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help > RE: Labeling Multiple-ROI Masks (Atlas Files)
Nov 12, 2015 12:11 AM | Alfonso Nieto-Castanon - Boston University
RE: Labeling Multiple-ROI Masks (Atlas Files)
Hi Buddhika,
The accompanying text file looks perfectly fine, could you please double-check that your original ROI file (i.e. NALL_Power.nii) contains the expected range of 1 to 229 numbers? You can do this for example using something like:
a = spm_vol('NALL_Power.nii');
b = spm_read_vols(a);
disp(unique(b)');
which should show 230 numbers (from 0 to 229). If in doubt please send me that file and I will quickly check if everything looks fine there as well.
Best
Alfonso
Originally posted by Buddhika Bellana:
The accompanying text file looks perfectly fine, could you please double-check that your original ROI file (i.e. NALL_Power.nii) contains the expected range of 1 to 229 numbers? You can do this for example using something like:
a = spm_vol('NALL_Power.nii');
b = spm_read_vols(a);
disp(unique(b)');
which should show 230 numbers (from 0 to 229). If in doubt please send me that file and I will quickly check if everything looks fine there as well.
Best
Alfonso
Originally posted by Buddhika Bellana:
Hi,
I have created a mask (i.e., "atlas file", according to the manual) based on a set of 229 coordinates using FSL. Similar to the AAL atlas file provided by CONN, the mask I made contains multiple separable ROIs (a 5mm sphere centered around each coordinate, with increasing intensity values for each coordinate, just like the AAL mask). CONN has no problem using this mask and produces timecourses for each ROI within the mask. However, unlike the AAL atlas that comes with CONN, I cannot get CONN to accept the accompanying text file containing the labels of each ROI within the mask, so when I look at the results each ROI lacks their respective label. I've attached my text file to this message.
Anyone else run into this issue? Are there specific instructions regarding the creation of the text files containing labels for multiple ROI masks? I've tried renaming the file, removing underscores and still can't get the labeling to work.
Any help would be greatly appreciated!
Buddhika
I have created a mask (i.e., "atlas file", according to the manual) based on a set of 229 coordinates using FSL. Similar to the AAL atlas file provided by CONN, the mask I made contains multiple separable ROIs (a 5mm sphere centered around each coordinate, with increasing intensity values for each coordinate, just like the AAL mask). CONN has no problem using this mask and produces timecourses for each ROI within the mask. However, unlike the AAL atlas that comes with CONN, I cannot get CONN to accept the accompanying text file containing the labels of each ROI within the mask, so when I look at the results each ROI lacks their respective label. I've attached my text file to this message.
Anyone else run into this issue? Are there specific instructions regarding the creation of the text files containing labels for multiple ROI masks? I've tried renaming the file, removing underscores and still can't get the labeling to work.
Any help would be greatly appreciated!
Buddhika
Threaded View
| Title | Author | Date |
|---|---|---|
| Buddhika Bellana | Nov 11, 2015 | |
| Buddhika Bellana | Nov 16, 2015 | |
| Alfonso Nieto-Castanon | Nov 12, 2015 | |
| Buddhika Bellana | Nov 12, 2015 | |
| Alfonso Nieto-Castanon | Nov 16, 2015 | |
| Buddhika Bellana | Nov 17, 2015 | |