help > conn17a ERROR: duplicate ROI labels
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Nov 1, 2016  12:11 PM
Shady El Damaty
Georgetown University
conn17a ERROR: duplicate ROI labels
Just tried out the new version of CONN (17a).  I added new ROIs in the Setup panel and clicked 'Done'

This resulted in the following error ::

Error using conn_process (line 763)
duplicated ROI name atlas.Vermis 10
Error in conn_process (line 15)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);

I debugged at that line and noticed that the roinames for all 116 of the AAL atlas were the same "atlas.Vermis 10."  This makes me think that there is a bug in the rex function that extracts all of the roi names from the params object.

names = 'Grey Matter' 'White Matter' 'CSF' 'atlas.Vermis 10' 'atlas.Vermis 10'

Any other ideas why this error exists or how to ameliorate it?
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Nov 1, 2016  08:11 PM
Alfonso Nieto-Castanon
McGovern Institute for Brain Research. MIT
RE: conn17a ERROR: duplicate ROI labels
Hi Shady,

Sorry I do not seem to be able to replicate this error, could you please send me or point me towards the version of the aal atlas that you are using here?
Thanks
Alfonso
Originally posted by Shady El Damaty:
Just tried out the new version of CONN (17a).  I added new ROIs in the Setup panel and clicked 'Done'

This resulted in the following error ::

Error using conn_process (line 763)
duplicated ROI name atlas.Vermis 10
Error in conn_process (line 15)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);

I debugged at that line and noticed that the roinames for all 116 of the AAL atlas were the same "atlas.Vermis 10."  This makes me think that there is a bug in the rex function that extracts all of the roi names from the params object.

names = 'Grey Matter' 'White Matter' 'CSF' 'atlas.Vermis 10' 'atlas.Vermis 10'

Any other ideas why this error exists or how to ameliorate it?
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Nov 2, 2016  01:11 PM
Shady El Damaty
Georgetown University
RE: conn17a ERROR: duplicate ROI labels
Hi Alfonso,

I was using the AAL atlas included in conn under /utils/otherrois.  I've noticed that this issue occurs with any atlas I try to load into the Setup other than the Gray, White & CSF files.

Would it be useful to have my conn *.mat file to help reproduce the problem?  The conn.mat file was originally generated in an earlier version of conn (15h).  I haven't tried starting a new project from scratch yet to see if the error reproduces.
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Nov 2, 2016  06:11 PM
Alfonso Nieto-Castanon
McGovern Institute for Brain Research. MIT
RE: conn17a ERROR: duplicate ROI labels
Hi Shady,

Yes, if you could please send me your conn_*.mat file that will help. I tried with a project created in 15h, then loaded in 17a, and then adding the aal.nii atlas and running the Setup step but I am still not able to replicate the problem. Could you please also check the following? a) in Setup.ROIs select your aal file and click on the ROI tools. Check ROI labels option and let me know what is being reported there; and b) in Matlab command-line type "which rex" without the quotes and let me know if it points towards something other than your latest conn release.

Thanks
Alfonso
Originally posted by Shady El Damaty:
Hi Alfonso,

I was using the AAL atlas included in conn under /utils/otherrois.  I've noticed that this issue occurs with any atlas I try to load into the Setup other than the Gray, White & CSF files.

Would it be useful to have my conn *.mat file to help reproduce the problem?  The conn.mat file was originally generated in an earlier version of conn (15h).  I haven't tried starting a new project from scratch yet to see if the error reproduces.
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Nov 3, 2016  03:11 PM
Shady El Damaty
Georgetown University
RE: conn17a ERROR: duplicate ROI labels
Hi Alfonso,

I ended up reverting back to the previous version to add my ROIs - however I followed your instructions and tried loading in a test atlas into version 17 and got the same error.
Error using conn_process (line 763)
duplicated ROI name test.Ver10 (Vermis 10)

The command which('rex') points to the correct release of conn.

When I click the Check ROI labels option in Setup.ROIs I see that all 132 of the ROI labels appear:
test.FP r (Frontal Pole Right)
test.FP l (Frontal Pole Left)
...
test.Ver10 (Vermis10).

I tried debugging the code by pausing the execution at line 763 and it seems that the labels are not being read correctly by the rex function. Vermis10 is inserted for all of atlas labels, which causes the error.

I'm absolutely stumped! I've attached my conn_*.mat file.  I hope you can reproduce it!  I can also try on another machine and get back to you.

PS I'm using MATLAB 2016a
Attachment: conn_forAlf.mat reply reply with quote
Nov 3, 2016  06:11 PM
Alfonso Nieto-Castanon
McGovern Institute for Brain Research. MIT
RE: conn17a ERROR: duplicate ROI labels
Hi Shady,

I believe I finally was able to replicate it (and fix it). Please try the attached patch and let me know if everything seems to be working fine now (this patch is for release 17a, simply copy the attached file to the conn distribution folder overwriting the file with the same name there) 

Thanks for reporting this and for all the additional info, and sorry for the extra trouble (if I got it right it was a somewhat strange interaction with other settings; e.g. if you unchecked in Setup.Options the 'create REX files' option it would have worked just fine).

Best
Alfonso
Originally posted by Shady El Damaty:
Hi Alfonso,

I ended up reverting back to the previous version to add my ROIs - however I followed your instructions and tried loading in a test atlas into version 17 and got the same error.
Error using conn_process (line 763)
duplicated ROI name test.Ver10 (Vermis 10)

The command which('rex') points to the correct release of conn.

When I click the Check ROI labels option in Setup.ROIs I see that all 132 of the ROI labels appear:
test.FP r (Frontal Pole Right)
test.FP l (Frontal Pole Left)
...
test.Ver10 (Vermis10).

I tried debugging the code by pausing the execution at line 763 and it seems that the labels are not being read correctly by the rex function. Vermis10 is inserted for all of atlas labels, which causes the error.

I'm absolutely stumped! I've attached my conn_*.mat file.  I hope you can reproduce it!  I can also try on another machine and get back to you.

PS I'm using MATLAB 2016a
Attachment: rex.m reply reply with quote
Nov 10, 2016  04:11 PM
Shady El Damaty
Georgetown University
RE: conn17a ERROR: duplicate ROI labels
Thank you for looking into this Alfonso! I've downloaded the file and updated my conn project.. currently trying to sort out an unrelated bug but will check if the fix works as soon as I can!
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Nov 12, 2016  03:11 PM
Shady El Damaty
Georgetown University
RE: conn17a ERROR: duplicate ROI labels
I tested this out and it works perfectly - thanks alfonso
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Dec 8, 2016  08:12 AM
RE: conn17a ERROR: duplicate ROI labels
Thank you for posting this. I had the same problem and the new rex.m fixed it.
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