Merge pull request #85 from neuropoly/rb/subjects_file

Creation of `subjects.csv` in the correct path and fixing minor bugs in the path name

README.md

@@ -225,21 +225,22 @@ e) Minc2simple
 ```
 pip install "git+https://github.com/NIST-MNI/minc2-simple.git@develop_new_build#subdirectory=python"
 ``` 
+f) Update the absolute of the `subjects.csv` in the `generate_template.py` script. The `subjects.csv` lies inside the `DATASET/derivatives/template` directory
 
-f) Create `template_pipleline.sh` 
+g) Create `template_pipleline.sh` 
 > **Note:**
 > Create the `template_pipeline.sh` inside the `template` folder.
 ```
 #!/bin/bash
 python -m scoop -vvv generate_template.py
 ```
 
-g) Batch on Alliance Canada
+h) Batch on Alliance Canada
 ```
 sbatch --time=24:00:00  --mem-per-cpu 4000 template_pipeline.sh # will probably require batching several times, depending on number of subjects
 ```
 
-h) Final output
+i) Final output
 <p>After the pipeline has finished running, the `.mnc` file needs to be converted to `.nii` format in order to get the final template. The pipeline would give outputs with the name: avg.XXX.mnc, where `XXX` is the nth iteration. To convert it to the `.nii` format, run the following command:</p>
 
 ```

preprocess_normalize.py

@@ -639,15 +639,15 @@ def create_mask_template(dataset_info):
     if os.path.isfile(path_template + '/template_mask.mnc'): os.remove(path_template + '/template_mask.mnc')
 
     os.system('nii2mnc ' + path_template + '/template_mask.nii.gz ' + ' ' + path_template + '/template_mask.mnc')
-    return path_template + '/template_mask.mnc'
+    return path_template + 'template_mask.mnc'
 
 def convert_data2mnc(dataset_info):
     path_template = dataset_info['path_data'] + 'derivatives/template/'
     list_subjects = dataset_info['include_list'].split(' ')
 
     path_template_mask = create_mask_template(dataset_info)
 
-    output_list = open('subjects.csv', "w")
+    output_list = open(path_template + 'subjects.csv', "w")
     writer = csv.writer(output_list, delimiter = ',', quotechar = ',', quoting = csv.QUOTE_MINIMAL)
 
     tqdm_bar = tqdm(total = len(list_subjects), unit = 'B', unit_scale = True, desc = "Status", ascii = True)
@@ -661,7 +661,7 @@ def convert_data2mnc(dataset_info):
         os.system('nii2mnc ' + fname_nii + ' ' + fname_mnc)
         os.remove(fname_nii) # remove duplicate nifti file!
 
-        writer.writerow([fname_mnc,path_template_mask])
+        writer.writerow([fname_mnc, path_template_mask])
 
         tqdm_bar.update(1)
     tqdm_bar.close()