Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions.
Regards, Wil -----Original Message----- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -----Original Message----- From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: > > Hi- > > > > I’ve come across a peculiar behavior with recon_checker, and am hoping > someone can shed some light on this. > > > > I have used it 100’s of times in the past, but not for about 2 months. > I recently processed a large set of cases I wanted to QC. When I ran > it, some, but not all, of the snaps were corrupted. Specifically the > talairach, aseg, surfs, and all the ‘detailed snaps’, which are > basically additional instances of the aforementioned types. The > inflated, curv, and parc are all just fine. As the process runs, all > images are being displayed in the pop-up windows, and the html page is > created. > > > > While there have been no system changes which should affect this, I > upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the > problem. The problem remains. And the problem remains w/ or w/o the > flag for detailed snaps. > > > > If all of the images were corrupted, I would have certainly concluded > something has gone awry with my system. The fact that only some of the > images are corrupted makes me scratch my head. > > > > Thoughts? Suggestions? > > > > Thanks, > > Wil > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
