Merge pull request #6 from BIDS-Apps/fsdir

make freesurfer_dir optional
bids-apps · Aug 15, 2017 · 0c89e96 · 0c89e96
2 parents f6eef41 + cfd3b85
commit 0c89e96
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diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ Your data has to be organized according to the
 [BIDS standard](http://bids.neuroimaging.io) and each subject needs at
 least one T1w image.
 In a first step, BARACUS runs [FreeSurfer's](http://freesurfer.net)
-`recon-all` command and saves the output in `--freesurfer_dir`.
+`recon-all` command and saves the output in `{out_dir}/freesurfer/`
 If the data has previously been analyzed with FreeSurfer version 5.3.0,
 and BARACUS finds them in `--freesurfer_dir` this step ist skippen.
 
@@ -67,36 +67,44 @@ aseg files extracted via asegstats2table.
 These examples demonstrate how to run the `bids/baracus` docker container.
 For a brief introduction how to run BIDS Apps see
 [this site](http://bids-apps.neuroimaging.io/tutorial/).
-In the examples `/project/bids_sourcedata`, `/project/freesurfer` and
-`/project/baracus` are directories
-on your hard drive, which are mapped into the docker container directories
-`/data/in`, `/data/freesurfer` and `/data/out`, respectively, via
-the `-v` flag.
+In the examples `/project/bids_sourcedata` and
+`/project/baracus` are directories on your hard drive, which are mapped
+into the docker container directories `/data/in` and `/data/out`,
+respectively, via the `-v` flag.
 
 #### Participants
 
     docker run -ti --rm \
     -v /project/bids_sourcedata/:/data/in \
-    -v /project/freesurfer/:/data/freesurfer \
     -v /project/baracus:/data/out \
     bids/baracus /data/in /data/out participant \
-    --license_key "XX" --freesurfer_dir /data/freesurfer
+    --license_key "XX"
 
 #### Group
 
     docker run -ti --rm \
     -v /project/bids_sourcedata/:/data/in \
-    -v /project/freesurfer/:/data/freesurfer \
     -v /project/baracus:/data/out \
     bids/baracus /data/in /data/out group \
+    --license_key "XX"
+
+#### Participants with previously processed FreeSurfer data
+If FreeSurfer data is already available, for example at
+`/project/freesurfer/` running the follwing command will use the
+previously processed data:
+
+    docker run -ti --rm \
+    -v /project/bids_sourcedata/:/data/in \
+    -v /project/freesurfer/:/data/freesurfer \
+    -v /project/baracus:/data/out \
+    bids/baracus /data/in /data/out participant \
     --license_key "XX" --freesurfer_dir /data/freesurfer
 
 ### Usage
 
-    docker run -ti --rm bids/${CIRCLE_PROJECT_REPONAME,,} -h
     usage: run_brain_age_bids.py [-h]
                                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
-                                 --freesurfer_dir FREESURFER_DIR
+                                 [--freesurfer_dir FREESURFER_DIR]
                                  [--models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]]
                                  --license_key LICENSE_KEY [--n_cpus N_CPUS] [-v]
                                  bids_dir out_dir {participant,group}
@@ -108,7 +116,7 @@ the `-v` flag.
     positional arguments:
       bids_dir              The directory with the input dataset formatted
                             according to the BIDS standard.
-      out_dir               Results are put here.
+      out_dir               Results are put into {out_dir}/baracus.
       {participant,group}   Level of the analysis that will be performed.
                             "participant": predicts single subject brain age,
                             "group": collects single subject predictions.
@@ -125,7 +133,8 @@ the `-v` flag.
       --freesurfer_dir FREESURFER_DIR
                             Folder with FreeSurfer subjects formatted according to
                             BIDS standard. If subject's recon-all folder cannot be
-                            found, recon-all will be run.
+                            found, recon-all will be run. If not specified
+                            freesurfer data will be saved to {out_dir}/freesurfer
       --models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]
       --license_key LICENSE_KEY
                             FreeSurfer license key - letters and numbers after "*"
@@ -136,6 +145,7 @@ the `-v` flag.
       -v, --version         show program's version number and exit
 
 
+
 ## FILE mode
 ### Example
     docker run -ti --rm \

diff --git a/circle.yml b/circle.yml
@@ -33,21 +33,21 @@ test:
     # ds114_test1
     - docker run --rm -ti -v ${HOME}/data/ds114_test1:/data/in -v ${HOME}/data/ds114_test1_freesurfer:/data/fs -v ${HOME}/outputs/ds114_test1:/data/out bids/${CIRCLE_PROJECT_REPONAME,,} /data/in /data/out participant --freesurfer_dir /data/fs --license_key="~/test.key"
     - docker run --rm -ti -v ${HOME}/data/ds114_test1:/data/in -v ${HOME}/data/ds114_test1_freesurfer:/data/fs -v ${HOME}/outputs/ds114_test1:/data/out bids/${CIRCLE_PROJECT_REPONAME,,} /data/in /data/out group --freesurfer_dir /data/fs --license_key="~/test.key"
-    - cat ${HOME}/outputs/ds114_test1/00_group/group_predicted_age.tsv
+    - cat ${HOME}/outputs/ds114_test1/baracus/00_group/group_predicted_age.tsv
 
     # test models
     - docker run --rm -ti -v ${HOME}/data/ds114_test1:/data/in -v ${HOME}/data/ds114_test1_freesurfer:/data/fs -v ${HOME}/outputs/ds114_test1_models:/data/out bids/${CIRCLE_PROJECT_REPONAME,,} /data/in /data/out participant --freesurfer_dir /data/fs --models Liem2016__OCI_norm Liem2016__full_2samp_training --license_key="~/test.key"
     - docker run --rm -ti -v ${HOME}/data/ds114_test1:/data/in -v ${HOME}/data/ds114_test1_freesurfer:/data/fs -v ${HOME}/outputs/ds114_test1_models:/data/out bids/${CIRCLE_PROJECT_REPONAME,,} /data/in /data/out group --freesurfer_dir /data/fs --license_key="~/test.key"
-    - cat ${HOME}/outputs/ds114_test1_models/00_group/group_predicted_age.tsv
-    
+    - cat ${HOME}/outputs/ds114_test1_models/baracus/00_group/group_predicted_age.tsv
+
     # test file mode
-    - docker run --rm -ti -v ${HOME}/outputs/ds114_test1/sub-01/data/:/data/in -v ${HOME}/outputs/ds114_test1_file_mode:/data/out --entrypoint=run_brain_age_files.py bids/baracus /data/out --lh_thickness_file /data/in/lh.thickness.mgh --rh_thickness_file /data/in/rh.thickness.mgh --lh_area_file /data/in/lh.area.mgh --rh_area_file /data/in/rh.area.mgh --aseg_file /data/in/aseg --participant_label sub-01
+    - docker run --rm -ti -v ${HOME}/outputs/ds114_test1/baracus/sub-01/data/:/data/in -v ${HOME}/outputs/ds114_test1_file_mode:/data/out --entrypoint=run_brain_age_files.py bids/baracus /data/out --lh_thickness_file /data/in/lh.thickness.mgh --rh_thickness_file /data/in/rh.thickness.mgh --lh_area_file /data/in/lh.area.mgh --rh_area_file /data/in/rh.area.mgh --aseg_file /data/in/aseg --participant_label sub-01
     - cat ${HOME}/outputs/ds114_test1_file_mode/sub-01/sub-01_predicted_age.tsv
 
     # ds114_test2
     - docker run --rm -ti -v ${HOME}/data/ds114_test2:/data/in -v ${HOME}/data/ds114_test2_freesurfer:/data/fs -v ${HOME}/outputs/ds114_test2:/data/out bids/${CIRCLE_PROJECT_REPONAME,,} /data/in /data/out participant --freesurfer_dir /data/fs --license_key="~/test.key"
     - docker run --rm -ti -v ${HOME}/data/ds114_test2:/data/in -v ${HOME}/data/ds114_test2_freesurfer:/data/fs -v ${HOME}/outputs/ds114_test2:/data/out bids/${CIRCLE_PROJECT_REPONAME,,} /data/in /data/out group --freesurfer_dir /data/fs --license_key="~/test.key"
-    - cat ${HOME}/outputs/ds114_test2/00_group/group_predicted_age.tsv
+    - cat ${HOME}/outputs/ds114_test2/baracus/00_group/group_predicted_age.tsv
 
 deployment:
   hub:

diff --git a/scripts/run_brain_age_bids.py b/scripts/run_brain_age_bids.py
@@ -19,7 +19,7 @@
                     'is extracted automatiacally from that folder. ')
     parser.add_argument('bids_dir', help='The directory with the input dataset '
                                          'formatted according to the BIDS standard.')
-    parser.add_argument('out_dir', help='Results are put here.')
+    parser.add_argument('out_dir', help='Results are put into {out_dir}/baracus.')
     parser.add_argument('analysis_level', help='Level of the analysis that will be performed. '
                                                '"participant": predicts single subject brain age, '
                                                '"group": collects single subject predictions.',
@@ -31,9 +31,11 @@
                                                     'provided all subjects should be analyzed. Multiple '
                                                     'participants can be specified with a space separated list.',
                         nargs="+")
-    parser.add_argument('--freesurfer_dir', required=True, help="Folder with FreeSurfer subjects formatted according "
-                                                                "to BIDS standard. If subject's recon-all folder "
-                                                                "cannot be found, recon-all will be run.")
+    parser.add_argument('--freesurfer_dir', help="Folder with FreeSurfer subjects formatted according "
+                                                 "to BIDS standard. If subject's recon-all folder "
+                                                 "cannot be found, recon-all will be run. "
+                                                 "If not specified freesurfer data will be saved to {"
+                                                 "out_dir}/freesurfer")
     parser.add_argument('--models', choices=models_list, default=["Liem2016__OCI_norm"], help='',
                         nargs="+")
     parser.add_argument('--license_key',
@@ -46,6 +48,17 @@
                         version='BARACUS version {}'.format(__version__))
     args = parser.parse_args()
 
+    # set up output dirs
+    if args.freesurfer_dir:
+        freesurfer_dir = args.freesurfer_dir
+    else:
+        freesurfer_dir = os.path.join(args.out_dir, "freesurfer")
+    out_dir = os.path.join(args.out_dir, "baracus")
+    if not os.path.isdir(freesurfer_dir):
+        os.makedirs(freesurfer_dir)
+    if not os.path.isdir(out_dir):
+        os.makedirs(out_dir)
+
     model_dir = resource_filename(Requirement.parse("baracus"), 'models')
 
     run("bids-validator " + args.bids_dir)
@@ -58,11 +71,11 @@
 
     if args.analysis_level == "participant":
 
-        data_files = run_prepare_all(args.bids_dir, args.freesurfer_dir, args.out_dir, subjects_to_analyze,
+        data_files = run_prepare_all(args.bids_dir, freesurfer_dir, out_dir, subjects_to_analyze,
                                      sessions_to_analyze, args.n_cpus, args.license_key)
 
         for subject, d in data_files.items():
-            d["out_dir"] = args.out_dir
+            d["out_dir"] = out_dir
             d["model_dir"] = model_dir
             d["models"] = args.models
             d["subject_label"] = subject
@@ -72,10 +85,10 @@
         print("Creating group table...")
         df = pd.DataFrame([])
         for subject in freesurfer_subjects_to_analyze:
-            in_file = os.path.join(args.out_dir, subject, subject + "_predicted_age.tsv")
+            in_file = os.path.join(out_dir, subject, subject + "_predicted_age.tsv")
             df = df.append(pd.read_csv(in_file, sep="\t"))
 
-        group_out_dir = os.path.join(args.out_dir, "00_group")
+        group_out_dir = os.path.join(out_dir, "00_group")
         if not os.path.isdir(group_out_dir):
             os.makedirs(group_out_dir)
         out_file = os.path.join(group_out_dir, "group_predicted_age.tsv")