Hi,
My main question is, is there a way of specifying in batch preferably (but also in GUI), that you want each session to be realigned intra-session (and not to the first volume of the first session or mean volume of every session)?
Below a detailed description of solutions I have tried, and what is not working.
Recently I encountered significant problems when using Realignment & Unwarping on data from 4 session across two different days. This step completely failed for some subjects, I think because it couldn't properly realign for some subjects across days.
My solution was to process each session at a time, which works much better after looking at the images on SPM.
I suppose this works much better because now realignment is done using the first image of each session, or the mean of each session (rather than overall mean of first image of the first session).
Now here's the problem:[list][*]I don't know how to specify this on the batch, so I prepare everything in the batch and launch each session individually from the GUI[*]I use distributed processing. When the jobs are merged, and everything is done, I notice that starting in session 3, the images are no longer attributed in the GUI, with the exception of subject 1 which is correctly attributed in the GUI... That is, the images exist for the other subjects, were created, and look fine. But the primary dataset of subjects other than 1, session 3, is still the "f" image...[*]The same that is described above happens to the 1st level covariates[/list]
I don't know if this is relevant, but session 3 happens to be the first of day 5.
I also get a warning about "Mismatched second-level covariate names with..." starting in session 3. This could potentially be the problem, but I don't see why this would affect attribution of the rest of the info
Thanks in advance!
My main question is, is there a way of specifying in batch preferably (but also in GUI), that you want each session to be realigned intra-session (and not to the first volume of the first session or mean volume of every session)?
Below a detailed description of solutions I have tried, and what is not working.
Recently I encountered significant problems when using Realignment & Unwarping on data from 4 session across two different days. This step completely failed for some subjects, I think because it couldn't properly realign for some subjects across days.
My solution was to process each session at a time, which works much better after looking at the images on SPM.
I suppose this works much better because now realignment is done using the first image of each session, or the mean of each session (rather than overall mean of first image of the first session).
Now here's the problem:[list][*]I don't know how to specify this on the batch, so I prepare everything in the batch and launch each session individually from the GUI[*]I use distributed processing. When the jobs are merged, and everything is done, I notice that starting in session 3, the images are no longer attributed in the GUI, with the exception of subject 1 which is correctly attributed in the GUI... That is, the images exist for the other subjects, were created, and look fine. But the primary dataset of subjects other than 1, session 3, is still the "f" image...[*]The same that is described above happens to the 1st level covariates[/list]
I don't know if this is relevant, but session 3 happens to be the first of day 5.
I also get a warning about "Mismatched second-level covariate names with..." starting in session 3. This could potentially be the problem, but I don't see why this would affect attribution of the rest of the info
Thanks in advance!