|
229 | 229 | "cell_type": "code",
|
230 | 230 | "execution_count": null,
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231 | 231 | "metadata": {},
|
232 |
| - "outputs": [ |
233 |
| - { |
234 |
| - "name": "stdout", |
235 |
| - "output_type": "stream", |
236 |
| - "text": [ |
237 |
| - "170904-06:02:02,387 workflow INFO:\n", |
238 |
| - "\t Executing node datagrabber in dir: /tmp/tmpiwew6ysu/datagrabber\n" |
239 |
| - ] |
240 |
| - }, |
241 |
| - { |
242 |
| - "data": { |
243 |
| - "text/plain": [ |
244 |
| - "\n", |
245 |
| - "anat = /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\n", |
246 |
| - "func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz" |
247 |
| - ] |
248 |
| - }, |
249 |
| - "execution_count": null, |
250 |
| - "metadata": {}, |
251 |
| - "output_type": "execute_result" |
252 |
| - } |
253 |
| - ], |
| 232 | + "outputs": [], |
254 | 233 | "source": [
|
255 | 234 | "dg.run().outputs"
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256 | 235 | ]
|
|
313 | 292 | "cell_type": "code",
|
314 | 293 | "execution_count": null,
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315 | 294 | "metadata": {},
|
316 |
| - "outputs": [ |
317 |
| - { |
318 |
| - "name": "stdout", |
319 |
| - "output_type": "stream", |
320 |
| - "text": [ |
321 |
| - "170904-06:02:02,435 workflow INFO:\n", |
322 |
| - "\t Executing node selectfiles in dir: /tmp/tmpd3odxyze/selectfiles\n" |
323 |
| - ] |
324 |
| - }, |
325 |
| - { |
326 |
| - "data": { |
327 |
| - "text/plain": [ |
328 |
| - "\n", |
329 |
| - "anat = /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\n", |
330 |
| - "func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz" |
331 |
| - ] |
332 |
| - }, |
333 |
| - "execution_count": null, |
334 |
| - "metadata": {}, |
335 |
| - "output_type": "execute_result" |
336 |
| - } |
337 |
| - ], |
| 295 | + "outputs": [], |
338 | 296 | "source": [
|
339 | 297 | "sf.run().outputs"
|
340 | 298 | ]
|
|
356 | 314 | "cell_type": "code",
|
357 | 315 | "execution_count": null,
|
358 | 316 | "metadata": {},
|
359 |
| - "outputs": [ |
360 |
| - { |
361 |
| - "name": "stdout", |
362 |
| - "output_type": "stream", |
363 |
| - "text": [ |
364 |
| - "170904-06:02:02,458 workflow INFO:\n", |
365 |
| - "\t Executing node selectfiles in dir: /tmp/tmp53bxb6rj/selectfiles\n" |
366 |
| - ] |
367 |
| - }, |
368 |
| - { |
369 |
| - "data": { |
370 |
| - "text/plain": [ |
371 |
| - "\n", |
372 |
| - "anat = ['/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz', '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz']" |
373 |
| - ] |
374 |
| - }, |
375 |
| - "execution_count": null, |
376 |
| - "metadata": {}, |
377 |
| - "output_type": "execute_result" |
378 |
| - } |
379 |
| - ], |
| 317 | + "outputs": [], |
380 | 318 | "source": [
|
381 | 319 | "from nipype import SelectFiles, Node\n",
|
382 | 320 | "from os.path import abspath as opap\n",
|
|
488 | 426 | "cell_type": "code",
|
489 | 427 | "execution_count": null,
|
490 | 428 | "metadata": {},
|
491 |
| - "outputs": [ |
492 |
| - { |
493 |
| - "name": "stdout", |
494 |
| - "output_type": "stream", |
495 |
| - "text": [ |
496 |
| - "170904-06:04:52,28 workflow INFO:\n", |
497 |
| - "\t Executing node fssource in dir: /tmp/tmpisu77m7r/fssource\n" |
498 |
| - ] |
499 |
| - } |
500 |
| - ], |
| 429 | + "outputs": [], |
501 | 430 | "source": [
|
502 | 431 | "fssource.inputs.subject_id = 'sub-01'\n",
|
503 | 432 | "result = fssource.run() "
|
|
514 | 443 | "cell_type": "code",
|
515 | 444 | "execution_count": null,
|
516 | 445 | "metadata": {},
|
517 |
| - "outputs": [ |
518 |
| - { |
519 |
| - "name": "stdout", |
520 |
| - "output_type": "stream", |
521 |
| - "text": [ |
522 |
| - "aparc_aseg: ['/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.a2009s+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.dktatlas+aseg.mgz']\n", |
523 |
| - "\n", |
524 |
| - "brainmask: /data/ds000114/derivatives/freesurfer/sub-01/mri/brainmask.mgz\n", |
525 |
| - "\n", |
526 |
| - "inflated: ['/data/ds000114/derivatives/freesurfer/sub-01/surf/rh.inflated', '/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated']\n", |
527 |
| - "\n" |
528 |
| - ] |
529 |
| - } |
530 |
| - ], |
| 446 | + "outputs": [], |
531 | 447 | "source": [
|
532 | 448 | "print('aparc_aseg: %s\\n' % result.outputs.aparc_aseg)\n",
|
533 | 449 | "print('brainmask: %s\\n' % result.outputs.brainmask)\n",
|
|
545 | 461 | "cell_type": "code",
|
546 | 462 | "execution_count": null,
|
547 | 463 | "metadata": {},
|
548 |
| - "outputs": [ |
549 |
| - { |
550 |
| - "name": "stdout", |
551 |
| - "output_type": "stream", |
552 |
| - "text": [ |
553 |
| - "170904-06:04:54,346 workflow INFO:\n", |
554 |
| - "\t Executing node fssource in dir: /tmp/tmpisu77m7r/fssource\n" |
555 |
| - ] |
556 |
| - } |
557 |
| - ], |
| 464 | + "outputs": [], |
558 | 465 | "source": [
|
559 | 466 | "fssource.inputs.hemi = 'lh'\n",
|
560 | 467 | "result = fssource.run()"
|
|
571 | 478 | "cell_type": "code",
|
572 | 479 | "execution_count": null,
|
573 | 480 | "metadata": {},
|
574 |
| - "outputs": [ |
575 |
| - { |
576 |
| - "data": { |
577 |
| - "text/plain": [ |
578 |
| - "'/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated'" |
579 |
| - ] |
580 |
| - }, |
581 |
| - "execution_count": null, |
582 |
| - "metadata": {}, |
583 |
| - "output_type": "execute_result" |
584 |
| - } |
585 |
| - ], |
| 481 | + "outputs": [], |
586 | 482 | "source": [
|
587 | 483 | "result.outputs.inflated"
|
588 | 484 | ]
|
|
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