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help > RE: Surface ROIs
Oct 5, 2018 08:10 PM | Daniel Berge - Hospital del Mar Medical Research Institute (IMIM)
RE: Surface ROIs
Hi Justyna,
I came accross the same issue some months ago. You have to copy the "FreeSurferColorLUT.txt" from freesurfer in each subject folder where the aparc.a2009s+aseg.nii is stored, and rename it exactly with the same name (except for the extension, which should be .txt). For instance, if you have foldersubj/ROI/aparc.a2009s+aseg.nii you should copy the FreeSurferColorLUT.txt in foldersubj/ROI, and rename it as /aparc.a2009s+aseg.txt.
Then, if you are using the conn batch to load the ROIs, it will automatically identify it as an atlas file, and thus, once you run the setup done, you should see in the denoising tab, as many ROI as the atlas has, usually called like aparc.a2009s+aseg.lh.ctx-anteriorcingulate .....
If you are just loading the ROIs through the GUI, just click the option "atlas file" or something like this, and again, after you run the setup, the ROIs should appear in the denoising step.
Hope this helps.
Dani Bergé
Originally posted by Justyna Beresniewicz:
I came accross the same issue some months ago. You have to copy the "FreeSurferColorLUT.txt" from freesurfer in each subject folder where the aparc.a2009s+aseg.nii is stored, and rename it exactly with the same name (except for the extension, which should be .txt). For instance, if you have foldersubj/ROI/aparc.a2009s+aseg.nii you should copy the FreeSurferColorLUT.txt in foldersubj/ROI, and rename it as /aparc.a2009s+aseg.txt.
Then, if you are using the conn batch to load the ROIs, it will automatically identify it as an atlas file, and thus, once you run the setup done, you should see in the denoising tab, as many ROI as the atlas has, usually called like aparc.a2009s+aseg.lh.ctx-anteriorcingulate .....
If you are just loading the ROIs through the GUI, just click the option "atlas file" or something like this, and again, after you run the setup, the ROIs should appear in the denoising step.
Hope this helps.
Dani Bergé
Originally posted by Justyna Beresniewicz:
Hi,
I am also trying to perform first level analysis using Freesurfer parcellation. As you advised in the previous post I used patient-specific parcellation file aprac.a2009s+aseg.nii (one for each subject). However, in the output file I obtained only one seed, and no division into ROIs. I should obtain 148 seed ROIs. I guess I am doing something really wrong. Could you please advise me what should I do in order to obtain correlations for all ROIs in the parcellation file?
Best regards,
Justyna
I am also trying to perform first level analysis using Freesurfer parcellation. As you advised in the previous post I used patient-specific parcellation file aprac.a2009s+aseg.nii (one for each subject). However, in the output file I obtained only one seed, and no division into ROIs. I should obtain 148 seed ROIs. I guess I am doing something really wrong. Could you please advise me what should I do in order to obtain correlations for all ROIs in the parcellation file?
Best regards,
Justyna
Threaded View
| Title | Author | Date |
|---|---|---|
| Sami Abboud | Feb 27, 2017 | |
| Alfonso Nieto-Castanon | Mar 1, 2017 | |
| Justyna Beresniewicz | Oct 5, 2018 | |
| Daniel Berge | Oct 5, 2018 | |
| Sami Abboud | Mar 1, 2017 | |
| Alfonso Nieto-Castanon | Mar 7, 2017 | |