| T O P I C R E V I E W |
| mb |
Posted - Sep 16 2004 : 5:31:25 PM
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? |
| 15 L A T E S T R E P L I E S (Newest First) |
| rkozink |
Posted - Aug 15 2006 : 11:57:40 AM
You're exactly right, Syam. I changed the "_b" to something that didn't start with a "b" and it worked fine! Thanks for the help everyone. |
| syam.gadde |
Posted - Aug 15 2006 : 11:23:02 AM
It looks like roianalysis_timecourse_iris does not like the '_b' in the filename. I'm not sure why -- perhaps IRIS uses a '_b' suffix for something and the script tries to back up the base filename before that. Can you use a name that doesn't have '_b' and see if that helps? |
| rkozink |
Posted - Aug 15 2006 : 10:54:59 AM
roiFileSpec = 'sprintf(''%s\\%s.img'',studies{study},studies{study})'; |
| syam.gadde |
Posted - Aug 15 2006 : 10:53:28 AM
What does the roiFileSpec line in your calling script look like? |
| rkozink |
Posted - Aug 15 2006 : 10:37:13 AM
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. |
| petty |
Posted - Aug 15 2006 : 10:31:25 AM
are you running this off of your local machine? because ROI_Smokeatt.01 does not exist, but Smokeatt.01 is on goldman. |
| rkozink |
Posted - Aug 15 2006 : 10:22:34 AM
I have checked and re-checked to make sure everything matches up and I'm still getting the error. |
| petty |
Posted - Aug 15 2006 : 10:19:30 AM
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. |
| rkozink |
Posted - Aug 15 2006 : 08:59:04 AM
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 |
| charles.michelich |
Posted - Sep 22 2004 : 5:52:42 PM
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
|
| gunes |
Posted - Sep 22 2004 : 5:42:06 PM
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 |
| charles.michelich |
Posted - Sep 22 2004 : 5:35:15 PM
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.
|
| petty |
Posted - Sep 22 2004 : 5:06:21 PM
??? 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. |
| charles.michelich |
Posted - Sep 17 2004 : 2:52:16 PM
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
|
| mb |
Posted - Sep 17 2004 : 12:53:08 PM
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 |
