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help > RE: ROI problem (csf)
Dec 3, 2015 01:12 AM | Alfonso Nieto-Castanon - Boston University
RE: ROI problem (csf)
Hi Sherihane and Jalmar,
I am attaching a patch that allows defining different threshold/erosion options for the WM and CSF ROIs (this patch is for release 15g, copy the attached file to the conn distribution folder overwriting the file with the same name there). To define these options you may use the syntax:
options = [.5 1 0 0];
conn_batch('Setup.cwthreshold',options);
The four values in the vector "options" indicate:
options(1): Threshold for binary White Matter mask (default .5)
options(2): Number of binary-erosion steps for White Matter mask (default 1)
options(3): Threshold for binary CSF mask (default .5)
options(4): Number of binary-erosion steps for CSF mask (default 1)
The example above, then, would leave the default options for the White Matter mask while disabling the erosion step for the CSF mask.
Hope this helps and let me know if you run into any issues
And regarding the question about patches and releases, yes, each CONN update/release always includes all of the patches that may have been created for the previous release, and the next release should be out some time next week (we typically try to follow roughly a monthly-update schedule but this one has taken a little longer than usual)
Best
Alfonso
Originally posted by Jalmar Teeuw:
I am attaching a patch that allows defining different threshold/erosion options for the WM and CSF ROIs (this patch is for release 15g, copy the attached file to the conn distribution folder overwriting the file with the same name there). To define these options you may use the syntax:
options = [.5 1 0 0];
conn_batch('Setup.cwthreshold',options);
The four values in the vector "options" indicate:
options(1): Threshold for binary White Matter mask (default .5)
options(2): Number of binary-erosion steps for White Matter mask (default 1)
options(3): Threshold for binary CSF mask (default .5)
options(4): Number of binary-erosion steps for CSF mask (default 1)
The example above, then, would leave the default options for the White Matter mask while disabling the erosion step for the CSF mask.
Hope this helps and let me know if you run into any issues
And regarding the question about patches and releases, yes, each CONN update/release always includes all of the patches that may have been created for the previous release, and the next release should be out some time next week (we typically try to follow roughly a monthly-update schedule but this one has taken a little longer than usual)
Best
Alfonso
Originally posted by Jalmar Teeuw:
We too would be interested in setting the
threshold and erosion levels for CSF and WM separately. We require
slightly more lenient settings for CSF in our paediatric dataset
with relatively large voxel size; white matter is fine with default
settings.
Will this patch (and any other patches distributed through this forum since the release of 15.g) be included in the next release of CONN? We want to start processing the datasets soon, but for the purpose of replication & reproducibility we'd prefer to cite an official release of CONN rather than having to mention all the separate patches applied to CONN 15.g.
Will this patch (and any other patches distributed through this forum since the release of 15.g) be included in the next release of CONN? We want to start processing the datasets soon, but for the purpose of replication & reproducibility we'd prefer to cite an official release of CONN rather than having to mention all the separate patches applied to CONN 15.g.
Threaded View
| Title | Author | Date |
|---|---|---|
| sherihane Bensemmane | Nov 30, 2015 | |
| Alfonso Nieto-Castanon | Nov 30, 2015 | |
| sherihane Bensemmane | Dec 1, 2015 | |
| Alfonso Nieto-Castanon | Dec 1, 2015 | |
| sherihane Bensemmane | Dec 2, 2015 | |
| sherihane Bensemmane | Dec 2, 2015 | |
| Alfonso Nieto-Castanon | Dec 2, 2015 | |
| Jalmar Teeuw | Dec 2, 2015 | |
| Alfonso Nieto-Castanon | Dec 3, 2015 | |
| Jalmar Teeuw | Feb 8, 2016 | |
| Alfonso Nieto-Castanon | Feb 13, 2016 | |
| Jalmar Teeuw | Feb 15, 2016 | |
| Alfonso Nieto-Castanon | Feb 17, 2016 | |
| Bob Kraft | Jun 14, 2016 | |
| Alfonso Nieto-Castanon | Jun 14, 2016 | |
| Bob Kraft | Jun 22, 2016 | |
| Jalmar Teeuw | Dec 4, 2015 | |
| sherihane Bensemmane | Dec 3, 2015 | |