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/TPIAMO_NET/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_Data_Tutorial.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
}