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help > RE: ROI problem (csf)
Nov 30, 2015 04:11 PM | Alfonso Nieto-Castanon - Boston University
RE: ROI problem (csf)
Hi Sherihane,
The error message indicates that for that there are no remaining CSF voxels in that mask after erosion (in order to minimize spillage from nearby regions CONN applies one-voxel erosion to the white/CSF masks). Normally this error message would simply indicate that there was some problem in the normalization/segmentation step of that subject's structural data, but in your case the file names might seem to indicate that you are using a template mask instead, so, if you prefer to simply skip the erosion step you can do that typing the following in Matab's command window before running the Setup step:
conn_batch('Setup.cwthreshold',[0 0]);
Hope this helps
Alfonso
Originally posted by sherihane Bensemmane:
The error message indicates that for that there are no remaining CSF voxels in that mask after erosion (in order to minimize spillage from nearby regions CONN applies one-voxel erosion to the white/CSF masks). Normally this error message would simply indicate that there was some problem in the normalization/segmentation step of that subject's structural data, but in your case the file names might seem to indicate that you are using a template mask instead, so, if you prefer to simply skip the erosion step you can do that typing the following in Matab's command window before running the Setup step:
conn_batch('Setup.cwthreshold',[0 0]);
Hope this helps
Alfonso
Originally posted by sherihane Bensemmane:
Hi,
I can't run the set up phase apparently it's unable to read my csf mask, but i don't understand why, it s a binary image in the same space as the anatomical and made the same way as the wm and gm. The error message i get is :
Error using conn_process (line 557)
No suprathreshold voxels in ROI file /data/local/sherihane/connectivity_conn/new_analysis/template/clean_template/clean_to_use/csf_clean_thr_bin.nii after erosion (original file contained 13623 suprathreshold voxels)
Error in conn_process (line 12)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:5]);
Error in conn (line 2377)
conn_process('setup');
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.a
SPM8 + Beamforming DEM FieldMap MEEGtools marsbar spmss vbm8
Matlab v.2012b
storage: 983.1Gb available
Thank you in advance
I can't run the set up phase apparently it's unable to read my csf mask, but i don't understand why, it s a binary image in the same space as the anatomical and made the same way as the wm and gm. The error message i get is :
Error using conn_process (line 557)
No suprathreshold voxels in ROI file /data/local/sherihane/connectivity_conn/new_analysis/template/clean_template/clean_to_use/csf_clean_thr_bin.nii after erosion (original file contained 13623 suprathreshold voxels)
Error in conn_process (line 12)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:5]);
Error in conn (line 2377)
conn_process('setup');
Error in conn_menumanager (line 109)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.a
SPM8 + Beamforming DEM FieldMap MEEGtools marsbar spmss vbm8
Matlab v.2012b
storage: 983.1Gb available
Thank you in advance
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 | |