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help > How to remove first-order derivatives of realignment parameters in conn_batch_humanconnectomeproject's
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Sep 10, 2019 04:09 PM | mohammad reza
How to remove first-order derivatives of realignment parameters in conn_batch_humanconnectomeproject's
onDear CONN developers,
Thank you for your great toolbox, I really enjoy using it!
I have a problem regarding the editing of CONN_batch_humanconnectomeproject. Since HCP has included the motion parameters and its derivatives in its motion parameter text file, I didn't want to add first-order temporal derivatives to the the realignment confound parameters. So in the conn_batch_humanconnectomeproject I added:
Unfortunately, after the processing of the data, the default setup won't get changed and CONN add first-order temporal derivatives of the realignments which results in 24 parameters of realignment. Also, even if "effect of rest" was not selected in the batch commands, after loading the results in the GUI, it was in the list of the confounds.
I know this problem can be solved by editing the GUI but due to the large sample size of HCP, I prefer using the batch commands.
Thank you!
Best,
Mohammad
Thank you for your great toolbox, I really enjoy using it!
I have a problem regarding the editing of CONN_batch_humanconnectomeproject. Since HCP has included the motion parameters and its derivatives in its motion parameter text file, I didn't want to add first-order temporal derivatives to the the realignment confound parameters. So in the conn_batch_humanconnectomeproject I added:
batch.Preprocessing.confounds.names={'White','CSF','scrubbing','realigment'};
batch.Preprocessing.confounds.dimensions={5,5,6,12};
batch.Preprocessing.confounds.deriv={0,0,0,0};
Unfortunately, after the processing of the data, the default setup won't get changed and CONN add first-order temporal derivatives of the realignments which results in 24 parameters of realignment. Also, even if "effect of rest" was not selected in the batch commands, after loading the results in the GUI, it was in the list of the confounds.
I know this problem can be solved by editing the GUI but due to the large sample size of HCP, I prefer using the batch commands.
Thank you!
Best,
Mohammad
Sep 10, 2019 07:09 PM | Alfonso Nieto-Castanon - Boston University
RE: How to remove first-order derivatives of realignment parameters in conn_batch_humanconnectomeproject's
Hi Mohammad,
Please try changing your "batch.Preprocessing.confounds" fieldnames to "batch.Denoising.confounds" and let me know if everything seems to be working fine now (for this you may simply re-run the Denoising step for testing purposes if you prefer).
Best
Alfonso
Originally posted by mohammad reza:
Please try changing your "batch.Preprocessing.confounds" fieldnames to "batch.Denoising.confounds" and let me know if everything seems to be working fine now (for this you may simply re-run the Denoising step for testing purposes if you prefer).
Best
Alfonso
Originally posted by mohammad reza:
onDear CONN developers,
Thank you for your great toolbox, I really enjoy using it!
I have a problem regarding the editing of CONN_batch_humanconnectomeproject. Since HCP has included the motion parameters and its derivatives in its motion parameter text file, I didn't want to add first-order temporal derivatives to the the realignment confound parameters. So in the conn_batch_humanconnectomeproject I added:
Unfortunately, after the processing of the data, the default setup won't get changed and CONN add first-order temporal derivatives of the realignments which results in 24 parameters of realignment. Also, even if "effect of rest" was not selected in the batch commands, after loading the results in the GUI, it was in the list of the confounds.
I know this problem can be solved by editing the GUI but due to the large sample size of HCP, I prefer using the batch commands.
Thank you!
Best,
Mohammad
Thank you for your great toolbox, I really enjoy using it!
I have a problem regarding the editing of CONN_batch_humanconnectomeproject. Since HCP has included the motion parameters and its derivatives in its motion parameter text file, I didn't want to add first-order temporal derivatives to the the realignment confound parameters. So in the conn_batch_humanconnectomeproject I added:
batch.Preprocessing.confounds.names={'White','CSF','scrubbing','realigment'};
batch.Preprocessing.confounds.dimensions={5,5,6,12};
batch.Preprocessing.confounds.deriv={0,0,0,0};
Unfortunately, after the processing of the data, the default setup won't get changed and CONN add first-order temporal derivatives of the realignments which results in 24 parameters of realignment. Also, even if "effect of rest" was not selected in the batch commands, after loading the results in the GUI, it was in the list of the confounds.
I know this problem can be solved by editing the GUI but due to the large sample size of HCP, I prefer using the batch commands.
Thank you!
Best,
Mohammad
Sep 13, 2019 08:09 PM | mohammad reza
RE: How to remove first-order derivatives of realignment parameters in conn_batch_humanconnectomeproject's
Dear Alfonso,
The problem solved, the "batch.Denoising.confounds" command works perfect!
Thank you!
Best,
Mohammad
The problem solved, the "batch.Denoising.confounds" command works perfect!
Thank you!
Best,
Mohammad