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help > RE: CONN Scripting Adding New Subjects w dif TR, scan order, slice number
Nov 24, 2022 04:11 PM | Alfonso Nieto-Castanon - Boston University
RE: CONN Scripting Adding New Subjects w dif TR, scan order, slice number
Hi,
To enter different TR values per subject simply enter a vector (with one value per subject) in the batch.Setup.RT field.
Alternatively you may also set batch.Setup.RT=nan and then have the specific TR values listed in a sidecar .json file (one .json file for each individual NIFTI file) indicating the TR values in a 'RepetitionTime' field.
Similarly, if you have functional runs with different slice orders, you may enter in Setup.preprocessing.sliceorder the value 'BIDS' and then have that information specified in the same .json files as above (now in a field named 'SliceTiming')
And regarding adding new subjects in general, if you use batch.Setup.isnew=1 that will start your project from scratch, disregarding any already-processed subects (which is fine if you want to reprocess all existing and new subjects in a project). If instead you just want to add new subjects to an already-defined project, I would suggest to create a new batch script where you set batch.Setup.isnew=0 and batch.Setup.add=1 and enter in your batch structure ONLY the information for the new subjects (and it does not matter in this case whether you use overwrite='Yes' since only the new subjects are being considered). See "help conn_batch" for additional details
Hope this helps
Alfonso
Originally posted by henryblair:
To enter different TR values per subject simply enter a vector (with one value per subject) in the batch.Setup.RT field.
Alternatively you may also set batch.Setup.RT=nan and then have the specific TR values listed in a sidecar .json file (one .json file for each individual NIFTI file) indicating the TR values in a 'RepetitionTime' field.
Similarly, if you have functional runs with different slice orders, you may enter in Setup.preprocessing.sliceorder the value 'BIDS' and then have that information specified in the same .json files as above (now in a field named 'SliceTiming')
And regarding adding new subjects in general, if you use batch.Setup.isnew=1 that will start your project from scratch, disregarding any already-processed subects (which is fine if you want to reprocess all existing and new subjects in a project). If instead you just want to add new subjects to an already-defined project, I would suggest to create a new batch script where you set batch.Setup.isnew=0 and batch.Setup.add=1 and enter in your batch structure ONLY the information for the new subjects (and it does not matter in this case whether you use overwrite='Yes' since only the new subjects are being considered). See "help conn_batch" for additional details
Hope this helps
Alfonso
Originally posted by henryblair:
Hi,
So I am using CONN and I have a scripted preprocessing and analysis. I was wondering if anyone had experience adding subjects from a new site wherein there were different scan parameters - TR, slice number, scan order. I am asking because I would like to make my project more powerful but the subjects I would like to add use a different repition time. I also have some general questions about my script, which I modified and found from a few different places online. I have pasted parts of my it below.
Thank you
TR= ____ % I will change this value (would this be part of the batch.setup.preprocessing..?)
...
batch.Setup.isnew=1; %honestly not sure what this means but I run it every time.
...
batch.Setup.preprocessing.steps='default_mni';
batch.Setup.preprocessing.sliceorder='interleaved (Siemens)'; %I may change this part
BATCH.Preprocessing.done=1;
BATCH.Preprocessing.overwrite='No'; %Will this mean all my other subjects (already denoised, analyzed) will not be impacted? Does it matter if I import a new file for covariates because I am adding more subjects. Alternatively do I need to write 'yes' also if I am adding more covariates. I know that its not a part of preprocessing but double checking
batch.Setup.done=1;
batch.Setup.overwrite='Yes'; %should this be set to yes. what would yes vs no do?
...
batch.Denoising.overwrite='Yes'; %should I overwrite denoising for past subjects? Not changing anything.
...
batch.Analysis.overwrite='Yes'; %assuming I should overwrite 'yes' if adding more subjects and changing covariate file
So I am using CONN and I have a scripted preprocessing and analysis. I was wondering if anyone had experience adding subjects from a new site wherein there were different scan parameters - TR, slice number, scan order. I am asking because I would like to make my project more powerful but the subjects I would like to add use a different repition time. I also have some general questions about my script, which I modified and found from a few different places online. I have pasted parts of my it below.
Thank you
TR= ____ % I will change this value (would this be part of the batch.setup.preprocessing..?)
...
batch.Setup.isnew=1; %honestly not sure what this means but I run it every time.
...
batch.Setup.preprocessing.steps='default_mni';
batch.Setup.preprocessing.sliceorder='interleaved (Siemens)'; %I may change this part
BATCH.Preprocessing.done=1;
BATCH.Preprocessing.overwrite='No'; %Will this mean all my other subjects (already denoised, analyzed) will not be impacted? Does it matter if I import a new file for covariates because I am adding more subjects. Alternatively do I need to write 'yes' also if I am adding more covariates. I know that its not a part of preprocessing but double checking
batch.Setup.done=1;
batch.Setup.overwrite='Yes'; %should this be set to yes. what would yes vs no do?
...
batch.Denoising.overwrite='Yes'; %should I overwrite denoising for past subjects? Not changing anything.
...
batch.Analysis.overwrite='Yes'; %assuming I should overwrite 'yes' if adding more subjects and changing covariate file
Threaded View
| Title | Author | Date |
|---|---|---|
| henryblair | Nov 9, 2022 | |
| Alfonso Nieto-Castanon | Nov 24, 2022 | |
| henryblair | Nov 23, 2022 | |