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help > RE: Misaligned export mask
Sep 9, 2021 12:09 PM | Alfonso Nieto-Castanon - Boston University
RE: Misaligned export mask
Hi Denise,
Thanks for the clarification. For that you may either resample the mask to the target size/resolution (e.g. using spm_imcalc), or perhaps easier extract the signal using some other software which does not require the mask and source data to have the same resolution or bounding box, e.g. (using CONN's rex function)
[data, names] = rex( 'mydata.nii', 'PCCmask.ROIs_1.img', 'level', 'clusters' );
Note that this expects the data and mask to be coregistered (in the same space) even if both files do not have the same resolution or bounding boxes.
Hope this helps
Alfonso
Originally posted by sungoku:
Thanks for the clarification. For that you may either resample the mask to the target size/resolution (e.g. using spm_imcalc), or perhaps easier extract the signal using some other software which does not require the mask and source data to have the same resolution or bounding box, e.g. (using CONN's rex function)
[data, names] = rex( 'mydata.nii', 'PCCmask.ROIs_1.img', 'level', 'clusters' );
Note that this expects the data and mask to be coregistered (in the same space) even if both files do not have the same resolution or bounding boxes.
Hope this helps
Alfonso
Originally posted by sungoku:
But this makes problems when extracting signals,
the extracting tool kept report error that the mask size was not
the same as images. Some error like this:
"Mask does not match.
Mask size is 147x183x154, not same with required size 181x217x181".
I need the mask to have exact the same size as normalised images. How can I do that ?
Originally posted by Alfonso Nieto-Castanon:
"Mask does not match.
Mask size is 147x183x154, not same with required size 181x217x181".
I need the mask to have exact the same size as normalised images. How can I do that ?
Originally posted by Alfonso Nieto-Castanon:
Hi
Denise,
The mask file looks perfectly fine to me (it seems to be a medial prefrontal mask) . If you use something like:
spm_check_registration /software/spm12/canonical/avg152T1.nii PCCmask.ROIs_1.img
you should be able to see the coregistration between this mask and a canonical template. Let me know if you still run into any issues and/or if I am missing something else here.
Best
Alfonso
Originally posted by Denise Pergolizzi:
The mask file looks perfectly fine to me (it seems to be a medial prefrontal mask) . If you use something like:
spm_check_registration /software/spm12/canonical/avg152T1.nii PCCmask.ROIs_1.img
you should be able to see the coregistration between this mask and a canonical template. Let me know if you still run into any issues and/or if I am missing something else here.
Best
Alfonso
Originally posted by Denise Pergolizzi:
Sorry about that, hdr attached. Thanks!
Threaded View
| Title | Author | Date |
|---|---|---|
| Denise Pergolizzi | Jan 27, 2016 | |
| Alfonso Nieto-Castanon | Jan 27, 2016 | |
| Denise Pergolizzi | Jan 28, 2016 | |
| Alfonso Nieto-Castanon | Jan 29, 2016 | |
| sungoku | Sep 6, 2021 | |
| Alfonso Nieto-Castanon | Sep 9, 2021 | |