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help > RE: text file with MNI (or Talairach) coordinates
May 1, 2014 05:05 AM | Alfonso Nieto-Castanon - Boston University
RE: text file with MNI (or Talairach) coordinates
Hi Mary
All WFU_Pickatlas atlases have been already converted to MNI space using Brett transform (see http://fmri.wfubmc.edu/downloads/WFU_Pic...), so if you generated your ROIs from the 'Human Atlas' box the resulting ROI files are correctly coregistered to 'normalized' (MNI) space. In CONN14 we started using the Lancaster transform (Lancaster et al. 2010) to generate the provided BA atlas, but the differences should be relatively minor. The main issue I would recommend keeping in mind when using WFU_Pickatlas is that their atlases are stored using a right-handed coordinate system, while most SPM files are stored using left-handed coordinate system. This is not a problem if you are using SPM5 or above (since this will read the appropriate orientation from the file header) but it may cause you some problems (flipping left/right hemispheres) if you are using at any point of the analyses SPM2 (since this version does not read the header info and it instead uses the defaults.analyze.flip info in spm_defaults.m to 'guess' the appropriate coordinate system).
Hope this helps
Alfonso
Originally posted by Mary Newsome:
All WFU_Pickatlas atlases have been already converted to MNI space using Brett transform (see http://fmri.wfubmc.edu/downloads/WFU_Pic...), so if you generated your ROIs from the 'Human Atlas' box the resulting ROI files are correctly coregistered to 'normalized' (MNI) space. In CONN14 we started using the Lancaster transform (Lancaster et al. 2010) to generate the provided BA atlas, but the differences should be relatively minor. The main issue I would recommend keeping in mind when using WFU_Pickatlas is that their atlases are stored using a right-handed coordinate system, while most SPM files are stored using left-handed coordinate system. This is not a problem if you are using SPM5 or above (since this will read the appropriate orientation from the file header) but it may cause you some problems (flipping left/right hemispheres) if you are using at any point of the analyses SPM2 (since this version does not read the header info and it instead uses the defaults.analyze.flip info in spm_defaults.m to 'guess' the appropriate coordinate system).
Hope this helps
Alfonso
Originally posted by Mary Newsome:
Hi. This question is about this portion of
the thread, "Alternatively you may also create a ROI image
file using WFU_pickatlas or some other tool and enter the resulting
.img files as ROIs in the toolbox."
I made an ROI in the WFU_Pickatlas, but later realized I likely made an error by creating it in Talairach space using the Talairach Daemon atlas option. I didn't see any MNI atlases in the version I have. When using WFU_Pickatlas, is there a particular atlas you would recommend to choose from the Human Atlas box on the left side of the gui?
Thanks so much for all of your help!
I made an ROI in the WFU_Pickatlas, but later realized I likely made an error by creating it in Talairach space using the Talairach Daemon atlas option. I didn't see any MNI atlases in the version I have. When using WFU_Pickatlas, is there a particular atlas you would recommend to choose from the Human Atlas box on the left side of the gui?
Thanks so much for all of your help!
Threaded View
| Title | Author | Date |
|---|---|---|
| Elise Lesage | Jan 5, 2012 | |
| Alfonso Nieto-Castanon | Jan 11, 2012 | |
| Mary Newsome | Apr 29, 2014 | |
| Alfonso Nieto-Castanon | May 1, 2014 | |