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mb
BIAC Alum
27 Posts |
 Posted - Sep 16 2004 : 5:31:25 PM
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I'm having trouble figuring out how to use the masked ROIs written by the count function in the timecourse function. I specified the same range and decDigits in the timecourse function as in count, but I get an error saying that the .hdr doesn't exist for the maskedROI written out by the count function (because it doesn't).
Is there some way to make the count function write out the .hdr file as well as/instead of the .bxh? Do I have to make them manually, or should I be doing something else entirely? |
Edited by - charles.michelich on Sep 16 2004 5:35:02 PM |
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 16 2004 : 5:32:34 PM
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Hi Mary Beth,
The issue is that your original ROIs are in Analyze 7.5 format and the masked ROIs created by roianalysis_count_iris are BXH format. The original and masked ROIs need to be in the same format. Since the masked ROIs are automatically generated with BXH headers, I suggest that you add BXH header to your original ROIs. You can do this using either bxhabsorb or by opening them in IRIS and saving them as BXH files.
Enjoy,
Chuck
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mb
BIAC Alum
27 Posts |
Posted - Sep 16 2004 : 6:31:34 PM
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So I used bxhabsorb to make .bxh files for each of my ROIs but know when I try to rerun roianalysis_count_iris, I get the following error:
??? Error using ==> roianalysis_count_iris
Improper index matrix reference.
Any suggestions?
Thanks,
mb |
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 16 2004 : 7:56:46 PM
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The message you saw was acutally an error in the creation of the message to indicate that an ROI file cannot be read. I have fixed the error handling. I suggest that you try reading the IRIS ROI file using readmr to track down the problem with the file.
quote:
Originally posted by mb
So I used bxhabsorb to make .bxh files for each of my ROIs but know when I try to rerun roianalysis_count_iris, I get the following error:
??? Error using ==> roianalysis_count_iris
Improper index matrix reference.
Any suggestions?
Thanks,
mb
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mb
BIAC Alum
27 Posts |
Posted - Sep 17 2004 : 12:53:08 PM
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So I created .bxh's for all of my ROIs and they seem to be correct, but now when I run roianalysis_timecourse_iris, I get the following error:
??? Error using ==> roianalysis_timecourse_iris
Error using ==> roistats_iris
Segments are missing anchor specifications!
I checked to make sure that all of my label files had anchor points and they do. What else should I check?
thanks, thanks, thanks a bunch - mb |
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 17 2004 : 2:52:16 PM
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One of your subjects did not have any regions specified in their ROI. This is possible when you run roianalysis_timecourse_iris using masked ROIs as inputs since some regions may not have any activity.
That said, the code should be able to handle this situation. I fixed roistats_iris to deal with this and updated the copy in User_Scripts. You analysis should work now.
quote:
Originally posted by mb
So I created .bxh's for all of my ROIs and they seem to be correct, but now when I run roianalysis_timecourse_iris, I get the following error:
??? Error using ==> roianalysis_timecourse_iris
Error using ==> roistats_iris
Segments are missing anchor specifications!
I checked to make sure that all of my label files had anchor points and they do. What else should I check?
thanks, thanks, thanks a bunch - mb
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 22 2004 : 5:06:21 PM
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??? Error using ==> roianalysis_timecourse_iris
Error using ==> getorientation
One of the directions vectors is not defined!
here's an error that i'm getting. the same script previously worked. ROIs are being read in as .hdr's in 'Analyze7.5_SPM' format. Any suggestions, this worked a couple of weeks ago. |
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 22 2004 : 5:35:15 PM
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Thanks for reporting this bug. I fixed the problem in roistats_iris that was causing the error you saw.
quote:
Originally posted by petty
??? Error using ==> roianalysis_timecourse_iris
Error using ==> getorientation
One of the directions vectors is not defined!
here's an error that i'm getting. the same script previously worked. ROIs are being read in as .hdr's in 'Analyze7.5_SPM' format. Any suggestions, this worked a couple of weeks ago.
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gunes
BIAC Alum
45 Posts |
Posted - Sep 22 2004 : 5:42:06 PM
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Chuck,
Now I am getting this error while running script with ".hdr".
??? Error using ==> roianalysis_timecourse_iris
Error using ==> roistats_iris
Reference to a cleared variable mseg.
Any suggestion?
Thanks.
Gunes |
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charles.michelich
BIAC Alum
USA
183 Posts |
Posted - Sep 22 2004 : 5:52:42 PM
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Thanks Gunes. That was a typo in the fix I released 20 minutes ago. I fixed the problem in roistats_iris that was causing the error you saw.
If you saw the following warning between 5:20 and 5:55 pm today, you should rerun the ROI analysis to make sure that the cardinal planes were the same.
Orientations for FILENAME and mseg do not match!
(They are the same cardinal plane, but have a different oblique angle)
quote:
Originally posted by gunes
Chuck,
Now I am getting this error while running script with ".hdr".
??? Error using ==> roianalysis_timecourse_iris
Error using ==> roistats_iris
Reference to a cleared variable mseg.
Any suggestion?
Thanks.
Gunes
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Edited by - charles.michelich on Sep 22 2004 6:05:05 PM |
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rkozink
Junior Member
31 Posts |
Posted - Aug 15 2006 : 08:59:04 AM
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I am having difficulties with roianalysis_timecourse_iris. I was running it yesterday and had no problems, but now I am getting the following error:
?? Error using ==> roianalysis_timecourse_iris
IRIS Label file "S:\Harvey\ROI_Smokeatt.01\306v1r1_bg\306v1r1.txt" does not exist!
It is not using the entire study name (306v1r1_bg) when it is looking for the label file. I went back and tried to rerun what I did yesterday since I knew it worked then, and I am now getting errors that it can't find files, which do exist in the location specified. Any suggestions?
Thanks
Rachel |
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petty
BIAC Staff
USA
453 Posts |
Posted - Aug 15 2006 : 10:19:30 AM
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| the label file has to be the exact same name as the ROI header file. also, make sure that folder listed above actually does exist. |
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rkozink
Junior Member
31 Posts |
Posted - Aug 15 2006 : 10:22:34 AM
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| I have checked and re-checked to make sure everything matches up and I'm still getting the error. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Aug 15 2006 : 10:31:25 AM
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| are you running this off of your local machine? because ROI_Smokeatt.01 does not exist, but Smokeatt.01 is on goldman. |
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rkozink
Junior Member
31 Posts |
Posted - Aug 15 2006 : 10:37:13 AM
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| Yes, I have this on a local drive. We have three different ROI files, _bg, _amyg, and _fgs. Yesterday I ran _amyg and _fgs without any problems. All three ROI files follow the exact same naming convention, so I don't understand why _bg is not working. I used the sample file to create my own timecourse_iris file, so it should be looking for 306v1r1_bg\306v1r1_bg.txt (which does exist) since "306v1r1_bg" is what I put as one of my studies. But as you can see from the error message, it is omitting the "_bg" part of the label file. |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Aug 15 2006 : 10:53:28 AM
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| What does the roiFileSpec line in your calling script look like? |
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IRIS ROI analysis problems
