Right I have fixed this in the master now. Peace,
Matt. From: "Mandelli, Maria Luisa" <[email protected]<mailto:[email protected]>> Date: Thursday, July 6, 2017 at 11:11 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Cc: "Brown, Tim" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found nop, I only changed the path for the environment setting after the following below it worked DownSampleFolder=${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k and I got my first map! Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Sent: Thursday, July 6, 2017 6:43:47 PM To: Mandelli, Maria Luisa; [email protected]<mailto:[email protected]> Cc: Brown, Tim Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found Have you been editing the script or did one of us introduce a bug? Peace, Matt. From: "Mandelli, Maria Luisa" <[email protected]<mailto:[email protected]>> Date: Thursday, July 6, 2017 at 1:19 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found Hi! so I think I found where is the problem. I m in FreeSurfer2CaretConvertAndRegisterNonlinear.sh script I have this definition of the following path left_metric=${DownSampleT1wFolder}/${Subject}.L.midthickness_va.${LowResMesh}k_fs_LR.shape.gii roi_left=${DownSampleFolder}/${Subject}.L.atlasroi.${LowResMesh}k_fs_LR.shape.gii right_metric=${DownSampleT1wFolder}/${Subject}.R.midthickness_va.${LowResMesh}k_fs_LR.shape.gii roi_right=${DownSampleFolder}/${Subject}.R.atlasroi.${LowResMesh}k_fs_LR.shape.gii where DownSampleT1wFolder is defined like below while there is no definition for DownSampleFolder DownSampleT1wFolder=${T1wFolder}/fsaverage_LR${LowResMesh}k what should be DownSampleFOlder? my guess is that should be MNINonLInear/fsaverageLR32k but I want to check with you first! thank you Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From:[email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of Mandelli, Maria Luisa <[email protected]<mailto:[email protected]>> Sent: Wednesday, July 5, 2017 3:39:03 PM To: Glasser, Matthew; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found yes the environment should be set correctly let me see if I can dig into it more and give you more details! Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Sent: Wednesday, July 5, 2017 3:20:45 PM To: Mandelli, Maria Luisa; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found How did you call the pipeline? Did you set the environment correctly? Peace, Matt. From: "Mandelli, Maria Luisa" <[email protected]<mailto:[email protected]>> Date: Wednesday, July 5, 2017 at 5:19 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found yes it s HCP pipeline: PostFreesurferBatch.sh it creates the file in the subject directory but then it doesnt set the path correctly I think... Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Sent: Wednesday, July 5, 2017 3:06:52 PM To: Mandelli, Maria Luisa; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] cifti-create-dense-scalar file not found Is this running an HCP pipeline or something else? If it is a pipeline, which pipeline is it? That file is available in the HCP Pipelines repository: https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/L.atlasroi.32k_fs_LR.shape.gii https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/R.atlasroi.32k_fs_LR.shape.gii Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Mandelli, Maria Luisa" <[email protected]<mailto:[email protected]>> Date: Wednesday, July 5, 2017 at 3:16 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] cifti-create-dense-scalar file not found Hello! I m running the pipeline for FreeSurfer processing (PostProcessing) and I m encountering in this error File doesn not exist Basically it doesnt find the path for left and right .atlasroi.32k_fs_LR.shape.gii not sure if I m missing to set up something else, they are in MNInonlinear folder Thank you very much for your help /mnt/macdata/groups/language/workbench-linux64-v1.2.3/workbench/bin_linux64/../exe_linux64/wb_command -cifti-create-dense-scalar /subjects/hcp350014/T1w/fsaverage_LR32k/hcp350014.midthickness_va.32k_fs_LR.dscalar.nii -left-metric /subjects/hcp350014/T1w/fsaverage_LR32k/hcp350014.L.midthickness_va.32k_fs_LR.shape.gii -roi-left /hcp350014.L.atlasroi.32k_fs_LR.shape.gii -right-metric /subjects/hcp350014/T1w/fsaverage_LR32k/hcp350014.R.midthickness_va.32k_fs_LR.shape.gii -roi-right /hcp350014.R.atlasroi.32k_fs_LR.shape.gii Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
