Feat/nipypes

.gitignore

@@ -23,6 +23,8 @@ var/
 .installed.cfg
 *.egg
 Pipfile.lock
+**/.ipynb_checkpoints
+**crash*
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -64,3 +66,4 @@ target/
 *.xls
 *.html
 slices*
+pyscript.m

neuro_pypes/anat/utils.py

@@ -30,9 +30,7 @@ def biasfield_correct(anat_filepath=traits.Undefined):
     n4.inputs.convergence_threshold = 1e-6
     #n4.inputs.bspline_order = 5
     n4.inputs.save_bias = True
-
     n4.inputs.input_image = anat_filepath
-
     return n4
 
 

neuro_pypes/fmri/nuisance.py

@@ -208,7 +208,7 @@ def rest_noise_filter_wf(wf_name='rest_noise_removal'):
             ("in_file", "realigned_files"),
             ("motion_params", "realignment_parameters"),
             ("brain_mask", "mask_file"),
-        ß]),
+        ]),
 
         # calculte motion regressors
         (rest_noise_input, motion_regs, [("motion_params", "motion_params")]),

neuro_pypes/preproc/slicetime.py

@@ -306,8 +306,7 @@ def _pick_first(sequence):
     ]
 
     # the input and output nodes
-    stc_input = setup_node(IdentityInterface(fields=input_fields),
-                           name="stc_input")
+    stc_input = setup_node(IdentityInterface(fields=input_fields), name="stc_input")
 
     stc_output = setup_node(IdentityInterface(fields=["timecorrected_files",
                                                       "time_repetition",

neuro_pypes/preproc/slicetime_params.py

@@ -203,7 +203,7 @@ def calculate_slice_order(n_slices, slice_mode):
         img = nib.load(in_file)
         times = get_nii_slice_times(img)
         if times is not None:
-            return order_from_times(times)
+            return list(order_from_times(times))
 
     # read the slice mode code from the file
     if slice_mode == 'unknown':

scripts/rest_fmri_preprocessing/README.md

@@ -0,0 +1,32 @@
+
+Build the neurita/neuro_docker container:
+
+```
+git clone https://github.com/Neurita/neuro_ansible.git
+```
+
+Install the dependencies of neuro_ansible. Then:
+
+```
+cd neuro_ansible
+make docker-run
+```
+Exit from the container and delete it.
+
+Run the container again with your options:
+```
+export DATA_DIR=$HOME/projects/multimodal_test_data
+export PYPES_DIR=$HOME/projects/neuro_pypes
+
+docker run -it -p 8888:8888 --name neuro -v $DATA_DIR:/data -v  $PYPES_DIR:/root/projects/neuro_pypes neurita/neuro_docker:0.2 /bin/bash
+```
+
+Inside the container:
+```
+pyenv activate neuro
+pip install jupyter jupyterlab
+```
+
+```
+jupyter lab --ip 0.0.0.0 --no-browser --allow-root
+```