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help > RE: Specifying freesurfer files in batch file
Nov 11, 2015 05:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Specifying freesurfer files in batch file
Hi Yoel,
Yes, it works just the same when using batch scripts, simply pointing the structural file of a subject to the T1/brain/etc structural file in the subject/mri/ freesurfer-generated subfolder allows CONN to locate the associated surface files if needed (and if you want to run surface-based analyses just remember to also set batch.Setup.voxelresolution=4 -this is equivalent as setting in the GUI Setup.Options tab the 'analysis space' field to 'surface')
Hope this helps
Alfonso
Originally posted by Yoel Sanchez Araujo:
Yes, it works just the same when using batch scripts, simply pointing the structural file of a subject to the T1/brain/etc structural file in the subject/mri/ freesurfer-generated subfolder allows CONN to locate the associated surface files if needed (and if you want to run surface-based analyses just remember to also set batch.Setup.voxelresolution=4 -this is equivalent as setting in the GUI Setup.Options tab the 'analysis space' field to 'surface')
Hope this helps
Alfonso
Originally posted by Yoel Sanchez Araujo:
Hi,
When working with the GUI you can locate your freesurfer brainmask.mgz for your structural images and conn then finds the associated surface images. I'm wondering if this works exactly the same way when using a batch script? Will setting batch.Setup.structurals{subn}='path/to/freesurfer/volume/subn'; result in the same type of behavior or is there an additional step needed?
Thank you!
When working with the GUI you can locate your freesurfer brainmask.mgz for your structural images and conn then finds the associated surface images. I'm wondering if this works exactly the same way when using a batch script? Will setting batch.Setup.structurals{subn}='path/to/freesurfer/volume/subn'; result in the same type of behavior or is there an additional step needed?
Thank you!
Threaded View
| Title | Author | Date |
|---|---|---|
| Yoel Sanchez Araujo | Nov 2, 2015 | |
| Alfonso Nieto-Castanon | Nov 11, 2015 | |