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help > problems with batch processing
Mar 29, 2017 03:03 PM | Sascha Froelich
problems with batch processing
Dear all,
I want to preprocess my data using batch preprocessing. This is my batch-file:
Thanks!
Best,
Sascha
EDIT: Nevermind everyone, I figured it out myself: Of course I have to spell out "BATCH" in all caps (instead of Batch.Setup it has to be BATCH.Setup etc.)
I want to preprocess my data using batch preprocessing. This is my batch-file:
clear BATCH;
Batch.New.RT=2;
Batch.New.sliceorder=[1:2:31,2:2:32];
Batch.New.FWHM=6;
Batch.New.VOX=2;BATCH.filename='/data_august/sascha/BEST/conn_best.mat';
Batch.Setup.isnew=1;
Batch.Setup.RT=2;
Batch.Setup.nsubjects=2;BATCH.New.steps={'realignment','slicetiming','coregistration','segmentation','normalization','smoothing','initialization'};
BATCH.New.functionals{1}{1}='/data_august/sascha/BEST/BEST-BN-001/rsfMRI/rsfMRI.nii';
BATCH.New.structurals{1}='/data_august/sascha/BEST/BEST-BN-001/ANAT/T1.nii';
BATCH.New.functionals{2}{1}='/data_august/sascha/BEST/BEST-BN-002/rsfMRI/rsfMRI.nii';
BATCH.New.structurals{2}='/data_august/sascha/BEST/BEST-BN-002/ANAT/T1.nii';
Batch.Preprocessing.filter=[.008 0.09];
Batch.Preprocessing.done=1;
conn_batch(BATCH);
When I execute it, conn asks me to manually enter the slice
acquisition order for each subject. Why? I specified the slice
order in the third line.Batch.New.RT=2;
Batch.New.sliceorder=[1:2:31,2:2:32];
Batch.New.FWHM=6;
Batch.New.VOX=2;BATCH.filename='/data_august/sascha/BEST/conn_best.mat';
Batch.Setup.isnew=1;
Batch.Setup.RT=2;
Batch.Setup.nsubjects=2;BATCH.New.steps={'realignment','slicetiming','coregistration','segmentation','normalization','smoothing','initialization'};
BATCH.New.functionals{1}{1}='/data_august/sascha/BEST/BEST-BN-001/rsfMRI/rsfMRI.nii';
BATCH.New.structurals{1}='/data_august/sascha/BEST/BEST-BN-001/ANAT/T1.nii';
BATCH.New.functionals{2}{1}='/data_august/sascha/BEST/BEST-BN-002/rsfMRI/rsfMRI.nii';
BATCH.New.structurals{2}='/data_august/sascha/BEST/BEST-BN-002/ANAT/T1.nii';
Batch.Preprocessing.filter=[.008 0.09];
Batch.Preprocessing.done=1;
conn_batch(BATCH);
Thanks!
Best,
Sascha
EDIT: Nevermind everyone, I figured it out myself: Of course I have to spell out "BATCH" in all caps (instead of Batch.Setup it has to be BATCH.Setup etc.)