User Tools

Site Tools


neuroimagen:cpac

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
neuroimagen:cpac [2019/05/23 09:56]
osotolongo [Integrando en el cluster]
neuroimagen:cpac [2020/08/04 10:58] (current)
Line 83: Line 83:
 ==== Integrando en el cluster ==== ==== Integrando en el cluster ====
 El esquema para correr en el cluster es el de lanzar las imagenes de singularity en paralelo. Hay que hacer varias  pruebas por si se solapan unas a otras pero en principio intentaremos lanzar unos 8 procesos por nodo (o menos). El esquema para correr en el cluster es el de lanzar las imagenes de singularity en paralelo. Hay que hacer varias  pruebas por si se solapan unas a otras pero en principio intentaremos lanzar unos 8 procesos por nodo (o menos).
 +
 +++++ Aqui el codigo |
  
 <code perl cpac.pl> <code perl cpac.pl>
Line 150: Line 152:
  print ORD '#SBATCH --mail-type=FAIL,TIME_LIMIT,STAGE_OUT'."\n"; #no quieres que te mande email de todo  print ORD '#SBATCH --mail-type=FAIL,TIME_LIMIT,STAGE_OUT'."\n"; #no quieres que te mande email de todo
  print ORD '#SBATCH -o '.$outdir.'/cpac-%j'."\n";  print ORD '#SBATCH -o '.$outdir.'/cpac-%j'."\n";
- print ORD '#SBATCH -c 8'."\n";+ print ORD '#SBATCH -c 20'."\n";
  print ORD '#SBATCH -p fast'."\n";  print ORD '#SBATCH -p fast'."\n";
  print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";  print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
Line 170: Line 172:
 my $order = 'sbatch --dependency=singleton '.$orderfile; my $order = 'sbatch --dependency=singleton '.$orderfile;
 exec($order); exec($order);
 +</code>
 +++++
 +**Nota**: Al correr //c-pac// en el cluster dan errores de I/O. Esto puede ser debido a un intenso uso de la red o de disco. He de reducir el nuemro de lanzamientos concurrentes y probar de nuevo.
 +
 +=== Output ===
 +
 +//C-PAC// genera un directorio de output por cada sujeto analizado
 +<code>
 +[osotolongo@detritus mopead]$ ls cpac_out/output/pipeline_analysis_nuisance/
 +sub-0001_ses-1  sub-0003_ses-1  sub-0005_ses-1  sub-0007_ses-1  sub-0009_ses-1  sub-0012_ses-1  sub-0015_ses-1  sub-0018_ses-1  sub-0020_ses-1  sub-0022_ses-1
 +sub-0002_ses-1  sub-0004_ses-1  sub-0006_ses-1  sub-0008_ses-1  sub-0010_ses-1  sub-0014_ses-1  sub-0017_ses-1  sub-0019_ses-1  sub-0021_ses-1  sub-0023_ses-1
 +</code>
 +
 +[[http://detritus.fundacioace.com/files/example_cpac_out.txt|El output completo para cada sujeto se puede ver aqui]].
 +
 +{{:neuroimagen:2019-05-30-112300_grim.png|}}
 +
 +=== Errores ===
 +
 +Los errores que se obtienen son muy diversos y parece indicar que tienen que ver mas con la calidad de la adquisicion que con el software en si mismo.No obstante al fallar en distintos puntos del procesamiento es posible que algunos de los sujetos fallidos contengan los archivos de output para algun postprocesdo especifico. En cada caso se ha de buscar si existen estos archivos.
 +
 +<code>
 +190529-07:56:45,394 nipype.workflow INFO:
 +         [Node] Setting-up "resting_preproc_sub-0004_ses-1.sinker_0_13" in "/scratch/working/resting_preproc_sub-0004_ses-1/sinker_0_13".
 +190529-07:56:46,61 nipype.workflow INFO:
 +         [Node] Running "sinker_0_13" ("nipype.interfaces.io.DataSink")
 +190529-07:56:46,617 nipype.workflow INFO:
 +         [Node] Finished "resting_preproc_sub-0004_ses-1.sinker_0_13".
 +srun: error: brick01: task 0: Exited with exit code 1
 +</code>
 +
 +<code>
 +190529-08:02:22,31 nipype.workflow INFO:
 +         [Node] Outdated cache found for "resting_preproc_sub-0003_ses-1.qc_snr_0.std_dev_anat".
 +190529-08:02:22,347 nipype.workflow INFO:
 +         [Node] Running "std_dev_anat" ("nipype.interfaces.fsl.preprocess.ApplyWarp"), a CommandLine Interface with command:
 +applywarp --in=/scratch/working/resting_preproc_sub-0003_ses-1/qc_snr_0/_scan_rest_run-1/std_dev/sub-0003_task-rest_run-1_bold_calc_tshift_resample_volreg_calc_maths_tstat.nii.gz --ref=/scratch/working/resting_preproc_sub-0003_ses-1/anat_preproc_bet_0/anat_skullstrip_orig_vol/sub-0003_T1w_resample_calc.nii.gz --out=/scratch/working/resting_preproc_sub-0003_ses-1/qc_snr_0/_scan_rest_run-1/std_dev_anat/sub-0003_task-rest_run-1_bold_calc_tshift_resample_volreg_calc_maths_tstat_warp.nii.gz --premat=/scratch/working/resting_preproc_sub-0003_ses-1/func_to_anat_bbreg_0/_scan_rest_run-1/bbreg_func_to_anat/sub-0003_task-rest_run-1_bold_calc_tshift_resample_volreg_calc_tstat_flirt.mat --interp=trilinear
 +190529-08:02:25,845 nipype.workflow INFO:
 +         [Node] Finished "resting_preproc_sub-0003_ses-1.qc_snr_0.std_dev_anat".
 +srun: error: brick01: task 0: Exited with exit code 1
 +</code>
 +
 +<code>
 +nipype.external.portalocker.LockException: (5, 'Input/output error')
 +190529-08:02:21,718 nipype.workflow INFO:
 +         [Node] Setting-up "resting_preproc_sub-0009_ses-1.qc_skullstrip_1.montage_skull.montage_a" in "/scratch/working/resting_preproc_sub-0009_ses-1/qc_skullstrip_1/montage_skull/montage_a".
 +190529-08:02:21,892 nipype.workflow INFO:
 +         [Node] Outdated cache found for "resting_preproc_sub-0009_ses-1.qc_skullstrip_1.montage_skull.montage_a".
 +190529-08:02:22,252 nipype.workflow INFO:
 +         [Node] Setting-up "_montage_a0" in "/scratch/working/resting_preproc_sub-0009_ses-1/qc_skullstrip_1/montage_skull/montage_a/mapflow/_montage_a0".
 +190529-08:02:22,286 nipype.workflow INFO:
 +         [Node] Outdated cache found for "_montage_a0".
 +190529-08:02:22,446 nipype.workflow INFO:
 +         [Node] Running "_montage_a0" ("CPAC.utils.function.Function")
 +190529-08:02:28,560 nipype.workflow INFO:
 +         [Node] Finished "_montage_a0".
 +190529-08:02:28,576 nipype.workflow INFO:
 +         [Node] Finished "resting_preproc_sub-0009_ses-1.qc_skullstrip_1.montage_skull.montage_a".
 +srun: error: brick01: task 0: Exited with exit code 1
 +</code>
 +
 +<code>
 +nipype.external.portalocker.LockException: (5, 'Input/output error')
 +190529-08:04:01,614 nipype.workflow INFO:
 +         [Node] Setting-up "resting_preproc_sub-0001_ses-1.hist_vmhc_fisher_zstd_1" in "/scratch/working/resting_preproc_sub-0001_ses-1/_scan_rest_run-1/_selector_CSF-2mmE-M_aC-CSF+WM-2mm-DPC5_M-SDB_P-2_BP-B0.01-T0.1/_fwhm_4/hist_vmhc_fisher_zstd_1".
 +190529-08:04:01,676 nipype.workflow INFO:
 +         [Node] Outdated cache found for "resting_preproc_sub-0001_ses-1.hist_vmhc_fisher_zstd_1".
 +190529-08:04:01,713 nipype.workflow INFO:
 +         [Node] Running "hist_vmhc_fisher_zstd_1" ("CPAC.utils.function.Function")
 +190529-08:04:01,899 nipype.workflow INFO:
 +         [Node] Finished "resting_preproc_sub-0001_ses-1.hist_vmhc_fisher_zstd_1".
 +srun: error: brick03: task 0: Exited with exit code 1
 +</code>
 +
 +<code>
 +         ***********************************
 +190529-09:10:47,524 nipype.workflow ERROR:
 +         could not run node: resting_preproc_sub-0014_ses-1.afni_centrality_0_eigenvector.afni_centrality.a0.b0
 +190529-09:10:47,527 nipype.workflow INFO:
 +         crashfile: /outputs/crash/crash-20190529-082639-osotolongo-afni_centrality.a0.b0-75dfa3ff-3c39-4800-b04d-c95080370a86.pklz
 +190529-09:10:47,530 nipype.workflow ERROR:
 +         could not run node: resting_preproc_sub-0014_ses-1.afni_centrality_1_eigenvector.afni_centrality.a0.b0
 +190529-09:10:47,533 nipype.workflow INFO:
 +         crashfile: /outputs/crash/crash-20190529-083301-osotolongo-afni_centrality.a0.b0-ee039f25-50ce-43c6-b64b-0d32355dd8c9.pklz
 +190529-09:10:47,535 nipype.workflow INFO:
 +         ***********************************
 +</code>
 +
 +<code>
 +nipype.external.portalocker.LockException: (5, 'Input/output error')
 +190529-09:37:12,642 nipype.workflow INFO:
 +         [Node] Running "_apply_ants_warp_mapnode6" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command:
 +antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input /scratch/working/resting_preproc_sub-0010_ses-1/temporal_dual_regression_0/_scan_rest_run-1/_selector_CSF-2mmE-M_aC-CSF+WM-2mm-DPC5_G-M_M-SDB_P-2_BP-B0.01-T0.1/_spatial_map_PNAS_Smith09_rsn10_spatial_map_file_..cpac_templates..PNAS_Smith09_rsn10.nii.gz/split_raw_volumes/temp_reg_map_0006.nii.gz --input-image-type 0 --interpolation Linear --output temp_reg_map_0006_antswarp.nii.gz --reference-image /usr/share/fsl/5.0/data/standard/MNI152_T1_3mm_brain.nii.gz --transform /scratch/working/resting_preproc_sub-0010_ses-1/anat_mni_ants_register_0/calc_ants_warp/transform3Warp.nii.gz --transform /scratch/working/resting_preproc_sub-0010_ses-1/anat_mni_ants_register_0/calc_ants_warp/transform2Affine.mat --transform /scratch/working/resting_preproc_sub-0010_ses-1/anat_mni_ants_register_0/calc_ants_warp/transform1Rigid.mat --transform /scratch/working/resting_preproc_sub-0010_ses-1/anat_mni_ants_register_0/calc_ants_warp/transform0DerivedInitialMovingTranslation.mat --transform /scratch/working/resting_preproc_sub-0010_ses-1/dr_tempreg_maps_files_fsl_to_itk_0/_scan_rest_run-1/_selector_CSF-2mmE-M_aC-CSF+WM-2mm-DPC5_G-M_M-SDB_P-2_BP-B0.01-T0.1/_spatial_map_PNAS_Smith09_rsn10_spatial_map_file_..cpac_templates..PNAS_Smith09_rsn10.nii.gz/change_transform_type/mapflow/_change_transform_type6/updated_affine.txt
 +190529-09:37:13,368 nipype.workflow INFO:
 +         [Node] Finished "_apply_ants_warp_mapnode6".
 +srun: error: brick01: task 0: Exited with exit code 1
 </code> </code>
  
neuroimagen/cpac.1558605397.txt.gz ยท Last modified: 2020/08/04 10:45 (external edit)