-
Notifications
You must be signed in to change notification settings - Fork 0
/
grmpyProcessing
247 lines (116 loc) · 3.27 KB
/
grmpyProcessing
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
---
layout: default
title: GRMPY_822831 Image Processing Workflow
parent: Flywheel
nav_order: 6
has_toc: false
---
# GRMPY_822831 Image Processing Workflow
This is documentation of how GRMPY_822831 was processed on Flywheel. All files referenced in input can be found attached to the project.
## Steps Overview:
Each step is a flywheel gear that has been launched on each subject in the project.
1. Heudiconv
2. fMRIPREP
3. XCP - CBF
4. XCP - Resting State Functional
5. XCP - Task Functional
## Step 1: Heudiconv
**Gear Name:** Flywheel HeuDiConv (fw-heudiconv)
**Version:** 0.2.10_0.2.4
**Inputs:**
Heuristic: grmpy_heuristic_v4.py
**Gear Configuration:**
action: Curate
do_whole_project: false
dry_run: false
extended_bids: true
**Output:** None. This curates the project in BIDS.
**Note:** When Processing GRMPY_822831, heudiconv was run on each subject individually. This is why do_whole_project was set to false.
## Step 2: fMRIPREP
**Gear Name:** fMRIPREP: A Robust Preprocessing Pipeline for fMRI Data [fw-heudiconv]
**Version:** 0.3.2_20.0.5
**Inputs:** license.txt
**Gear Configuration:**
anat_only: false
aroma_melodic_dimensionality: -200
bold2t1w_dof: 6
cifti_output: None
dummy_scans: 0
dvars_spike_threshold: 1.5
fd_spike_threshold: 0.5
fmap_bspline: false
fmap_no_demean: false
force_bbr: false
force_no_bbr: false
force_syn: false
fs_no_reconall: false
longitudinal: false
low_mem: false
medial_surface_nan: false
no_submm_recon: false
no_track: false
output_spaces: MNI152NLin2009cAsym
return_all_components: false
save_intermediate_work: false
save_outputs: false
sge-cpu: 8
sge-ram: 64G
sge-short: false
singularity-debug: false
singularity-writable: false
skip_bids_validation: false
skull_strip_fixed_seed: false
skull_strip_template: OASIS30ANTs
sloppy_mode: false
t2s_coreg: false
timeout: 2
use_all_sessions: false
use_aroma: false
use_syn_sdc: false
**Output:**
An html report: filename.html.zip
Processed Output: fmriprep_filename.zip
Source Code: fmriprep_run.sh
## Step 3: XCP - CBF
**Gear Name:** XCPENGINE: pipeline for processing of structural and functional data.
**Version:** 0.0.1_1.00
**Inputs:**
fMRIPREP Output: fmriprep_filename.zip
Design File: cbf_scorescrub_basil_v3.dsn
ASL Nifti: asl_image.nii.gz
**Gear Configuration:**
analysis_type: cbf
**Output:**
Processed Output: xcpEngineouput_cbf.zip
Cohort File: cohortfile.csv
## Step 4: XCP - Resting State Functional
**Gear Name:** XCPENGINE: pipeline for processing of structural and functional data.
**Version:** 0.0.1_1.00
**Inputs:**
fMRIPREP Output: fmriprep_filename.zip
Design File: fc-36p_despike.dsn
**Gear Configuration:**
analysis type: func
analysis type: xcp
**Output:**
Processed Output: xcpEngineouput_xcp.zip
Cohort File: cohortfile.csv
## Step 5: XCP - Task Functional
**Gear Name:** XCPENGINE: pipeline for processing of structural and functional data.
**Version:** 0.0.1_1.00
**Inputs:**
fMRIPREP Output: fmriprep_filename.zip
Design File:
Zip of necessary files: taskfile.zip
*Note:* files within the .zip are:
0back.txt
1back.txt
2back.txt
inst.txt
task.json
**Gear Configuration:**
analysis type: task
analysis type: xcp
**Output:**
Processed Output: xcpEngineouput_xcp.zip
Cohort File: cohortfile.csv