cli.afni_task_subj and cli.afni_resting_subj working

emu-project · May 17, 2022 · 35d48ee · 35d48ee
1 parent 033d6fd
commit 35d48ee
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Showing 8 changed files with 12 additions and 10 deletions.
diff --git a/func_processing/cli/afni_resting_group.py b/func_processing/cli/afni_resting_group.py
@@ -11,9 +11,9 @@
 Final output is:
     <proj_dir>/derivatives/afni/analyses/FINAL_RS-<seed>*
 
-Examples
+Example
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runRSGroup \
     --output=${code_dir}/logs/runAfniRestGroup_log \
     --mem-per-cpu=4000 \

diff --git a/func_processing/cli/afni_resting_subj.py b/func_processing/cli/afni_resting_subj.py
@@ -19,17 +19,18 @@
 Seed-based regression matrix is:
     decon_task-rest_<anaticor>_<seed>_ztrans+tlrc.
 
-Examples
+Example
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runAfniRest \
     --output=${code_dir}/logs/runAfniRest_log \
     --mem-per-cpu=4000 \
     --partition=IB_44C_512G \
     --account=iacc_madlab \
     --qos=pq_madlab \
     ${code_dir}/cli/afni_resting_subj.py \
-    -c $code_dir
+    -c $code_dir \
+    -j ${code_dir}/examples/rs_seed.json
 """
 
 

diff --git a/func_processing/cli/afni_task_group.py b/func_processing/cli/afni_task_group.py
@@ -10,7 +10,7 @@
 
 Example
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runTaskGroup \
     --output=${code_dir}/logs/runAfniTaskGroup_log \
     --mem-per-cpu=4000 \

diff --git a/func_processing/cli/afni_task_subj.py b/func_processing/cli/afni_task_subj.py
@@ -19,7 +19,7 @@
 
 Example
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runAfniTask \
     --output=${code_dir}/logs/runAfniTask_log \
     --mem-per-cpu=4000 \

diff --git a/func_processing/cli/ashs.py b/func_processing/cli/ashs.py
@@ -13,7 +13,7 @@
 
 Example
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runAshs \
     --output=${code_dir}/logs/runAshs_log \
     --mem-per-cpu=4000 \

diff --git a/func_processing/cli/fmriprep.py b/func_processing/cli/fmriprep.py
@@ -14,7 +14,7 @@
 
 Example
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runPrep \
     --output=${code_dir}/logs/runPrep_log \
     --mem-per-cpu=4000 \

diff --git a/func_processing/cli/reface.py b/func_processing/cli/reface.py
@@ -6,7 +6,7 @@
 
 Examples
 --------
-code_dir="$(pwd)"/func_processing
+code_dir=/home/nmuncy/compute/func_processing/func_processing
 sbatch --job-name=runReface \
     --output=${code_dir}/logs/runReface_log \
     --mem-per-cpu=4000 \

diff --git a/func_processing/examples/rs_seed.json b/func_processing/examples/rs_seed.json
@@ -0,0 +1 @@
+{"rPCC": "5 -55 25"}