From e2964758b394ffc6399c21fd09256122d83b1f0f Mon Sep 17 00:00:00 2001 From: Michael Riedel Date: Mon, 29 Jun 2020 15:50:31 -0400 Subject: [PATCH] fixed some imports, finalized group-level workflow --- connectivity/interfaces.py | 2 +- connectivity/rs.py | 66 +- datasets/download_hcp.ipynb | 2136 +---------------- datasets/hcp1200.py | 1 + .../test_hcp1200_download-checkpoint.ipynb | 100 - .../test_rsfc_workflow-checkpoint.ipynb | 95 - 6 files changed, 47 insertions(+), 2353 deletions(-) delete mode 100644 tests/test_hcp1200_download/.ipynb_checkpoints/test_hcp1200_download-checkpoint.ipynb delete mode 100644 tests/test_rsfc/.ipynb_checkpoints/test_rsfc_workflow-checkpoint.ipynb diff --git a/connectivity/interfaces.py b/connectivity/interfaces.py index b9ff182..f1a57e3 100644 --- a/connectivity/interfaces.py +++ b/connectivity/interfaces.py @@ -7,7 +7,7 @@ Shamelessly taken from https://github.com/poldracklab/ds003-post-fMRIPrep-analysis/blob/master/interfaces.py """ from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec -from nipype.interfaces.base import traits, TraitedSpec +from nipype.interfaces.base import File, traits, TraitedSpec, isdefined class PtoZInputSpec(FSLCommandInputSpec): diff --git a/connectivity/rs.py b/connectivity/rs.py index 23c496e..ddee249 100644 --- a/connectivity/rs.py +++ b/connectivity/rs.py @@ -18,6 +18,11 @@ def pickfirst(files): return files +def calcres(smoothest_input): + resels = int(228453/smoothest_input) + return resels + + def rs_preprocess(in_file, fwhm, work_dir, output_dir): from nipype.workflows.fmri.fsl.preprocess import create_featreg_preproc @@ -183,18 +188,16 @@ def rs_grouplevel(copes, varcopes, output_dir, work_dir): from nipype.interfaces.fsl.model import MultipleRegressDesign from nipype.interfaces.fsl.model import FLAMEO from nipype.interfaces.fsl.model import SmoothEstimate - from interfaces import Cluster + from connectivity.interfaces import Cluster from nipype.interfaces.fsl.utils import Merge - from nipype.interfaces.fsl.Info import standard_image - from interfaces import PtoZ - - def calcres(smoothest_input): - resels = int(smoothest_input[0]/smoothest_input[1]) + from nipype.interfaces.fsl import Info + from connectivity.interfaces import PtoZ grplevelworkflow = pe.Workflow(name="grplevelworkflow") + grplevelworkflow.base_dir = work_dir merger = Merge() - merger.inputs.dimensions = 't' + merger.inputs.dimension = 't' merger.inputs.in_files = copes merger.inputs.merged_file = op.join(work_dir, 'cope.nii.gz') merger.run() @@ -203,27 +206,28 @@ def calcres(smoothest_input): merger.inputs.merged_file = op.join(work_dir, 'varcope.nii.gz') merger.run() - model = MultipleRegressDesign() + model = pe.Node(interface=MultipleRegressDesign(), name='model') model.inputs.contrasts = [['mean', 'T', ['roi'], [1]]] - model.intputs.regressors = dict(roi=np.ones(len(copes))) + model.inputs.regressors = dict(roi=np.ones(len(copes)).tolist()) flameo = pe.Node(interface=FLAMEO(), name='flameo') flameo.inputs.cope_file = op.join(work_dir, 'cope.nii.gz') flameo.inputs.var_cope_file = op.join(work_dir, 'varcope.nii.gz') flameo.inputs.run_mode = 'flame1' - flameo.inputs.mask = standard_image('MNI152_T1_2mm_brain_mask.nii.gz') + flameo.inputs.mask_file = Info.standard_image('MNI152_T1_2mm_brain_mask.nii.gz') - grplevelworkflow.connect(model, 'design_con', flameo, 'inputs.t_con_file') - grplevelworkflow.connect(model, 'design_grp', flameo, 'inputs.cov_split_file') - grplevelworkflow.connect(model, 'design_mat', flameo, 'inputs.design_file') + grplevelworkflow.connect(model, 'design_con', flameo, 't_con_file') + grplevelworkflow.connect(model, 'design_grp', flameo, 'cov_split_file') + grplevelworkflow.connect(model, 'design_mat', flameo, 'design_file') - smoothest = Node(SmoothEstimate(), name='smooth_estimate') + smoothest = pe.Node(SmoothEstimate(), name='smooth_estimate') grplevelworkflow.connect(flameo, 'zstats', smoothest, 'zstat_file') - smoothest.inputs.mask_file = mask_file + smoothest.inputs.mask_file = Info.standard_image('MNI152_T1_2mm_brain_mask.nii.gz') - cluster = Node(Cluster(), name='cluster') + cluster = pe.Node(Cluster(), name='cluster') + ptoz = pe.Node(PtoZ(), name='ptoz') grplevelworkflow.connect(smoothest, 'resels', cluster, 'resels') - grplevelworkflow.connect(smoothest, (['volume', 'resels'], calcres), ptoz, 'resels') + grplevelworkflow.connect(smoothest, ('resels', calcres), ptoz, 'resels') grplevelworkflow.connect(ptoz, 'zstat', cluster, 'threshold') cluster.inputs.connectivity = 26 cluster.inputs.out_threshold_file = True @@ -231,12 +235,23 @@ def calcres(smoothest_input): cluster.inputs.out_localmax_txt_file = True cluster.inputs.voxthresh = True - grplevelworkflow.connect(flame, 'zstats', cluster, 'in_file') + grplevelworkflow.connect(flameo, 'zstats', cluster, 'in_file') datasink = pe.Node(nio.DataSink(), name='sinker') datasink.inputs.base_directory = work_dir - grplevelworkflow.connect(flameo, 'outputs') + grplevelworkflow.connect(flameo, 'zstats', datasink, 'z') + grplevelworkflow.connect(cluster, 'threshold_file', datasink, 'z_thresh') + + grplevelworkflow.run() + + shutil.rmtree(op.join(work_dir, 'grplevelworkflow')) + #copy data to directory + shutil.copyfile(op.join(work_dir, 'z', 'zstat1.nii.gz'), op.join(output_dir, 'z.nii.gz')) + shutil.copyfile(op.join(work_dir, 'z_thresh', 'zstat1_threshold.nii.gz'), op.join(output_dir, 'z_level-voxel_corr-FWE.nii.gz')) + + shutil.rmtree(work_dir) + def rs_workflow(x=None, y=None, z=None, rs_data_dir=None, work_dir=None): @@ -292,11 +307,12 @@ def rs_workflow(x=None, y=None, z=None, rs_data_dir=None, work_dir=None): stat_files = sorted(glob(op.join(rs_data_dir, 'derivatives', coords_str, ppt, '*', '*.nii.gz'))) for tmp_stat_file in stat_files: shutil.copy(tmp_fn, output_dir) - - exit() - copes = sorted(glob(op.join(rs_data_dir, 'derivatives', roi_prefix, ppt, 'cope*.nii.gz'))) - varcopes = sorted(glob(op.join(rs_data_dir, 'derivatives', roi_prefix, ppt, 'varcope*.nii.gz'))) - output_dir = op.join(rs_data_dir, 'derivatives', roi_prefix) - nii_work_dir = op.join(work_dir, 'rsfc', roi_prefix) + copes = sorted(glob(op.join(rs_data_dir, 'derivatives', coords_str, '*', 'cope*.nii.gz'))) + varcopes = sorted(glob(op.join(rs_data_dir, 'derivatives', coords_str, '*', 'varcope*.nii.gz'))) + + output_dir = op.join(rs_data_dir, 'derivatives', coords_str) + nii_work_dir = op.join(work_dir, 'rsfc', coords_str) + if not op.isdir(nii_work_dir): + os.makedirs(nii_work_dir) rs_grouplevel(copes, varcopes, output_dir, nii_work_dir) diff --git a/datasets/download_hcp.ipynb b/datasets/download_hcp.ipynb index c5377bf..b99a086 100644 --- a/datasets/download_hcp.ipynb +++ b/datasets/download_hcp.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -17,7 +17,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -26,2137 +26,9 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[WARNING] realpath of PWD=/Users/miriedel/Desktop/GitHub/niconn/datasets is /Users/miriedel/Desktop/GitHub/niconn/datasets whenever os.getcwd()=/Users/miriedel/hcp1200. From now on will be returning os.getcwd(). Directory symlinks in the paths will be resolved \n", - "[INFO] Cloning dataset to \n", - "[INFO] Attempting to clone from http://datasets.datalad.org/hcp-openaccess to /Users/miriedel/hcp1200/hcp-openaccess \n", - "[INFO] Attempting to clone from http://datasets.datalad.org/hcp-openaccess/.git to /Users/miriedel/hcp1200/hcp-openaccess \n" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "847efcd6af6e4050b83ac91fad9794af", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Cloning (counting objects)', style=ProgressStyle(descript…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Cloning (compressing objects)', max=34.0, style=ProgressS…" - ] - }, - "metadata": {}, - 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] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Results/rfM .. lean.nii.gz', max=993816207.0, style=Progr…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Results/rfM .. lean.nii.gz', max=993323547.0, style=Progr…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Results/rfM .. lean.nii.gz', max=993612385.0, style=Progr…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Results/rfM .. lean.nii.gz', max=993018162.0, style=Progr…" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "s3 = boto3.resource('s3')\n", "\n", diff --git a/datasets/hcp1200.py b/datasets/hcp1200.py index eb015a8..866e899 100644 --- a/datasets/hcp1200.py +++ b/datasets/hcp1200.py @@ -34,6 +34,7 @@ def download_ppt(hcp_data_dir=None, pid=None): for tmp_pid in pid: install(op.join(hcp_data_dir, tmp_pid, 'MNINonLinear', 'Results')) tmp_rs_dir = sorted(glob(op.join(hcp_data_dir, tmp_pid, 'MNINonLinear', 'Results', 'rfMRI_*'))) + tmp_rs_dir = [x for x in tmp_rs_dir if '7T' not in x] for tmp_rs_run in tmp_rs_dir: tmp_rs_run = tmp_rs_run.split('/')[-1] get(op.join(hcp_data_dir, tmp_pid, 'MNINonLinear', 'Results', tmp_rs_run, '{0}_hp2000_clean.nii.gz'.format(tmp_rs_run))) diff --git a/tests/test_hcp1200_download/.ipynb_checkpoints/test_hcp1200_download-checkpoint.ipynb b/tests/test_hcp1200_download/.ipynb_checkpoints/test_hcp1200_download-checkpoint.ipynb deleted file mode 100644 index 238cab2..0000000 --- a/tests/test_hcp1200_download/.ipynb_checkpoints/test_hcp1200_download-checkpoint.ipynb +++ /dev/null @@ -1,100 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import sys\n", - "sys.path.append('/Users/miriedel/Desktop/GitHub/niconn/')\n", - "from datasets.hcp1200 import hcp1200_download" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "hcp_data_dir = '/Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download/hcp_data_dir'" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[WARNING] realpath of PWD=/Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download is /Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download whenever os.getcwd()=/Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download/hcp_data_dir. From now on will be returning os.getcwd(). Directory symlinks in the paths will be resolved \n", - "[INFO] Cloning dataset to \n", - "[INFO] Attempting to clone from http://datasets.datalad.org/hcp-openaccess to /Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download/hcp_data_dir/hcp-openaccess \n", - "[INFO] Attempting to clone from http://datasets.datalad.org/hcp-openaccess/.git to /Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download/hcp_data_dir/hcp-openaccess \n" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "a2437b91aa1e41df9723a644d0b9b3e6", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Cloning (counting objects)', style=ProgressStyle(descript…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "HBox(children=(FloatProgress(value=0.0, description='Cloning (compressing objects)', max=34.0, style=ProgressS…" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[INFO] Completed clone attempts for \n" - ] - } - ], - "source": [ - "hcp1200_download(hcp_data_dir=hcp_data_dir)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.1" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/tests/test_rsfc/.ipynb_checkpoints/test_rsfc_workflow-checkpoint.ipynb b/tests/test_rsfc/.ipynb_checkpoints/test_rsfc_workflow-checkpoint.ipynb deleted file mode 100644 index fd80b63..0000000 --- a/tests/test_rsfc/.ipynb_checkpoints/test_rsfc_workflow-checkpoint.ipynb +++ /dev/null @@ -1,95 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "200623-13:15:52,490 nipype.utils INFO:\n", - "\t Running nipype version 1.4.2 (latest: 1.5.0)\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/dicom/__init__.py:53: UserWarning: \n", - "This code is using an older version of pydicom, which is no longer \n", - "maintained as of Jan 2017. You can access the new pydicom features and API \n", - "by installing `pydicom` from PyPI.\n", - "See 'Transitioning to pydicom 1.x' section at pydicom.readthedocs.org \n", - "for more information.\n", - "\n", - " warnings.warn(msg)\n" - ] - } - ], - "source": [ - "import sys\n", - "import os\n", - "sys.path.append('/Users/miriedel/Desktop/GitHub/niconn/')\n", - "from connectivity.rs import rs_download_ppt" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "rs_data_dir = '/Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download/hcp_data_dir/HCP1200'\n", - "os.chdir(rs_data_dir)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[WARNING] realpath of PWD=/Users/miriedel/Desktop/GitHub/niconn/tests/test_rsfc is /Users/miriedel/Desktop/GitHub/niconn/tests/test_rsfc whenever os.getcwd()=/Users/miriedel/Desktop/GitHub/niconn/tests/test_hcp1200_download/hcp_data_dir. From now on will be returning os.getcwd(). Directory symlinks in the paths will be resolved \n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "395251\n", - "ok\n" - ] - } - ], - "source": [ - "rs_download_ppt(rs_data_dir=rs_data_dir, n_ppt=1)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.1" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -}