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Processing pipelines for the HCP
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Image Exception Error running FreeSurferPipeline.sh #228

Closed margotwagner closed 2 years ago

margotwagner commented 2 years ago

I am trying to install the HCPpipeline on Linux and run it for the single subject example data provided. After following the installation instructions for all the prerequisites and the pipeline, as well as the 'Installation and Usage Instructions', I ran PreFreeSurferPipelineBatch.sh. It appeared to run without any problems (no error messages and the last log of PreFreeSurferPipeline.sh: Completed!. I then ran FreeSurferPipelineBatch.sh where I got the following error:

Image Exception : #63 :: No image files match: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore /home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/FreeSurferPipeline.sh: line 565: 32702 Aborted fslmaths ${T1wImage} -thr 0 ${zero_threshold_T1wImage} Mon May 9 09:27:10 PDT 2022:FreeSurferPipeline.sh: While running '/home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/FreeSurferPipeline.sh --subject=100307 --subjectDIR=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w --t1=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc_restore.nii.gz': Mon May 9 09:27:10 PDT 2022:FreeSurferPipeline.sh: ERROR: fslmaths command failed with return_code: 134

There seems to be a file with contents stored at home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz, so I am confused.

Here are the FreeSurferPipelineBatch.sh logs:

======================================== DIRECTORY: /home/mwagner/projects/hcp/HCPPIPEDIR PRODUCT: HCP Pipeline Scripts VERSION: v4.3.0

Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: FREESURFER_HOME: /home/mwagner/bin/freesurfer Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: Platform Information Follows: Linux porter 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 GNU/Linux Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: We were not able to locate one of the following required tools: Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: recon-all.v6.hires, conf2hires, or longmc Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: To be able to run this script using the standard versions of these tools, Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: we added /home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/custom to the beginning of the PATH. Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: If you intended to use some other version of these tools, please configure Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: your PATH before invoking this script, such that the tools you intended to Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: use can be found on the PATH. Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: WARNING: PATH set to: /home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/custom:/home/mwagner/bin/workbench/bin_linux64:/home/mwagner/bin/fsl/bin:/home/mwagner/bin/fsl/bin:/home/mwagner/anaconda3/condabin:/home/mwagner/bin/freesurfer/bin:/home/mwagner/bin/freesurfer/fsfast/bin:/home/mwagner/bin/freesurfer/tktools:/home/mwagner/bin/freesurfer/mni/bin:/home/mwagner/bin/Blender-2.79-CellBlender:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/local/bin:/usr/bin:/bin:/usr/games:/snap/bin:/var/cfengine/bin:/home/mwagner/bin/pycharm-community-2019.2.2/bin:/home/mwagner/bin/workbench/bin_linux64 Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: Showing HCP Pipelines version

DIRECTORY: /home/mwagner/projects/hcp/HCPPIPEDIR PRODUCT: HCP Pipeline Scripts VERSION: v4.3.0

Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: Showing recon-all.v6.hires version Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: /home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/custom/recon-all.v6.hires freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Mon May 9 09:27:08 PDT 2022:FreeSurferPipeline.sh: Showing tkregister version /home/mwagner/bin/freesurfer/tktools/tkregister stable6 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Showing mri_concatenate_lta version /home/mwagner/bin/freesurfer/bin/mri_concatenate_lta stable6 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Showing mri_surf2surf version /home/mwagner/bin/freesurfer/bin/mri_surf2surf stable6 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Showing fslmaths location /home/mwagner/bin/fsl/bin/fslmaths Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: INFO: Determined that FreeSurfer full version string is: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: INFO: Determined that FreeSurfer version is: 6.0.0 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Using named parameters Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Subject Directory: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Subject: 100307 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: T1w Image: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: T1w Brain: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Include -conf2hires flag in recon-all: TRUE Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Starting main functionality Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Retrieve positional parameters Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: SubjectDIR: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: SubjectID: 100307 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: T1wImage: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: T1wImageBrain: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: T2wImage: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc_restore.nii.gz Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: recon_all_seed: Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: flair: FALSE Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: existing_subject: FALSE Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: extra_reconall_args: Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: conf2hires: TRUE Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Figure out the number of cores to use. Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: num_cores: 8 Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: Thresholding T1w image to eliminate negative voxel values Mon May 9 09:27:09 PDT 2022:FreeSurferPipeline.sh: ...This produces a new file named: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz Mon May 9 09:27:10 PDT 2022:FreeSurferPipeline.sh: ERROR: fslmaths command failed with return_code: 134 Mon May 9 09:27:10 PDT 2022:FreeSurferPipeline.sh: ABORTING

Image Exception : #63 :: No image files match: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore /home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/FreeSurferPipeline.sh: line 565: 32702 Aborted fslmaths ${T1wImage} -thr 0 ${zero_threshold_T1wImage} Mon May 9 09:27:10 PDT 2022:FreeSurferPipeline.sh: While running '/home/mwagner/projects/hcp/HCPPIPEDIR/FreeSurfer/FreeSurferPipeline.sh --subject=100307 --subjectDIR=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w --t1=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T2w_acpc_dc_restore.nii.gz': Mon May 9 09:27:10 PDT 2022:FreeSurferPipeline.sh: ERROR: fslmaths command failed with return_code: 134

Here are the logs from running PreFreeSurferPipelineBatch.sh:

======================================== DIRECTORY: /home/mwagner/projects/hcp/HCPPIPEDIR PRODUCT: HCP Pipeline Scripts VERSION: v4.3.0

Fri May 6 13:42:10 PDT 2022:PreFreeSurferPipeline.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 13:42:10 PDT 2022:PreFreeSurferPipeline.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 13:42:10 PDT 2022:PreFreeSurferPipeline.sh: HCPPIPEDIR_Global: /home/mwagner/projects/hcp/HCPPIPEDIR/global/scripts Fri May 6 13:42:10 PDT 2022:PreFreeSurferPipeline.sh: Platform Information Follows: Linux porter 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 GNU/Linux Fri May 6 13:42:10 PDT 2022:PreFreeSurferPipeline.sh: Parsing Command Line Options Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: Finished Parsing Command Line Options Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: StudyFolder: /home/mwagner/projects/hcp/Pipelines_ExampleData Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: Subject: 100307 Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wInputImages: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/unprocessed/3T/T1w_MPR1/100307_3T_T1w_MPR1.nii.gz@ Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T2wInputImages: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/unprocessed/3T/T2w_SPC1/100307_3T_T2w_SPC1.nii.gz@ Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wTemplate: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T1_0.7mm.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wTemplateBrain: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T1_0.7mm_brain.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wTemplate2mm: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T1_2mm.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T2wTemplate: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T2_0.7mm.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T2wTemplateBrain: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T2_0.7mm_brain.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T2wTemplate2mm: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T2_2mm.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: TemplateMask: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: Template2mmMask: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: BrainSize: 150 Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: FNIRTConfig: /home/mwagner/projects/hcp/HCPPIPEDIR/global/config/T1_2_MNI152_2mm.cnf Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: MagnitudeInputName: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/unprocessed/3T/T1w_MPR1/100307_3T_FieldMap_Magnitude.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: PhaseInputName: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/unprocessed/3T/T1w_MPR1/100307_3T_FieldMap_Phase.nii.gz Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: GEB0InputName: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: TE: 2.46 Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodeNegative: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodePositive: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: SEEchoSpacing: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: SEUnwarpDir: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wSampleSpacing: 0.0000074 Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T2wSampleSpacing: 0.0000021 Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: UnwarpDir: z Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: GradientDistortionCoeffs: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: AvgrdcSTRING: SiemensFieldMap Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: TopupConfig: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: BiasFieldSmoothingSigma: Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: UseJacobian: true Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wBiasCorrect: Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: CustomBrain: NONE Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: ProcessingMode: HCPStyleData Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T1wFolder: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: T2wFolder: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T2w Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: AtlasSpaceFolder: /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/MNINonLinear Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/xfms/ Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T2w/xfms/ Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/MNINonLinear/xfms/ Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: POSIXLY_CORRECT= Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: Processing Modality: T1w Fri May 6 13:42:12 PDT 2022:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION Fri May 6 13:42:18 PDT 2022:PreFreeSurferPipeline.sh: Not Averaging T1w Images Fri May 6 13:42:18 PDT 2022:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING Fri May 6 13:42:19 PDT 2022:PreFreeSurferPipeline.sh: Aligning T1w image to /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T1_0.7mm.nii.gz to create native volume space Fri May 6 13:42:19 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/ACPCAlignment Fri May 6 13:42:20 PDT 2022:ACPCAlignment.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 13:42:20 PDT 2022:ACPCAlignment.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 13:42:20 PDT 2022:ACPCAlignment.sh: START Final FOV is: 0.000000 256.000000 0.000000 320.000000 58.000000 214.000000

Fri May 6 13:44:08 PDT 2022:ACPCAlignment.sh: END Fri May 6 13:44:08 PDT 2022:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking Fri May 6 13:44:08 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/BrainExtraction_FNIRTbased Fri May 6 13:44:09 PDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 13:44:09 PDT 2022:BrainExtraction_FNIRTbased.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 13:44:09 PDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates Fri May 6 13:44:09 PDT 2022:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT Fri May 6 13:54:51 PDT 2022:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT Fri May 6 13:54:51 PDT 2022:PreFreeSurferPipeline.sh: Processing Modality: T2w Fri May 6 13:54:51 PDT 2022:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION Fri May 6 13:54:53 PDT 2022:PreFreeSurferPipeline.sh: Not Averaging T2w Images Fri May 6 13:54:53 PDT 2022:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING Fri May 6 13:54:55 PDT 2022:PreFreeSurferPipeline.sh: Aligning T2w image to /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates/MNI152_T2_0.7mm.nii.gz to create native volume space Fri May 6 13:54:55 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T2w/ACPCAlignment Fri May 6 13:54:55 PDT 2022:ACPCAlignment.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 13:54:55 PDT 2022:ACPCAlignment.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 13:54:55 PDT 2022:ACPCAlignment.sh: START Final FOV is: 0.000000 256.000000 0.000000 320.000000 60.000000 214.000000

Fri May 6 13:56:33 PDT 2022:ACPCAlignment.sh: END Fri May 6 13:56:33 PDT 2022:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking Fri May 6 13:56:33 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T2w/BrainExtraction_FNIRTbased Fri May 6 13:56:33 PDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 13:56:33 PDT 2022:BrainExtraction_FNIRTbased.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 13:56:33 PDT 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /home/mwagner/projects/hcp/HCPPIPEDIR/global/templates Fri May 6 13:56:33 PDT 2022:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT Fri May 6 14:07:07 PDT 2022:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT Fri May 6 14:07:07 PDT 2022:PreFreeSurferPipeline.sh: Performing SiemensFieldMap Readout Distortion Correction Fri May 6 14:07:07 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg Fri May 6 14:07:07 PDT 2022:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 14:07:07 PDT 2022:T2wToT1wDistortionCorrectAndReg.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 14:07:07 PDT 2022:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR_Global: /home/mwagner/projects/hcp/HCPPIPEDIR/global/scripts Fri May 6 14:07:09 PDT 2022:T2wToT1wDistortionCorrectAndReg.sh: START

FieldMapPreprocessingAll.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR FieldMapPreprocessingAll.sh: FSLDIR: /home/mwagner/bin/fsl FieldMapPreprocessingAll.sh: HCPPIPEDIR_Global: /home/mwagner/projects/hcp/HCPPIPEDIR/global/scripts Fri May 6 14:07:09 PDT 2022:FieldMapPreprocessingAll.sh: Field Map Preprocessing and Gradient Unwarping Fri May 6 14:07:09 PDT 2022:FieldMapPreprocessingAll.sh: START 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/mwagner/projects/hcp/Pipelines_ExampleData/100307/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/FieldMap for use with FEAT. Fri May 6 14:07:15 PDT 2022:FieldMapPreprocessingAll.sh: DONE: fsl_prepare_fieldmap.sh Fri May 6 14:07:18 PDT 2022:FieldMapPreprocessingAll.sh: Field Map Preprocessing and Gradient Unwarping Fri May 6 14:07:18 PDT 2022:FieldMapPreprocessingAll.sh: END Running FAST segmentation FLIRT pre-alignment Running BBR 0.347956 0.999981 -0.006128 0.001073 0.000000 0.006168 0.999082 -0.042399 0.000000 -0.000813 0.042404 0.999100 0.000000 -1.303270 -3.381539 6.134600 1.000000 Fri May 6 14:23:45 PDT 2022:T2wToT1wDistortionCorrectAndReg.sh: END Fri May 6 14:23:45 PDT 2022:PreFreeSurferPipeline.sh: Performing Bias Field Correction using sqrt(T1w x T2w) Fri May 6 14:23:45 PDT 2022:PreFreeSurferPipeline.sh: mkdir -p /home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/BiasFieldCorrection_sqrtT1wXT2w Fri May 6 14:23:45 PDT 2022:BiasFieldCorrection_sqrtT1wXT2w.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 14:23:45 PDT 2022:BiasFieldCorrection_sqrtT1wXT2w.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 14:23:45 PDT 2022:BiasFieldCorrection_sqrtT1wXT2w.sh: CARET7DIR: /home/mwagner/bin/workbench/bin_linux64 Fri May 6 14:23:45 PDT 2022:BiasFieldCorrection_sqrtT1wXT2w.sh: START: BiasFieldCorrection 0.240758 0.975645 .8552660 Fri May 6 14:25:32 PDT 2022:BiasFieldCorrection_sqrtT1wXT2w.sh: END: BiasFieldCorrection Fri May 6 14:25:32 PDT 2022:PreFreeSurferPipeline.sh: Creating one-step resampled version of {T1w,T2w}_acpc_dc outputs Fri May 6 14:30:11 PDT 2022:PreFreeSurferPipeline.sh: Performing Atlas Registration to MNI152 (FLIRT and FNIRT) Fri May 6 14:30:11 PDT 2022:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: HCPPIPEDIR: /home/mwagner/projects/hcp/HCPPIPEDIR Fri May 6 14:30:11 PDT 2022:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: FSLDIR: /home/mwagner/bin/fsl Fri May 6 14:30:12 PDT 2022:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: START: AtlasRegistration to MNI152 Fri May 6 14:45:32 PDT 2022:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: END: AtlasRegistration to MNI152 Fri May 6 14:45:32 PDT 2022:PreFreeSurferPipeline.sh: Completed!

glasserm commented 2 years ago

what do you get if you type:

ls /home/mwagner/projects/Pipelines_ExampleData/100307/T1w/T1w_acpc_dc_restore.nii.gz

In the terminal?

margotwagner commented 2 years ago

I didn't update the project directory correctly for all of FreeSurfer, thanks!