flexibleConCreation

Create standard contrasts + adjust for missing conditions flexibly

FIRST:

• Specify + estimate your model.
• This set of scripts requires that you already have an estimated SPM.mat that you'd like to run contrasts on.

TO CREATE CONTRAST VARS:

• (1) create txt file: contrastNames_analysis.txt, one contrast name per line (example in flexibleConCreation/conInfo/)
• (2) create txt file: contrastWeights_analysis.txt, a matrix of weights, one contrast per line, tab delimited (example in flexibleConCreation/conInfo/)
• (3) create txt file: condsRemoved_analysis.txt, a sub x cond matrix specifying missing (1) and existing (0) conditions (example in flexibleConCreation/conInfo/)
• (4) make contrast mats for each sub, using matlab script scripts/makeCustomConMats.m (output goes to flexibleConCreation/customCons/, but you should change that)

STOP!

• You might want to check whether your output files look as they should. You can do this by loading the customContrast .mats into the Matlab workspace, and then comparing the variable "finalConMat" to your original contrastWeights txt file.
• Find a subject who has no missing conditions across any run. Their finalConMat variable should be identical to your text file.
• Find a subject who has at least one missing condition. Their finalConMat variable should be similar to the text file, with the missing columns removed.
• Find a contrast that includes a nonzero number in one of the missing conditions. The weights should have been rescaled appropriately so that all positive numbers add to 1, and all negative numbers add to 1 (check this).

NOTE:

• Normally we create a template script for a template subject, and replicate it across subs.
• In this case, we'll first make a template script for a single contrast (for sub 1), and then replicate it across CONTRASTS.
• Then, we can use the N contrasts created to make a script for a template sub.
• Finally, we replicate across subs as we usually would.

MAKE CONTRAST TEMPLATE FOR SUB 1, CON999:

• An example is in spmFiles/templates/
• Should have index 999 at the end of the filename
• It will use "load matlab variables" and "access matlab variables" modules.
• YOU MUST: (1) Update the path to the customContrasts .mat file for that subject (2) Update the path for the SPM.mat that was created from your model specification/estimation for that subject

CREATE TEMPLATE FOR SUB 1:

• Replicate the contrast template script you just made, for contrasts 1 through N, using the bash code in scripts/replicateConJobs.txt
• It's really primitive and uses "sed" to replace contrast numbers, but it works!
• Just copy and paste the code from the text file into the terminal, + it'll be nearly instantaneous
• You should now have N contrast scripts, for contrasts 1 thru N, for subject 1
• Load these N contrast scripts into batch editor (in order), and save the whole thing as a .mat

REPLICATE FOR ALL SUBS:

• Use spmbatch.m to replicate for all subjects as usual