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activatedvoxel edited this page Jun 14, 2012 · 13 revisions

Welcome to the CBS wiki!

To Do

  • Make .gif deletion in getsubjects.m happen by default, but not crash the script if it doesn't work
  • Make getsubject help more complete, specifiy how to enter data (in quotes, brackets, what do do if don't want to specify one of the choices - like fieldmap).
  • Complete testing of genPreprocBatches.py

##Bsub brain storming

  1. changes to exisiting genbatch scripts

alex's genbatch to throw errors if can't make the batch due to things like different number of runs

  1. A new small matlab script should be made that takes the batch, loads it, load spm defaults, and runs the jobman or art command in a try/catch that needs to write out errors if matlab crashes/batch doesn't run.

  2. We need a script to bsub #2. It would be great if this was somehow attached to the genbatch, so that the user can just submit one script to make and execute batches.
    --this needs to monitor when the individual subj bsubs finish. --also needs to gather errors, both from batch creation, and from batch execution, put in some final summary --probably similar for all the genbatches....

INFO: run1: 3 outliers run2: 4 outliers run3: 1 outlier 6 conditions

Pre: t-contrast (e.g., matlabbatch{3}.spm.stats.con.consess{10}.tcon.convec): [0.33333 0 0 0 0 0 0 0 0 0 0 0 0.33333 0 0 0 0 0 0 0 0 0 0 0 0.33333 0 0 0 0 0 0 0 0 0 0 0]

f-contrast: #cols: runs*(conditions + motion) note: motion is usually 6 (sometimes 0) #rows: runs(conditions) [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0]

Post: t-contrast: [0.33333 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33333 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33333 0 0 0 0 0 0 0 0 0 0 0 0] + + + + + + + + f-contrast: + + + + + + + + [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0] `

Initial test of genArtBatches:

genArtBatches('/mri01_users/mcmains/spm_scripting/test_1',1,0,1,2,3) Change to/mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_12ch/analysis writing cfg file and load SPM Change to~/mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_32ch/analysis writing cfg file and load SPM Successfully created ~/mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_32ch/art_analysis/art_exec001.m

cd ../test_1

ls 110808_12v32vis_SubjA_12ch/art_analysis/ art_config001.cfg

ls 110808_12v32vis_SubjA_32ch/art_analysis/ art_config001.cfg art_exec001.m

So looks like it didn't make the .m for first subject

Second test of genArt

cd ../CBS

genArtBatches('/mri01_users/mcmains/spm_scripting/test_1',1,0,1,2,3) Change to/mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_12ch/analysis Making new directory as follows: mkdir /mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_12ch/art_analysis writing cfg file and load SPM Change to/mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_32ch/analysis writing cfg file and load SPM Successfully created ~/mri01_users/mcmains/spm_scripting/test_1/110808_12v32vis_SubjA_32ch/art_analysis/art_exec001.m pwd

ans =

/ncf/mri/01/users/mcmains/spm_scripting/CBS

cd ../test_1

cd 110808_12v32vis_SubjA_12ch/ ls analysis art_analysis batch preproc RAW

ls art_analysis/ art_config001.cfg

ls ../110808_12v32vis_SubjA_32ch/art_analysis/ art_config001.cfg art_exec001.m

Looks like it still didn't make the .m file for the first one.


Level-1 Regressors: rp_f-run001-001.txt
Art Regressors + Motion: art_regression_outliers_and_movement_swrf-run001-001.mat
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