Merge pull request #28 from neu-spiral/develop

Develop

Author: esennesh

create_mean_images_compressed.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+for file in $1/*.nii.gz ##path to relevant dataset group
+do
+  base=`basename ${file} .nii.gz`.nii
+  gunzip -c ${file} > ${base}
+  fslmaths "${base}" -Tmean -bin "${base}_mean"
+done
+
+fslmerge -t allmeanmasks4d *.nii.gz
+fslmaths allmeanmasks4d -Tmean propDatavox3d
+fslmaths propDatavox3d -thr 1 wholebrain

environment.yml

@@ -40,6 +40,8 @@ dependencies:
   - jupyter_client=5.2.2=py36_0
   - jupyter_console=5.2.0=py36he59e554_1
   - jupyter_core=4.4.0=py36h7c827e3_0
+  - jupyterlab=0.31.12=py36_0
+  - jupyterlab_launcher=0.10.5=py36_0
   - libedit=3.1=heed3624_0
   - libffi=3.2.1=hd88cf55_4
   - libgcc-ng=7.2.0=h7cc24e2_2
@@ -116,19 +118,25 @@ dependencies:
   - pytorch=0.3.1=py36_cuda9.0.176_cudnn7.0.5_2
   - torchvision=0.2.0=py36h17b6947_1
   - pip:
+    - alembic==0.9.9
+    - banal==0.3.5
+    - dataset==1.0.8
     - deepdish==0.3.6
     - flatdict==2.0.1
     - future==0.16.0
     - htfatorch==0.0.0
     - hypertools==0.4.2
+    - mako==1.0.7
     - nibabel==2.2.1
     - nilearn==0.4.0
+    - normality==0.5.12
     - numexpr==2.6.4
     - pandas==0.22.0
     - ppca==0.0.3
     - probtorch==0.0+5a2c637
+    - python-editor==1.0.3
     - seaborn==0.8.1
+    - sqlalchemy==1.2.7
     - tables==3.4.2
     - torch==0.3.1.post2
-prefix: /home/work/anaconda3/envs/HTFATorch
-
+prefix: /home/eli/anaconda3/envs/HTFATorch