Hi,
I’ve running preprocess_bold function on my previously hcp preprocessed data. I’ve followed the steps reported here: oriadev / qunex / wiki / UsageDocs / BOLDPreprocessing — Bitbucket
During the procedure the following message is printed:
===> Final report for command preprocess_bold
... 06B ---> bolds: 1 ready [1], 0 not ready [], 0 already processed [], 1 ran ok [1], 0 failed [], 0 skipped []
===> Successful completion of all tasks
but after that the following message appear:
Running external command: octave -q --no-init-file --eval "try fc_preprocess('/home/admin01/qunex/output/ruminanti_P2/sessions/06B', 1, 0, 'shrcl', 'm,V,WM,WB', [], '', 0.800000, '', '', true, '.dtseries.nii', 'radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme', 'hipass=linear|regress=spline|lopass=linear', 'boldname=bold|surface_smooth=2.000000|volume_smooth=2.000000|voxel_smooth=1.000000|hipass_filter=0.008000|lopass_filter=0.090000|omp_threads=0|framework_path=|wb_command_path=|smooth_mask=nonzero|dilate_mask=/opt/qunex/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz|glm_matrix=both|glm_residuals=save|glm_name=|bold_tail=_Atlas|ref_bold_tail=|bold_variant=|img_suffix='); catch ME, general_report_crash(ME); exit(1), end; exit"
You can follow command's progress in:
/home/admin01/qunex/output/ruminanti_P2/processing/logs/comlogs/tmp_preprocess_bold_B1_06B_2022-09-01_09.44.43.870881.log
Looking at the log folder, the log file (reported below) don’t mention any failure. So I don’t understand if the preproc has been completed correctly or if there’s some error I’m missing.
I report the complete prompt log below:
Generated by QuNex
------------------------------------------------------------------------
Version: 0.93.6
User: root
System: 317be48ce35c
OS: RedHat Linux #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSE.md' which is a part of the QuNex Suite source code package:
https://bitbucket.org/oriadev/qunex/src/master/LICENSE.md
---> Setting up Octave
........................ Running QuNex v0.93.6 ........................
--- Full QuNex call for command: preprocess_bold
gmri preprocess_bold --sessionsfolder="/home/admin01/qunex/output/ruminanti_P2/sessions" --overwrite="yes" --modality="BOLD" --boldsuffix="Atlas" --bolds="all" --sessions="/home/admin01/qunex/output/ruminanti_P2/processing/batch_hcp8.txt"
---------------------------------------------------------
WARNING: Use of parameters with changed name(s)!
The following parameters have new names:
... hcp_Pipeline is now hcp_pipeline!
Please correct the listed parameter names in command line or batch file!
WARNING: Use of deprecated parameter value(s)!
The following parameter values have changed:
... original (hcp_filename) is now userdefined!
Please correct the listed parameter values in command line or batch file!
WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '_Atlas'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '_Atlas'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.93.6 on 2022-09-01_09.44.43.836922
#
=================================================================
gmri preprocess_bold \
--sessionsfolder="/home/admin01/qunex/output/ruminanti_P2/sessions" \
--overwrite="yes" \
--modality="BOLD" \
--boldsuffix="Atlas" \
--bolds="all" \
--sessions="/home/admin01/qunex/output/ruminanti_P2/processing/batch_hcp8.txt" \
=================================================================
Starting multiprocessing sessions in /home/admin01/qunex/output/ruminanti_P2/processing/batch_hcp8.txt with a pool of 16 concurrent processes
---- Running local
Adding processing of session 06B to the pool at Thursday, 01. September 2022 09:44:43
---------------------------------------------------------
Session id: 06B
[started on Thursday, 01. September 2022 09:44:43]
Preprocessing all BOLD files as specified in --bolds.
Files in 'images/functional will be processed.
Running Preprocessing bold runs ...
Processing 1 BOLDs in parallel
Working on: bold1 ...
... checking for data
... movement data present
... bold statistics data present
... bold scrubbing data present
... bold nuisance signal data present
... bold data present
running matlab/octave fc_preprocess on /home/admin01/qunex/output/ruminanti_P2/sessions/06B/images/functional bold 1
---> preprocess_bold test file [bold1_Atlas_s_hpss_res-mVWMWB_lpss.dtseries.nii] present
---> logfile: /home/admin01/qunex/output/ruminanti_P2/processing/logs/comlogs/done_preprocess_bold_B1_06B_2022-09-01_09.44.43.870881.log
Bold preprocessing completed on Thursday, 01. September 2022 09:51:35
---------------------------------------------------------
===> Final report for command preprocess_bold
... 06B ---> bolds: 1 ready [1], 0 not ready [], 0 already processed [], 1 ran ok [1], 0 failed [], 0 skipped []
===> Successful completion of all tasks
Running external command: octave -q --no-init-file --eval "try fc_preprocess('/home/admin01/qunex/output/ruminanti_P2/sessions/06B', 1, 0, 'shrcl', 'm,V,WM,WB', [], '', 0.800000, '', '', true, '.dtseries.nii', 'radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme', 'hipass=linear|regress=spline|lopass=linear', 'boldname=bold|surface_smooth=2.000000|volume_smooth=2.000000|voxel_smooth=1.000000|hipass_filter=0.008000|lopass_filter=0.090000|omp_threads=0|framework_path=|wb_command_path=|smooth_mask=nonzero|dilate_mask=/opt/qunex/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz|glm_matrix=both|glm_residuals=save|glm_name=|bold_tail=_Atlas|ref_bold_tail=|bold_variant=|img_suffix='); catch ME, general_report_crash(ME); exit(1), end; exit"
You can follow command's progress in:
/home/admin01/qunex/output/ruminanti_P2/processing/logs/comlogs/tmp_preprocess_bold_B1_06B_2022-09-01_09.44.43.870881.log
------------------------------------------------------------
log file:
# Generated by QuNex 0.93.6 on 2022-09-01_10.08.49.240930
#
------------------------------------------------------------
Running external command via QuNex:
octave -q --no-init-file --eval "try fc_preprocess('/home/admin01/qunex/output/ruminanti_P2/sessions/06A', 1, 0, 'shrcl', 'm,V,WM,WB', [], '', 0.800000, '', '', true, '.dtseries.nii', 'radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme', 'hipass=linear|regress=spline|lopass=linear', 'boldname=bold|surface_smooth=2.000000|volume_smooth=2.000000|voxel_smooth=1.000000|hipass_filter=0.008000|lopass_filter=0.090000|omp_threads=0|framework_path=|wb_command_path=|smooth_mask=nonzero|dilate_mask=/opt/qunex/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz|glm_matrix=both|glm_residuals=save|glm_name=|bold_tail=_Atlas|ref_bold_tail=|bold_variant=|img_suffix='); catch ME, general_report_crash(ME); exit(1), end; exit"
Test file:
/home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s_hpss_res-mVWMWB_lpss.dtseries.nii
------------------------------------------------------------
Running preproces script v0.9.17 [.dtseries.nii]
--------------------------------
Parameters:
---------------
sessionf: /home/admin01/qunex/output/ruminanti_P2/sessions/06A
bold: 1
omit: 0
doIt: shrcl
rgss: m,V,WM,WB
task: [0 0]
efile:
TR: 0.80
eventrstring:
variant:
overwrite: 1
tail: .dtseries.nii
scrub: radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme
ignores: hipass=linear|regress=spline|lopass=linear
options: boldname=bold|surface_smooth=2.000000|volume_smooth=2.000000|voxel_smooth=1.000000|hipass_filter=0.008000|lopass_filter=0.090000|omp_threads=0|framework_path=|wb_command_path=|smooth_mask=nonzero|dilate_mask=/opt/qunex/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz|glm_matrix=both|glm_residuals=save|glm_name=|bold_tail=_Atlas|ref_bold_tail=|bold_variant=|img_suffix=
Options used:
----------------
boldname: bold
surface_smooth: 2
volume_smooth: 2
voxel_smooth: 1
lopass_filter: 0.09
hipass_filter: 0.008
framework_path:
wb_command_path:
omp_threads: 0
smooth_mask: nonzero
dilate_mask: /opt/qunex/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz
glm_matrix: both
glm_residuals: save
glm_name:
bold_tail: _Atlas
ref_bold_tail:
bold_variant:
img_suffix:
---> removing old files:
... /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s.dtseries.nii
... /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s_hpss.dtseries.nii
Smoothing /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas.dtseries.nii
---> running wb_command -cifti-smoothing
... smoothing ... done!
High-pass filtering /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s.dtseries.nii
---> reading /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s.dtseries.nii ... done!
===> Temporal filtering (15/10/22)
---> triming: 0 on start, 0 on end
---> remaining bad frames: 0, action: linear
---> hipass frame 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
... saved!
Removing residual /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s_hpss.dtseries.nii excluding 0 bad frames ... saved!
Low-pass filtering /home/admin01/qunex/output/ruminanti_P2/sessions/06A/images/functional/bold1_Atlas_s_hpss_res-mVWMWB.dtseries.nii
===> Temporal filtering (15/10/22)
---> triming: 0 on start, 0 on end
---> remaining bad frames: 0, action: linear
---> lopass frame 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
... saved!
==> preproces BOLD finished successfully
===> Successful completion of task
Thanks for the help,
Chiara