do resting state data processing without FreeSurfer

[robilobi]

Hi all, does anybody know if it is possible to use the BI-pipeline, without referring to a Freesurfer data structure?Also, by using anatonmical data that were segemented in other software? Thank you! roberta

[akeshavan]

Hello! You could try workflow 8b5b5 (type bips -c 8b5b5 in the command line) and make sure to choose the FSL FAST segmentation instead of Atropos (it isn't implemented yet).

[robilobi]

Hi, thank you! I run the freesurfer preprocessing on the T1 data, so that I can use the bips -c 7757. Still, I get this error message related to the PCA at the CompCor node (see below).

Do you maybe have a suggestion on what I should look at?

Thank you! Roberta

sauer:/SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/fsdir/crashdir$ nipype_display_crash crash-20141118-093631-bianco-binarize.a0.pklz False False File: crash-20141118-093631-bianco-binarize.a0.pklz Node: preproc.preproc.CompCor.extract_csf_mask.binarize.a0 Working directory: /SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/fsdir/work/preproc/preproc/CompCor/extract_csf_mask/_subject_id_VP24/binarize

Node inputs:

abs = args = bin_col_num = bin_val = bin_val_not = binary_file = count_file = dilate = environ = {'SUBJECTS_DIR': '/afs/cbs.mpg.de/software/freesurfer/5.3.0/amd64/2.15/subjects'} erode = 2 erode2d = frame_no = ignore_exception = False in_file = invert = mask_file = mask_thresh = match = [4, 5, 14, 15, 24, 31, 43, 44, 63] max = merge_file = min = out_type = rmax = rmin = subjects_dir = /afs/cbs.mpg.de/software/freesurfer/5.3.0/amd64/2.15/subjects terminal_output = stream ventricles = wm = wm_ven_csf = True zero_edges = zero_slice_edge =

Traceback: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 38, in run node.run(updatehash=updatehash) File "/usr/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1424, in run self._run_interface() File "/usr/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1534, in _run_interface self._result = self._run_command(execute) File "/usr/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1650, in _run_command cmd = self._interface.cmdline File "/usr/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1366, in cmdline self._check_mandatory_inputs() File "/usr/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 903, in _check_mandatory_inputs raise ValueError(msg) ValueError: Binarize requires a value for input 'in_file'. For a list of required inputs, see Binarize.help()

[akeshavan]

Is the subject_id you used to grab the data the exact same name as the freesurfer subject_id in your SUBJECTS_DIR?

[robilobi]

Yes it is. All the directories are correct, what else could be the problem?

[robilobi]

Please, have a look at the .json file that I set. The data structure looks like that: SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/freesurfer/VP01 /SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/VP01/functional/rest/resting.nii

{ "SliceOrder": [ 0, 615, 1230, 438, 1053, 263, 878, 88, 703, 1318, 528, 1140, 350, 965, 175, 790, 0, 615, 1230, 438, 1053, 263, 878, 88, 703, 1318, 528, 1140, 350, 965, 175, 790, 0, 615, 1230, 438, 1053, 263, 878, 88, 703, 1318, 528, 1140, 350, 965, 175, 790, 0, 615, 1230, 438, 1053, 263, 878, 88, 703, 1318, 528, 1140, 350, 965, 175, 790 ], "TE_diff": 0.0, "TR": 1400.0, "advanced_script": "", "base_dir": "/SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA", "compcor_select": [ true, true ], "crash_dir": "/SCR/EXPERIMENTS/PIAMOtop/TPIAMONET/DATA/REST/crashdir", "debug": false, "desc": "\nfMRI preprocessing workflow\n===========================\n\nThis workflow can be used to preprocess resting-state and task fMRI. \n\n.. admonition: For Task fMRI\n\n * Do not regress anything from the timeseries (Nuisance Filter tab should have nothing selected)\n * The lowpass frequency of the bandpass filter tab should be set to -1\n\nFor a tutorial on this workflow, click here.\n\n.. _here: ../../Preprocessing_Resting_State_DataTutorial.html\n\nClick for more documentation.\n\n.. _Click: ../../interfaces/generated/bips.workflows.workflow2.html\n\n", "do_despike": false, "do_detrend": true, "do_scaling": true, "do_slicetiming": true, "do_whitening": false, "do_zscore": false, "echospacing": 0.0, "field_dir": "", "filtering_algorithm": "fsl", "func_template": "%s/functional/rest/resting.nii", "fwhm": [ 6.0 ], "highpass_freq": 0.01, "hpcutoff": 128.0, "loops": [ 5 ], "lowpass_freq": 0.1, "magnitude_template": "%s/magnitude.nii.gz", "motion_correct_node": "nipy", "norm_thresh": 300.0, "num_noise_components": 6, "order": "motion_slicetime", "phase_template": "%s/phase.nii.gz", "plugin": "PBS", "plugin_args": {}, "reg_params": [ true, true, true, false, true, false ], "regress_before_PCA": true, "run_datagrabber_without_submitting": true, "run_using_plugin": false, "save_script_only": false, "sigma": 2, "sink_dir": "/SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/REST/results", "smooth_type": "isotropic", "speedup": [ 5 ], "subjects": [ "VP01" ], "surf_dir": "/SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/freesurfer", "surface_fwhm": 0.0, "test_mode": false, "timeout": 14.0, "timepoints_to_remove": 5, "update_hash": false, "use_advanced_options": false, "use_fieldmap": false, "use_metadata": false, "uuid": "7757e3168af611e1b9d5001e4fb1404c", "working_dir": "/SCR/EXPERIMENTS/PIAMOtop/TPIAMO_NET/DATA/REST/work", "z_thresh": 3.0 }