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help > RE: Changing the atlas
Jul 8, 2012 10:07 PM | Alfonso Nieto-Castanon - Boston University
RE: Changing the atlas
Dear Farras,
To use a different ROI atlas file you may simply select the new atlas file from the gui (e.g. in Setup->rois, simply enter a new ROI line in the ROIs list, enter a name for this atlas, and then select all subjects and select the atlas116.img file) or use a batch script entering the new atlas information in the field batch.setup.rois (see the batch manual for more details). Yet another option is to simply include the atlas116.img file in the conn/rois/ folder and that will include all the ROIs in this atlas by default on every new project that you create. Any of these options will use the ROIs defined in your atlas file as new ROIs (for seed-to-voxel and/or ROI-to-ROI analyses). The line that you are changing, nevertheless, is used for display/information-purposes only (when you right-click on a voxel in any whole-brain display within the conn gui, it will tell you its spatial coordinates as well as the BA area that this voxel may belong to). Unfortunately I have not included yet a simpler option to change the default BA atlas used for these displays, so if this is what you would like to change, I am afraid that for now editing that line is the simplest option to achieve this (I will make sure to add in the next release of the toolbox a simpler option to allow you to use other atlases for these displays). Let me know if this clarifies.
Best
Alfonso
Originally posted by Farras Abdelnour:
To use a different ROI atlas file you may simply select the new atlas file from the gui (e.g. in Setup->rois, simply enter a new ROI line in the ROIs list, enter a name for this atlas, and then select all subjects and select the atlas116.img file) or use a batch script entering the new atlas information in the field batch.setup.rois (see the batch manual for more details). Yet another option is to simply include the atlas116.img file in the conn/rois/ folder and that will include all the ROIs in this atlas by default on every new project that you create. Any of these options will use the ROIs defined in your atlas file as new ROIs (for seed-to-voxel and/or ROI-to-ROI analyses). The line that you are changing, nevertheless, is used for display/information-purposes only (when you right-click on a voxel in any whole-brain display within the conn gui, it will tell you its spatial coordinates as well as the BA area that this voxel may belong to). Unfortunately I have not included yet a simpler option to change the default BA atlas used for these displays, so if this is what you would like to change, I am afraid that for now editing that line is the simplest option to achieve this (I will make sure to add in the next release of the toolbox a simpler option to allow you to use other atlases for these displays). Let me know if this clarifies.
Best
Alfonso
Originally posted by Farras Abdelnour:
Dear all,
I've been using an atlas with 116 ROI on conjunction with conn.m. For this, I needed to slightly modify the program around line 267 as follows:
filename = fullfile(fileparts(which('conn')),'rois',''atlas116.img');
As I will be using different atlases, is there a way to feed conn.m the atlas type without having to actually modify the program every time a new atlas is used?
With thanks,
Farras
I've been using an atlas with 116 ROI on conjunction with conn.m. For this, I needed to slightly modify the program around line 267 as follows:
filename = fullfile(fileparts(which('conn')),'rois',''atlas116.img');
As I will be using different atlases, is there a way to feed conn.m the atlas type without having to actually modify the program every time a new atlas is used?
With thanks,
Farras
Threaded View
| Title | Author | Date |
|---|---|---|
| Farras Abdelnour | Jun 7, 2012 | |
| Alfonso Nieto-Castanon | Jul 8, 2012 | |
| Larry Lai | Dec 21, 2017 | |
| Vahab Youssofzadeh | Dec 23, 2017 | |
| Farras Abdelnour | Jul 8, 2012 | |