diff --git a/bip/data/FileTree.tree b/bip/data/FileTree.tree
index 8d0eafdf77bf4bafff2eceaa4c67171c41f6ab51..7b6cffbc24aaa530c4752e18be723653e190f9e3 100644
--- a/bip/data/FileTree.tree
+++ b/bip/data/FileTree.tree
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:ba0df3594b01805dc61beeee6be87eaf42087dd5e4d4f28ecd6c2d2587cfe14a
-size 21918
+oid sha256:0d593e72e427400f23ec2829c5353cea47df1516fd3908e3a1b6c0c94f5692e6
+size 22258
diff --git a/bip/data/dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz b/bip/data/dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz
new file mode 100755
index 0000000000000000000000000000000000000000..058c22d8b553e6191e9fac59c9d1b1ac3d47a12c
--- /dev/null
+++ b/bip/data/dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3c2bc4a2aab93d388afc8387a2c0af9c20c92beefb6f28030fb4e8c1ffa8989d
+size 52093
diff --git a/bip/data/dMRI/TBSS/JHU-labels.xml b/bip/data/dMRI/TBSS/JHU-labels.xml
new file mode 100755
index 0000000000000000000000000000000000000000..b27c3bb353fcd8d993e2706556114863009439c7
--- /dev/null
+++ b/bip/data/dMRI/TBSS/JHU-labels.xml
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2d76ce80d1b0a50dccda2698d5eec55c8984a7f1bb438f79111d67a26fc4dc1c
+size 4594
diff --git a/bip/data/dMRI/TBSS/JHU-tracts.xml b/bip/data/dMRI/TBSS/JHU-tracts.xml
new file mode 100755
index 0000000000000000000000000000000000000000..089414b2e80b5ed9a8673813757523470b679eb0
--- /dev/null
+++ b/bip/data/dMRI/TBSS/JHU-tracts.xml
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d97e37ecca7c8675976f8e7d222e58aa3ce8b20243040c588c6cfcc5b1ab2a65
+size 2094
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
new file mode 100755
index 0000000000000000000000000000000000000000..5c5b166182dd81c560dd7b43ecbcd8d9a9b264b4
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_T1_FIRST_vols.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+#
+# IDP_T1_FIRST_vols.py - Generating IDP file with measure of FIRST volumes of T1
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from fsl import wrappers
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ T1_first_all_fast_firstseg: In(optional=True),
+ logs_dir: Ref,
+ IDP_T1_FIRST_vols: Out):
+
+ with redirect_logging('IDP_T1_FIRST_vols', outdir=logs_dir):
+ result = ("NaN " * 15).strip()
+
+ if os.path.exists(T1_first_all_fast_firstseg):
+ v=wrappers.fslstats(T1_first_all_fast_firstseg).H(58,0.5,58.5).run()
+ # indices that we are interested in
+ ind = [9, 48, 10, 49, 11, 50, 12, 51, 16, 52, 17, 53, 25, 57, 15]
+ result = [str(int(v[x])) for x in ind]
+ result = " ".join(result)
+
+
+ with open(IDP_T1_FIRST_vols, 'wt', encoding="utf-8") as f:
+ f.write(f'{result}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
new file mode 100755
index 0000000000000000000000000000000000000000..05b78132b59e379e8215f6408c9ca5b72606bebd
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_T1_SIENAX.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+#
+# IDP_T1_SIENAX.py - Generating IDP file with SIENAX metrics of T1.
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ T1_sienax_report: In,
+ T1_sienax_txt: Ref,
+ logs_dir: Ref,
+ IDP_T1_SIENAX: Out):
+
+ with redirect_logging('IDP_T1_SIENAX', outdir=logs_dir):
+
+ result = ("NaN " * 11).strip()
+
+ if os.path.exists(T1_sienax_report):
+ with open(T1_sienax_report, "r", encoding="utf-8") as f:
+ text = f.readlines()
+ # indices that we are interested in
+ result = text[0].split()[1] + " "
+ result += text[2].split()[1] + " " + text[2].split()[2] + " "
+ result += text[3].split()[1] + " " + text[3].split()[2] + " "
+ result += text[4].split()[1] + " " + text[4].split()[2] + " "
+ result += text[5].split()[1] + " " + text[5].split()[2] + " "
+ result += text[6].split()[1] + " " + text[6].split()[2]
+
+ with open(IDP_T1_SIENAX, 'wt', encoding="utf-8") as f:
+ f.write(f'{result}\n')
+
+ copyfile(src=IDP_T1_SIENAX, dst=T1_sienax_txt)
diff --git a/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py b/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py
new file mode 100755
index 0000000000000000000000000000000000000000..fc0089a64e8003d0b29a733c7df181af100a34ee
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_T2_FLAIR_WMH.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+#
+# IDP_T2_FLAIR_WMH.py - Generating IDP file with WMH segmentation metrics
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from shutil import copyfile
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ T2_FLAIR_bianca_volume: In,
+ logs_dir: Ref,
+ IDP_T2_FLAIR_WMH: Out):
+
+ with redirect_logging('IDP_T2_FLAIR_WMH', outdir=logs_dir):
+ copyfile(src=T2_FLAIR_bianca_volume, dst=IDP_T2_FLAIR_WMH)
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
new file mode 100755
index 0000000000000000000000000000000000000000..fd2cfd450a50c8c131a84b51d88ae0085edc8701
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_diff_TBSS.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+#
+# IDP_diff_TBSS.py - Generating IDP file with TBSS metrics
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ JHUrois_FA: In(optional=True),
+ logs_dir: Ref,
+ JHUrois_prefix: Ref,
+ IDP_diff_TBSS: Out):
+
+ with redirect_logging('IDP_diff_TBSS', outdir=logs_dir):
+
+ nan_result = ("NaN " * 48).strip()
+
+ result = ""
+
+ for mod in ["FA", "MD", "MO", "L1", "L2", "L3", "ICVF", "OD", "ISOVF"]:
+
+ file_name = JHUrois_prefix + mod + ".txt"
+ print(file_name)
+ if os.path.exists(file_name):
+ with open(file_name, "r") as f:
+ mini_result = f.read()
+ mini_result = mini_result.replace("\n", " ")
+ mini_result = mini_result.replace(" ", " ")
+ mini_result = mini_result.replace(" ", " ")
+ mini_result = mini_result.replace("[", "")
+ mini_result = mini_result.replace("]", "").strip()
+ else:
+ mini_result = nan_result
+
+ result += mini_result + " "
+
+ result = result.strip()
+
+ with open(IDP_diff_TBSS, 'wt', encoding="utf-8") as f:
+ f.write(f'{result}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
new file mode 100755
index 0000000000000000000000000000000000000000..02625c4a40d8962515ffd122005e0410d09ce9a1
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_diff_eddy_outliers.py
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+#
+# IDP_diff_eddy_outliers.py - Generating IDP file with eddy outliers metrics
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ eddy_outlier_report: In(optional=True),
+ logs_dir: Ref,
+ IDP_diff_eddy_outliers: Out):
+
+ with redirect_logging('IDP_diff_eddy_outliers', outdir=logs_dir):
+
+ num_outliers = 0
+
+ if os.path.exists(eddy_outlier_report):
+ with open(eddy_outlier_report, "r", encoding="utf-8") as f:
+ num_outliers = str(len(f.readlines()))
+ else:
+ num_outliers = "NaN"
+
+ with open(IDP_diff_eddy_outliers, 'wt', encoding="utf-8") as f:
+ f.write(f'{num_outliers}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_func_TSNR.py b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
new file mode 100755
index 0000000000000000000000000000000000000000..92e0b3ff227606857383a4f118cea83ac9f68a5c
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_func_TSNR.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+#
+# IDP_func_TSNR.py - Generating IDP file with measure of TSNR of fMRI
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from fsl import wrappers
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging, tempdir
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ filtered_func_data: In(optional=True),
+ filtered_func_data_clean: In(optional=True),
+ tfMRI_filtered_func_data: In(optional=True),
+ logs_dir: Ref,
+ tmp_dir: Ref,
+ IDP_func_TSNR: Out):
+
+ with redirect_logging('IDP_func_TSNR', outdir=logs_dir),\
+ tempdir(tmp_dir):
+
+ fMRI_SNR = tmp_dir + '/fMRI_SNR.nii.gz'
+
+ result =""
+
+ for file_name in [filtered_func_data, filtered_func_data_clean,
+ tfMRI_filtered_func_data]:
+ if os.path.exists(file_name):
+ wrappers.fslmaths(file_name).Tstd().run(fMRI_SNR)
+ wrappers.fslmaths(file_name).Tmean().div(fMRI_SNR).run(fMRI_SNR)
+ v=wrappers.fslstats(fMRI_SNR).l(0.1).p(50).run()
+ print(v)
+ v = 1/v
+ print(v)
+ result += f"{v} "
+ else:
+ result += "NaN "
+
+ result = result.strip()
+
+ with open(IDP_func_TSNR, 'wt', encoding="utf-8") as f:
+ f.write(f'{result}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_func_head_motion.py b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
new file mode 100755
index 0000000000000000000000000000000000000000..f673831b7b703fd7a5de4f7852cb2db3fa9e7c50
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_func_head_motion.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+#
+# IDP_func_head_motion.py - Generating IDP file with measure of fMRI head motion
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ rfMRI_mc_rel_mean: In(optional=True),
+ tfMRI_mc_rel_mean: In(optional=True),
+ logs_dir: Ref,
+ IDP_func_head_motion: Out):
+
+ with redirect_logging('IDP_func_head_motion', outdir=logs_dir):
+ result=""
+
+ if os.path.exists(rfMRI_mc_rel_mean):
+ with open(rfMRI_mc_rel_mean, "r", encoding="utf-8") as f:
+ val_1 = json.load(f)
+ else:
+ val_1 = "NaN"
+
+ if os.path.exists(tfMRI_mc_rel_mean):
+ with open(tfMRI_mc_rel_mean, "r", encoding="utf-8") as f:
+ val_2 = json.load(f)
+ else:
+ val_2 = "NaN"
+
+ with open(IDP_func_head_motion, 'wt', encoding="utf-8") as f:
+ f.write(f'{val_1} {val_2}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
new file mode 100755
index 0000000000000000000000000000000000000000..a9c5503d716635d8a21284cdfecc378156cba487
--- /dev/null
+++ b/bip/pipelines/IDPs_gen/IDP_subject_COG_table.py
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+#
+# IDP_subject_centre.py - Generating IDP file with the acquisition centre.
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+#
+
+import os
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+ T1_orig: In,
+ T1_QC_COG: In,
+ T1_dcm_txt: In,
+ dMRI_dcm_txt: Ref,
+ rfMRI_dcm_txt: Ref,
+ SWI_dcm_txt: Ref,
+ T2_dcm_txt: Ref,
+ tfMRI_dcm_txt: Ref,
+ logs_dir: Ref,
+ IDP_subject_COG_table: Out):
+
+ with redirect_logging('IDP_subject_COG_table', outdir=logs_dir):
+
+ result = ""
+ with open(T1_QC_COG, "r", encoding="utf-8") as f:
+ COG = f.read().strip()
+
+ table = "NaN"
+ table_text = "(0019, 1012) [TablePositionOrigin]"
+
+ for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
+ dMRI_dcm_txt, tfMRI_dcm_txt]:
+
+ if os.path.exists(file_name):
+ with open(file_name, 'rt', encoding="utf-8") as f:
+ cont = f.readlines()
+ for x in cont:
+ if x.startswith(table_text):
+ table = x.replace(table_text, "")
+ table = table.strip().replace("SL: ", "").strip()
+ table = table.split()[2].replace("]","")
+ break
+ if table != "NaN":
+ break
+
+ with open(IDP_subject_COG_table, 'wt', encoding="utf-8") as f:
+ f.write(f'{COG} {table}\n')
diff --git a/bip/pipelines/IDPs_gen/IDP_subject_centre.py b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
index 1bcbbc6181508c23e5a166feb68aa80ccbb72cf8..fb570d3272575a282bdc1f944acc7276e30f4ca0 100755
--- a/bip/pipelines/IDPs_gen/IDP_subject_centre.py
+++ b/bip/pipelines/IDPs_gen/IDP_subject_centre.py
@@ -27,31 +27,36 @@ def run(ctx,
tfMRI_dcm_txt: Ref,
logs_dir: Ref,
IDP_subject_centre: Out):
+
+ with redirect_logging('IDP_subject_centre', outdir=logs_dir):
- line = ""
+ line = ""
+ address_text = "(0008, 0081) Institution Address"
- for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
- dMRI_dcm_txt, tfMRI_dcm_txt]:
+ for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt,
+ dMRI_dcm_txt, tfMRI_dcm_txt]:
- if os.path.exists(file_name):
- with open(file_name, 'rt', encoding="utf-8") as f:
- cont = f.readlines()
- for x in cont:
- if x.startswith("(0008, 0081) Institution Address"):
- line = x.replace("(0008, 0081) Institution Address", "")
- line = line.strip().replace("ST: ", "").strip()
- line = line.replace("'","").replace(",","__").replace(" ","_")
- break
- if line != "":
- break
+ if os.path.exists(file_name):
+ with open(file_name, 'rt', encoding="utf-8") as f:
+ cont = f.readlines()
- if line != "":
- # TODO: Allow users to change the file with the sites
- with open(ctx.get_data("IDPs/sites_UKBB.json"), "r", encoding="utf-8") as f:
- sites = json.load(f)
+ for x in cont:
+ if x.startswith(address_text):
+ line = x.replace(address_text, "")
+ line = line.strip().replace("ST: ", "").strip()
+ line = line.replace("'","").replace(",","__")
+ line = line.replace(" ","_")
+ break
+ if line != "":
+ break
- centre = sites[line]
+ if line != "":
+ # TODO: Allow users to change the file with the sites
+ json_name = "IDPs/sites_UKBB.json"
+ with open(ctx.get_data(json_name), "r", encoding="utf-8") as f:
+ sites = json.load(f)
+
+ centre = sites[line]
- with redirect_logging('IDP_subject_centre', outdir=logs_dir):
with open(IDP_subject_centre, 'wt', encoding="utf-8") as f:
f.write(f'{centre}\n')
diff --git a/bip/pipelines/IDPs_gen/IDPs_gen.py b/bip/pipelines/IDPs_gen/IDPs_gen.py
index 49bd3447a7cf2decf6f4f9380c4b16f69e813a1f..89f15a6df3a1aaa07198dc202f574112b675af52 100755
--- a/bip/pipelines/IDPs_gen/IDPs_gen.py
+++ b/bip/pipelines/IDPs_gen/IDPs_gen.py
@@ -10,9 +10,13 @@
#
import logging
-from bip.utils.log_utils import redirect_logging
-from bip.pipelines.IDPs_gen import IDP_subject_ID
-from bip.pipelines.IDPs_gen import IDP_subject_centre
+from bip.utils.log_utils import redirect_logging
+from bip.pipelines.IDPs_gen import IDP_subject_ID, IDP_subject_centre
+from bip.pipelines.IDPs_gen import IDP_subject_COG_table
+from bip.pipelines.IDPs_gen import IDP_T1_FIRST_vols, IDP_T1_SIENAX
+from bip.pipelines.IDPs_gen import IDP_T2_FLAIR_WMH
+from bip.pipelines.IDPs_gen import IDP_func_head_motion, IDP_func_TSNR
+from bip.pipelines.IDPs_gen import IDP_diff_eddy_outliers, IDP_diff_TBSS
log = logging.getLogger(__name__)
@@ -24,9 +28,50 @@ def add_to_pipeline(ctx, pipe, tree, targets):
with redirect_logging('pipe_IDPs_gen', outdir=logs_dir):
pipe(IDP_subject_ID.run,
- submit=dict(jobtime=200, name="BIP_IDPs_subject_ID_" + subj),
+ submit=dict(jobtime=200, name="BIP_IDP_subject_ID_" + subj),
kwargs={'ctx' : ctx})
targets.append('IDP_subject_ID')
+
+ pipe(IDP_func_head_motion.run,
+ submit=dict(jobtime=200, name="BIP_IDP_func_head_motion_" + subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_func_head_motion')
+
+ pipe(IDP_func_TSNR.run,
+ submit=dict(jobtime=200, name="BIP_IDP_func_TSNR_" + subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_func_TSNR')
+
+ pipe(IDP_diff_eddy_outliers.run,
+ submit=dict(jobtime=200, name="BIP_IDP_diff_eddy_outliers_"+ subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_diff_eddy_outliers')
+
+ pipe(IDP_T1_SIENAX.run,
+ submit=dict(jobtime=200, name="BIP_IDP_T1_SIENAX_" + subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_T1_SIENAX')
+
+ pipe(IDP_T1_FIRST_vols.run,
+ submit=dict(jobtime=200, name="BIP_IDP_T1_FIRST_vols_" + subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_T1_FIRST_vols')
+
+ pipe(IDP_T2_FLAIR_WMH.run,
+ submit=dict(jobtime=200, name="BIP_IDP_T2_FLAIR_WMH_" + subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_T2_FLAIR_WMH')
+
+ pipe(IDP_diff_TBSS.run,
+ submit=dict(jobtime=200, name="BIP_IDP_diff_TBSS_"+ subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_diff_TBSS')
+
+ pipe(IDP_subject_COG_table.run,
+ submit=dict(jobtime=200, name="BIP_IDP_subject_COG_table_" + subj),
+ kwargs={'ctx' : ctx})
+ targets.append('IDP_subject_COG_table')
+
pipe(IDP_subject_centre.run,
submit=dict(jobtime=200, name="BIP_IDP_subject_centre_" + subj),
kwargs={'ctx' : ctx})
diff --git a/bip/pipelines/dMRI_diff/diff_eddy.py b/bip/pipelines/dMRI_diff/diff_eddy.py
index ae947ca1800d963fc14aafbbc39233a88ffa0963..9baeee980e10e7fba8bcd15b018f94f4356a8ea7 100755
--- a/bip/pipelines/dMRI_diff/diff_eddy.py
+++ b/bip/pipelines/dMRI_diff/diff_eddy.py
@@ -39,7 +39,8 @@ def run(ctx,
eddy_bvals: Out,
eddy_bvecs: Out,
eddy_index: Out,
- eddy_data: Out):
+ eddy_data: Out,
+ eddy_outlier_report: Out):
with redirect_logging('diff_eddy', outdir=logs_dir):
diff --git a/bip/pipelines/dMRI_diff/diff_tbss.py b/bip/pipelines/dMRI_diff/diff_tbss.py
index 04c5482733918b312f5ced61e15d21b37eb35eaf..82dfce2270664e1eeb1faf53517f163ad1097dd0 100755
--- a/bip/pipelines/dMRI_diff/diff_tbss.py
+++ b/bip/pipelines/dMRI_diff/diff_tbss.py
@@ -131,9 +131,11 @@ def run(ctx,
wrappers.fslmaths(TBSS_mean_FA_skeleton).thr(thresh).bin().run(TBSS_mean_FA_skeleton_mask)
wrappers.fslmaths(TBSS_all_FA).mas(TBSS_mean_FA_skeleton_mask).run(TBSS_all_FA_skeletonised)
- atlas = ctx.get_atlas('JHU/JHU-ICBM-labels-1mm.nii.gz')
+ atlas = ctx.get_data('/dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz')
mean = wrappers.fslstats(TBSS_all_FA_skeletonised, K=atlas).M.run()
+ # TODO: Funnily enough, this atlas has changed over time, so for v2
+ # of the pipeline, we will need to change the IDPs
with open(JHUrois_FA, 'wt', encoding="utf-8") as f:
f.write(f'{mean}')
diff --git a/bip/pipelines/fMRI_rest/rfMRI_melodic.py b/bip/pipelines/fMRI_rest/rfMRI_melodic.py
index 6e6c3b9c4aaa3dc407a01a5cdc387590321e40f8..9c048f9f9fd69444725038452e561d4cd41aa026 100755
--- a/bip/pipelines/fMRI_rest/rfMRI_melodic.py
+++ b/bip/pipelines/fMRI_rest/rfMRI_melodic.py
@@ -29,7 +29,8 @@ def run(ctx,
rfMRI_standard: Out,
filtered_func_data: Out,
melodic_mix: Out,
- rfMRI_mc_parameters: Out):
+ rfMRI_mc_parameters: Out,
+ rfMRI_mc_rel_mean: Out):
with redirect_logging('rfMRI_melodic', outdir=logs_dir):
wrappers.feat(fsf=rfMRI_fsf)
diff --git a/bip/pipelines/fMRI_task/tfMRI_feat.py b/bip/pipelines/fMRI_task/tfMRI_feat.py
index 0c58b8371d4eab3a9bb3bb39ec8e93db70023573..1a9a26cb0ca01322ca413356147a533e6e76bc3c 100755
--- a/bip/pipelines/fMRI_task/tfMRI_feat.py
+++ b/bip/pipelines/fMRI_task/tfMRI_feat.py
@@ -18,9 +18,10 @@ from pipe_tree import In, Out, Ref
log = logging.getLogger(__name__)
def run(ctx,
- tfMRI_fsf: In,
- logs_dir: Ref,
- tfMRI_feat: Out):
+ tfMRI_fsf: In,
+ logs_dir: Ref,
+ tfMRI_feat: Out,
+ tfMRI_filtered_func_data: Out):
with redirect_logging('tfMRI_feat', outdir=logs_dir):
wrappers.feat(fsf=tfMRI_fsf)