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help > RE: Structural/functional image overlay error
Jul 30, 2015 07:07 PM | Alfonso Nieto-Castanon - Boston University
RE: Structural/functional image overlay error
Hi Morgan,
Perhaps the simplest approach to do this would be the following:
1) skip the wizard and enter your original (before any preprocessing steps) functional and anatomical data in Setup.Functional and Setup.Structural, respectively.
2) then click on 'Preprocessing' and manually flip the appropriate subjects (i.e. add the 'manually reorient functionals' and 'manually reorient structural' steps to your list of preprocessing steps, then select the 'flip along x-direction' option for each of those steps, uncheck the 'all subjects' option and select only those subjects that you want to flip, and click 'Done')
3) then click on 'Preprocessing' again and now select the standard pipeline that you would want to apply (e.g. select 'default MNI direct normalization' pipeline and click 'add', then click 'Done') and proceed normally from this point on
Hope this helps
Alfonso
Originally posted by Morgan Foreman:
Perhaps the simplest approach to do this would be the following:
1) skip the wizard and enter your original (before any preprocessing steps) functional and anatomical data in Setup.Functional and Setup.Structural, respectively.
2) then click on 'Preprocessing' and manually flip the appropriate subjects (i.e. add the 'manually reorient functionals' and 'manually reorient structural' steps to your list of preprocessing steps, then select the 'flip along x-direction' option for each of those steps, uncheck the 'all subjects' option and select only those subjects that you want to flip, and click 'Done')
3) then click on 'Preprocessing' again and now select the standard pipeline that you would want to apply (e.g. select 'default MNI direct normalization' pipeline and click 'add', then click 'Done') and proceed normally from this point on
Hope this helps
Alfonso
Originally posted by Morgan Foreman:
Thanks for your help, Alfonso.
I took a look at all of the 'check coregistration' options you suggested and couldn't find an issue.
As a work around I created a new project and used the Wizard to select data and have preprocessing go through Conn. This worked out well (no issues with coregistration when I got to denoising!) but now I have a new question: my images are all brains with stroke infarcts, some in the left hemisphere and some in the right. I would like to set up my Conn analysis so that all infarcts are in the left hemisphere (so rather than left side corresponding to left hemisphere, left side corresponds to ipsilesional hemisphere). Any suggestions on how to make this happen while still using the wizard? I can flip the necessary structural T1 images, but the corresponding functional images will not be flipped.
Thank you for your help,
Morgan
I took a look at all of the 'check coregistration' options you suggested and couldn't find an issue.
As a work around I created a new project and used the Wizard to select data and have preprocessing go through Conn. This worked out well (no issues with coregistration when I got to denoising!) but now I have a new question: my images are all brains with stroke infarcts, some in the left hemisphere and some in the right. I would like to set up my Conn analysis so that all infarcts are in the left hemisphere (so rather than left side corresponding to left hemisphere, left side corresponds to ipsilesional hemisphere). Any suggestions on how to make this happen while still using the wizard? I can flip the necessary structural T1 images, but the corresponding functional images will not be flipped.
Thank you for your help,
Morgan
Threaded View
| Title | Author | Date |
|---|---|---|
| Morgan Foreman | Jul 29, 2015 | |
| Alfonso Nieto-Castanon | Jul 30, 2015 | |
| Morgan Foreman | Jul 30, 2015 | |
| Alfonso Nieto-Castanon | Jul 30, 2015 | |
| gol mi | Sep 9, 2017 | |