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]
<[email protected]> on behalf of Mandelli, Maria Luisa
<[email protected]>
Sent: Wednesday, July 5, 2017 3:39:03 PM
To: Glasser, Matthew; [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]>
Sent: Wednesday, July 5, 2017 3:20:45 PM
To: Mandelli, Maria Luisa; [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/
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HCP-Users mailing list
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http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
