Activity for Thomas DeRamus
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Thomas DeRamus posted a comment on discussion Help
It looks great! Just needs to be shifted a bit. Thanks so much!
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It ran to completion and the initial template looks great! If the whole job runs to completion I'll go ahead and close the issue.
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Got it. Yeah it looks like the jobs may be iterating because it's queueing more jobs with different tags. I'm probably just impatient. 463821 qTRD bash tderamus R 1:45:36 1 trendscn010.rs.gsu.edu 463836 qTRD antsdef3 tderamus R 0:02 1 trendscn008.rs.gsu.edu 463837 qTRD antsdef3 tderamus R 0:02 1 trendscn007.rs.gsu.edu 463838 qTRD antsdef3 tderamus R 0:02 1 trendscn007.rs.gsu.edu 463835 qTRD antsdef3 tderamus R 0:22 1 trendscn008.rs.gsu.edu
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Well I say that but it pops back in the queue every so often. 463832 qTRD antsdef2 tderamus R 0:20 1 trendscn008.rs.gsu.edu 463833 qTRD antsdef2 tderamus R 0:20 1 trendscn004.rs.gsu.edu 463834 qTRD antsdef2 tderamus R 0:20 1 trendscn004.rs.gsu.edu 463831 qTRD antsdef2 tderamus R 0:22 1 trendscn008.rs.gsu.edu
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It does not. Thankfully that issue seems to be resolved with the right --partition flag, but it seems to hang up once the jobs have been run. I know the output says PENDING, but it's been done for quite a while. No longer see it in the squeue. antsMultivariateTemplateConstruction2.sh -d 3 -i 4 -k 1 -t SyN -m CC -c 5 -o /data/mialab/users/tderamus/Data_Fu^Con_DevCog/derivatives/Template_Maker/DevTemplate $zorkus (reverse-i-search)`sba': ^Catch TemplateMaker.job [tderamus@trendscn010 Template_Maker]$...
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Oh. So just edit the script directly?
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Did so. Same issue. Works just fine with serial but have quite a few images I need to do this with...... antsMultivariateTemplateConstruction2.sh -d 3 -i 4 -k 1 -t SyN -m CC -c 5 -o /data/mialab/users/tderamus/Data_Fusion_DevCog/derivatives/Template_Maker/DevTemplate $zorkus Creating template /data/mialab/users/tderamus/Data_Fusion_DevCog/derivatives/Template_Maker/DevTemplatetemplate0.nii.gz from a population average image from the inputs. /data/mialab/users/tderamus/Data_Fusion_DevCog/derivatives/Template_Maker/First_sub-M68228769_Session1_task-restclosed_bold.nii.gz...
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Forgot to attach these.
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Threw a different error this time: [tderamus@trendscn010 Template_Maker]$ zorkus=find "$(pwd)" -name "*task*.nii.gz" | head -n4 [tderamus@trendscn010 Template_Maker]$ antsMultivariateTemplateConstruction2.sh -d 3 -i 4 -k 1 -t SyN -m CC -c 5 -o DevTemplate $zorkus Creating template DevTemplatetemplate0.nii.gz from a population average image from the inputs. /data/mialab/users/tderamus/Data_Fusion_DevCog/derivatives/Template_Maker/First_sub-M68228769_Session1_task-restclosed_bold.nii.gz /data/mialab/users/tderamus/Data_Fusion_DevCog/derivatives/Template_Maker/First_sub-M87116562_Session1_task-restopen_bold.nii.gz...
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Same error even when it's reduced to 3 dimensions: antsMultivariateTemplateConstruction2.sh -d 3 -j 6 -k 1 -n 0 -r 1 -t SyN -c 5 -o MY First_sub-M87192301_Session1_task-restopen_bold.nii.gz First_sub-M87192301_Session1_task-restclosed_bold.nii.gz First_sub-M68290751_Session1_task-restclosed_bold.nii.gz First_sub-M68290751_Session1_task-restopen_bold.nii.gz Creating template MYtemplate0.nii.gz from a population average image from the inputs. First_sub-M87192301_Session1_task-restopen_bold.nii.gz First_sub-M87192301_Session1_task-restclosed_bold.nii.gz...
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I tried the full path and that didn't do it. I was hoping to do it with 4D data give the argument in the help: -d: ImageDimension: 2 or 3 (for 2 or 3 dimensional registration of single volume) ImageDimension: 4 (for template generation of time-series data) But it doesn't seem like that's working. I'll try the first image in the series and see what happens.
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Hi all. I'm trying to build a subject-specific template for some pediatric timeseries data. antsMultivariateTemplateConstruction2.sh -d 4 -j 6 -k 1 -n 0 -r 1 -t SyN -c 5 -o MY sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz All of the timeseries are in a folder, but the slurm scripts being generated don't seem to look like slurm scripts and it looks...
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