/qsirecon-NODDI/sub-PNC
 derivatives/qsirecon-NODDI/sub-PNC.html
 derivatives/qsirecon-NODDI/sub-PNC/dwi
 derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_dwimap.fib.gz
-derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-AMICOconfig_dwimap.pickle.gz
+derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-amicoconfig_dwimap.pickle.gz
 derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-direction_dwimap.json
 derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-direction_dwimap.nii.gz
 derivatives/qsirecon-NODDI/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-noddi_param-icvf_dwimap.json

qsirecon/tests/data/autotrack_outputs.txt

@@ -10,8 +10,8 @@ derivatives/qsirecon-DSIStudio/logs/CITATION.tex
 derivatives/qsirecon-DSIStudio/sub-ABCD
 derivatives/qsirecon-DSIStudio/sub-ABCD.html
 derivatives/qsirecon-DSIStudio/sub-ABCD/dwi
-derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-Association_ArcuateFasciculusL_streamlines.tck.gz
-derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-Association_ArcuateFasciculusR_streamlines.tck.gz
+derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusL_streamlines.tck.gz
+derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusR_streamlines.tck.gz
 derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundlestats.csv
 derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_dwimap.fib.gz
 derivatives/qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_mapping.map.gz

qsirecon/tests/data/dipy_dki_outputs.txt

@@ -10,24 +10,24 @@ derivatives/qsirecon-DKI/logs/CITATION.tex
 derivatives/qsirecon-DKI/sub-ABCD
 derivatives/qsirecon-DKI/sub-ABCD.html
 derivatives/qsirecon-DKI/sub-ABCD/dwi
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AD_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AD_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AK_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-AK_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-KFA_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-KFA_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MD_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MD_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MKT_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MKT_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MK_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-MK_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RD_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RD_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RK_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-RK_dwimap.nii.gz
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-FA_dwimap.json
-derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-FA_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ad_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ad_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ak_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-ak_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-kfa_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-kfa_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-md_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-md_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mkt_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mkt_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mk_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-mk_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rd_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rd_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rk_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-dki_param-rk_dwimap.nii.gz
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.json
+derivatives/qsirecon-DKI/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.nii.gz
 logs
 logs/CITATION.bib
 logs/CITATION.html