It sounds like FreeSurfer didn’t run properly. The end of your FreeSurferPipeline.sh.o23511 file states:
ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Are you sure that you deleted all the files from your previous attempt, because the message above indicates that you did not. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of YC Yao <yao_yongch...@icloud.com<mailto:yao_yongch...@icloud.com>> Date: Friday, October 14, 2016 at 10:29 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] errors with HCP_Pipelines structural processing Hi Tim, Thank you for your detailed replay, I have fixed the errors read: mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file /home/yoson/Applications/HCP_Pipelines/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 63: /100307/T1w/100307/mri/c_ras.mat: No such file or directory As you suppose, the reason for having these errors is the wrong path directing to brain.finalsurfs.mgz, so after checking the script I use to invoke PostFreeSurferPipeline.sh, I find out that I set the the value /Users/YOSON/Projects/HcpPipelinesExampleDataGDC to a wrong variable name SStudyFolder where I duplicate the capital S.However, successive errors appear even after I set the right path. In case errors would have occurred in the first two part, I deleted all generated files and re-runed pre-freesurfer and freesurfer process. After that, I found that the FreeSurferPipeline.sh.e 23511 and PreFreeSurferPipeline.sh.e13527 were blank, while there were errors in PostFreeSurferPipeline.sh.e23895. The errors read: mghRead(/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file mghRead(/home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz, -1): could not open file Cannot open volume /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/wmparc_1mm for reading! I checked the data repository, and could not find /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/100307/mri/brain.finalsurfs.mgz and /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/wmparc_1mm. Here is the info of PreFreeSurferPipeline.sh.o13527: Fri Oct 14 15:28:05 CST 2016 - PreFreeSurferPipeline.sh - Platform Information Follows: Linux yoson-Precision-Tower-3620 4.4.0-42-generic #62-Ubuntu SMP Fri Oct 7 23:11:45 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Fri Oct 14 15:28:05 CST 2016 - PreFreeSurferPipeline.sh - Parsing Command Line Options Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Finished Parsing Command Line Options Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - StudyFolder: /home/yoson/Projects/HcpPipelinesExampleDataGDC Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Subject: 100307 Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wInputImages: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T1w_MPR1/100307_3T_T1w_MPR1.nii.gz@ Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wInputImages: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T2w_SPC1/100307_3T_T2w_SPC1.nii.gz@ Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wTemplate: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_0.7mm.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wTemplateBrain: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wTemplate2mm: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_2mm.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wTemplate: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T2_0.7mm.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wTemplateBrain: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wTemplate2mm: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T2_2mm.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - TemplateMask: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Template2mmMask: /home/yoson/Applications/HCP_Pipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - BrainSize: 150 Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - FNIRTConfig: /home/yoson/Applications/HCP_Pipelines/global/config/T1_2_MNI152_2mm.cnf Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - MagnitudeInputName: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T1w_MPR1/100307_3T_FieldMap_Magnitude.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - PhaseInputName: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/unprocessed/3T/T1w_MPR1/100307_3T_FieldMap_Phase.nii.gz Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - GEB0InputName: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - TE: 2.46 Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - SpinEchoPhaseEncodeNegative: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - SpinEchoPhaseEncodePositive: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - DwellTime: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - SEUnwarpDir: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wSampleSpacing: 0.0000074 Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wSampleSpacing: 0.0000021 Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - UnwarpDir: z Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - GradientDistortionCoeffs: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - AvgrdcSTRING: SiemensFieldMap Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - TopupConfig: NONE Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - BiasFieldSmoothingSigma: Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - UseJacobian: true Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - FSLDIR: /usr/share/fsl/5.0 Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - HCPPIPEDIR: /home/yoson/Applications/HCP_Pipelines Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - HCPPIPEDIR_Global: /home/yoson/Applications/HCP_Pipelines/global/scripts Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - HCPPIPEDIR_PreFS: /home/yoson/Applications/HCP_Pipelines/PreFreeSurfer/scripts Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T1wFolder: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - T2wFolder: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - AtlasSpaceFolder: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/MNINonLinear Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/xfms/ Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/xfms/ Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/MNINonLinear/xfms/ Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - POSIXLY_CORRECT= Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Processing Modality: T1w Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - NOT PERFORMING GRADIENT DISTORTION CORRECTION Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Not Averaging T1w Images Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - ONLY ONE AVERAGE FOUND: COPYING Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - Aligning T1w image to 0.7mm MNI T1wTemplate to create native volume space Fri Oct 14 15:28:06 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/ACPCAlignment START: ACPCAlignment Final FOV is: 0.000000 256.000000 0.000000 320.000000 58.000000 214.000000 END: ACPCAlignment Fri Oct 14 15:31:39 CST 2016 - PreFreeSurferPipeline.sh - Performing Brain Extraction using FNIRT-based Masking Fri Oct 14 15:31:39 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/BrainExtraction_FNIRTbased START: BrainExtraction_FNIRT END: BrainExtraction_FNIRT Fri Oct 14 15:39:20 CST 2016 - PreFreeSurferPipeline.sh - Processing Modality: T2w Fri Oct 14 15:39:20 CST 2016 - PreFreeSurferPipeline.sh - NOT PERFORMING GRADIENT DISTORTION CORRECTION Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - Not Averaging T2w Images Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - ONLY ONE AVERAGE FOUND: COPYING Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - Aligning T2w image to 0.7mm MNI T2wTemplate to create native volume space Fri Oct 14 15:39:21 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/ACPCAlignment START: ACPCAlignment Final FOV is: 0.000000 256.000000 0.000000 320.000000 60.000000 214.000000 END: ACPCAlignment Fri Oct 14 15:42:32 CST 2016 - PreFreeSurferPipeline.sh - Performing Brain Extraction using FNIRT-based Masking Fri Oct 14 15:42:32 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/BrainExtraction_FNIRTbased START: BrainExtraction_FNIRT END: BrainExtraction_FNIRT Fri Oct 14 15:50:12 CST 2016 - PreFreeSurferPipeline.sh - Performing SiemensFieldMap Readout Distortion Correction Fri Oct 14 15:50:12 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/T2wToT1wDistortionCorrectAndReg START: T2WToT1wDistortionCorrectAndReg.sh START: Field Map Preprocessing and Gradient Unwarping Loading volumes Phase loaded Magnitude loaded Mask loaded Rewrapping phase range to [-pi,pi] Number of phase splits = 8 Calculating starting matrices (6143 by 6143) Finished connection_matrices 18546 constraints left 8771 constraints left 6835 constraints left 5338 constraints left 3472 constraints left 1841 constraints left 192 constraints left Did while loop 6142 times Done. Created /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/FieldMap for use with FEAT. DONE: fsl_prepare_fieldmap.sh END: Field Map Preprocessing and Gradient Unwarping Running FAST segmentation FLIRT pre-alignment Running BBR 0.348442 0.999983 -0.005782 0.001238 0.000000 0.005833 0.998931 -0.045856 0.000000 -0.000971 0.045863 0.998947 0.000000 -1.228439 -3.729267 6.633881 1.000000 END: T2WToT1wDistortionCorrectAndReg.sh Fri Oct 14 16:10:31 CST 2016 - PreFreeSurferPipeline.sh - Performing Bias Field Correction Fri Oct 14 16:10:31 CST 2016 - PreFreeSurferPipeline.sh - mkdir -p /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/BiasFieldCorrection_sqrtT1wXT1w START: BiasFieldCorrection 0.240737 0.975605 .8552365 END: BiasFieldCorrection Fri Oct 14 16:12:55 CST 2016 - PreFreeSurferPipeline.sh - Performing Atlas Registration to MNI152 (FLIRT and FNIRT) START: AtlasRegistration to MNI152 END: AtlasRegistration to MNI152 Fri Oct 14 16:23:58 CST 2016 - PreFreeSurferPipeline.sh - Completed And the info of FreeSurferPipeline.sh.o23511: Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - Parsing Command Line Options Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - Finished Parsing Command Line Options Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - SubjectID: 100307 Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - SubjectDIR: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - T1wImage: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/T1w_acpc_dc_restore.nii.gz Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - T1wImageBrain: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - T2wImage: /home/yoson/Projects/HcpPipelinesExampleDataGDC/100307/T1w/T2w_acpc_dc_restore.nii.gz Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - recon_all_seed: Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - seed_cmd_appendix: Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - HCPPIPEDIR: /home/yoson/Applications/HCP_Pipelines Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - HCPPIPEDIR_FS: /home/yoson/Applications/HCP_Pipelines/FreeSurfer/scripts Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which flirt: /usr/share/fsl/5.0/bin/flirt Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - flirt -version: FLIRT version 6.0 Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which applywarp: /usr/share/fsl/5.0/bin/applywarp Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which fslstats: /usr/share/fsl/5.0/bin/fslstats Fri Oct 14 18:02:19 CST 2016 - FreeSurferPipeline.sh - which fslmaths: /usr/share/fsl/5.0/bin/fslmaths Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which recon-all: /home/yoson/Applications/freesurfer/bin/recon-all Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - recon-all --version: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which mri_convert: /home/yoson/Applications/freesurfer/bin/mri_convert Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which mri_em_register: /home/yoson/Applications/freesurfer/bin/mri_em_register Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - mri_em_register --version: ======= NUMBER OF OPENMP THREADS = 4 ======= stable5 Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - which mri_watershed: /home/yoson/Applications/freesurfer/bin/mri_watershed Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - mri_watershed --version: stable5 Fri Oct 14 18:02:20 CST 2016 - FreeSurferPipeline.sh - Make Spline Interpolated Downsample to 1mm Fri Oct 14 18:02:40 CST 2016 - FreeSurferPipeline.sh - Initial Recon-all Steps ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. I really appreciate your help. Best, YC Yao _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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