Option to pick only last structural when there are multiple MPRAGEs
Put this in your user script
aap.options.autoidentifystructural_chooselast=1;
Additional parameters can be passed to realignment/slicetime correction
Description: You can now pass extra parameters to aamod_realign and aamod_slicetiming via the aap.spmanalysis fields:
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aap.spmanalysis.reslicewhich |
% 0 = do not reslice any image (CBU default) |
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% 1 = do not reslice first image (if realigned to first) |
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% 2 = reslice all images (e.g, if want to perform slicetiming after realignment) |
aap.spmanalysis.writemean |
% 1 = write mean (default), 0 = do not |
aap.spmanalysis.refslice |
% reference slice for slicetiming correction (CBU default=1) |
Also, more of the standard SPM defaults apply to aamod_realign (rather than being hard-coded in aamod_realign).
Authors: Rik Henson, Doris Eckstein
Changed source of EPI file prefix
Previously, a single parameter allowed changing of the EPI file prefixes that were looked for, so that slice timing could be included or not. This was the aap.directory_conventions.forrealign_fileprefix, which as either 'f' for no slice timing or 'af' if slice timing was used. It was appended by realign and all subsequent modules.
This did not allow much flexibility for other stages to be included (e.g., realign & unwarp, which adds 'u') or for slice timing to be shifted to after realignment.
I have now moved the file prefixes to the 'tasklist' parameter list, which is where it really belongs. Instead of one long list, tasks are now added using the new aas_addtask command. For stages that take EPI input, the aas_addtask command can optionally include a third parameter that specifies the prefix of the EPIs for this stage. So, a section of a typical tasklist specification ends looks like this:
aap=aas_addtask(aap,'aamod_realignunwrap','f');
aap=aas_addtask(aap,'aamod_slicetiming','uf');
aap=aas_addtask(aap,'aamod_coreg_noss','auf');
aap=aas_addtask(aap,'aamod_norm_noss','auf');
aap=aas_addtask(aap,'aamod_norm_write','auf');
aap=aas_addtask(aap,'aamod_smooth','wauf');
Hopefully, this provides much more flexibility for stage reordering, or additional stages.
Author: Rhodri Cusack
Changed .mat file for normalisation
Description: Changed name of _sn.mat and _sn_inv.mat files produced by normalisation to ms* instead of s* to reflect their origin in second pass
Author: Doris Eckstein
New recipes
The default processing stream has changed in the new "general" recipes, with slice timing now AFTER realignment. This is thought to be better if slices have been acquired in a sequential rather than interleaved order. The files have also been tidied up. There is a full description of the recipes and of some issues in choosing an appropriate recipe on this new page AutomaticAnalysisRecipes.
Conversion of aribitrary special series
New aa mechanism for converting arbitrary series: - add fifth parameter to aas_addsubject command specifying series to be converted - use recipe
- aarecipe_notforfmri_ver00
They'll be converted and put in [subjectdir]/specialseries
See example in /imaging/local/spm/aa/aa_ver1_devel/examples/aa_user_notforfmri.m
Author: Rhodri Cusack