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syam.gadde
BIAC Staff
USA
421 Posts |
 Posted - Oct 16 2014 : 2:38:17 PM
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--corrlabel specifies the image for the atlas. Defaults are:
--corrlabel /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/aal_MNI_V4.nii
--corrtext /usr/local/packages/MATLAB/WFU_PickAtlas_3.0.1/wfu_pickatlas/MNI_atlas_templates/aal_MNI_V4.txt
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jlh125
Starting Member
USA
3 Posts |
Posted - Feb 16 2016 : 4:10:06 PM
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| I wondered how best to use this script if you had multiple resting state runs from the same subject? Our group had two ~4 mins scans per subject. Is it reasonable to just combine the two resting state NIFTI files before Step 7 of the script (and simply concatenate the .par files output from step 2 for scrubbing)? Would that be reasonable? |
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Jeff_Browndyke
Junior Member
35 Posts |
Posted - Feb 16 2016 : 4:22:44 PM
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| I'm not certain how the BIAC resting pipeline handles data, but I don't believe simply concatenating resting state runs is advisable as it would cause problems for any linear detrending correction. |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Feb 16 2016 : 4:52:15 PM
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In this case, the suggestion was to concatenate the two runs after most of the pre-processing (including time-based filtering), but just before the parcellation and correlation, so each input would have been detrended individually.
Just don't be surprised if it sacrifices the volumes at the "splice" point, depending on the metric you use for scrubbing, as the two .par files (from mcflirt) are based on different reference volumes in each run, and so there may be a discontinuity at the concatenation. FD and "motion" metrics will be affected most by the discontinuity, DVARS may not notice it. |
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jlh125
Starting Member
USA
3 Posts |
Posted - Feb 16 2016 : 5:24:14 PM
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quote:
Originally posted by syam.gadde
In this case, the suggestion was to concatenate the two runs after most of the pre-processing (including time-based filtering), but just before the parcellation and correlation, so each input would have been detrended individually.
Just don't be surprised if it sacrifices the volumes at the "splice" point, depending on the metric you use for scrubbing, as the two .par files (from mcflirt) are based on different reference volumes in each run, and so there may be a discontinuity at the concatenation. FD and "motion" metrics will be affected most by the discontinuity, DVARS may not notice it.
That is what I thought might happen. That wouldn't be ideal, but might be acceptable for some pilot analyses. Any alternative suggestions? |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Feb 16 2016 : 6:40:30 PM
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| I wasn't saying you should be worried about it, just be aware. I don't think you'll miss the two or so volumes that it might remove, given the length of your runs. |
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jlh125
Starting Member
USA
3 Posts |
Posted - Feb 19 2016 : 11:36:55 AM
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| Just a quick clarification (specifically related to combining multiple runs), are the resting state run de-meaned? (and if so, when in the script?) |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Feb 19 2016 : 11:56:04 AM
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| It seems there is some re-meaning (i.e. adding back the mean) after WM/CSF regression, and then some rescaling of the data, all in step4 and step6. However, as far as step7/correlation is concerned, if two regions are linearly-correlated in both runs individually, I think that will be reflected in the concatenated runs too, even without explicitly demeaning the inputs, assuming similar variance in the two runs. However I am not a statistician and you could certainly demean the inputs yourself before sending them to step 7 if you wanted to be safe. |
Edited by - syam.gadde on Feb 19 2016 11:57:19 AM |
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resting_pipeline-beta
