Dear Elveda,

Please attach your atlas *.txt file to better understand what the format problem might be. In general if your atlas myatlas.nii file contains ROI ids/numbers that range, for example, from 1 to 5, and you would like to associated with these numbers the labels "ROI1" to "ROI5", you can define the associated labels file using any of the following methods:

1) create an associated .txt file containing only the associated labels (in order). See for example BA.txt file. E.g.

myatlas.txt
ROI1
ROI2
ROI3
ROI4
ROI5

2) create an associated .txt file containing two tab-separated columns, indicating ROI ids followed by ROI labels (ROIs listed in any order). See for example any freesurfer *LUT.txt file. E.g.

myatlas.txt
3 ROI3
4 ROI4
1 ROI1
2  ROI2
5  ROI5

3) create an associated .csv file containing two comma-separated columns, indicating ROI labels followed by ROI ids (ROIs listed in any order).  E.g.

myatlas.csv
ROI3, 3
ROI4, 4
ROI1, 1
ROI2, 2
ROI5, 5

4) create an associated .xls file containing two columns, indicating ROI ids followed by ROI labels (ROIs listed in any order, columns listed in any order; id's should be numeric, labels should be strings; file may include a first-row header or not). E.g.

myatlas.xls
ROI3 3
ROI4 4
ROI1 1
ROI2 2
ROI5 5

The first format above only works when your atlas file contains sequential numbers from 1 to N, while the last three formats work for any numbering scheme for your ROI atlas file (e.g. non-sequential numbers)

Hope this helps
Alfonso


Originally posted by Elveda Yildirim: