[caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
Donna Dierker
donna at brainvis.wustl.edu
Thu Jun 18 09:04:16 CDT 2009
On 06/16/2009 08:31 PM, midoli wrote:
> Thanks All and sorry for the late reply.
>
> It's MacOSX 10.5.6.
>
> I reinstalled MacOSX 10.5.6. and caret5, then tried again.
> I found that:
> [open data file] --> [choose xx.hdr] --> then caret5 asked me some
> question, like "if you would create a spec file", "what kind of file
> it was (functional, anatomy and so on) ".....
>
> on this step, if I chose the wrong answer, caret5 would crash.
I'm not disputing that it crashed here; I'm sure it did. But at the
step of identifying what type of volume you were opening, there really
isn't a wrong answer to this question. I often open volumes of other
types (e.g., segmentations, paint, or functional volumes) as anatomical
volumes, just so I can get a grayscale representation of it. The volume
type mainly affects which overlay type you can access it under on the
Overlay/Underlay - Volume menu.
So while it did crash here, it wasn't your "wrong answer" that caused it.
By the way, if you are the person who uploaded a volume named
beta_0003.hdr on 6/14, I was able to open it in Caret with no problem,
and mayo_analyze turned up nothing unusual (output attached).
>
> I followed Donna's instruction, tried to find ".caret*" file. I typed
> "ls -al .caret*", but there was no file found :(
> ( I tried it on several directory. I asked my friend to help me, he is
> a software engineer and he could not find .caret*, too.)
Maybe this is because you weren't able to get Caret working long enough
to generate a .caret5_preferences file. (My earlier reply was sent from
home, where I could not readily identify the filename.) In any event,
if it doesn't exist, then it is not the culprit.
>
> -----------------------------------------
> By the way, I installed caret5 window version too, but it could not
> load any "scence".
> the OS was "window XP professional".
> If I selected[choose spec file] -- [PALS_B12.RIGHT.DEMO.73730.spec] --
> [Load Scenes] -- selected [Inflated, Lateral view (PALS-B13 RIGHT)]
> --[Show Selected Scene], then it crashed.. the error message was "out
> of memory". (I have tried to choose different spec file and different
> scenes, and everytime I selected "show selected Scene, it crashed.)
>
>
> I have tried it on two personal computers (windows system) . One was
> 2G RAM (windows XP professional), and other was 5G RAM (windows 2003).
> The "windows task manager" showed that the memory used arose to 9xx MB
> then crashed. Although there was 5G RAM, It could not assign task to
> >1G RAM.
Wow. You're really having lousy luck with Caret!
I wish I could think of something else to try for either platform, but
I'm stumped. We have it working on both MacOSX and Windows here in the
lab, and these particular triggers (loading volume, show scenese) are
not familiar trouble spots.
You aren't by chance using a network drive to access the data, are you?
If so, does the problem persist when accessed locally? We use network
drives here all the time, but occasionally they can be a source of
trouble, depending on both the drive/platform combination.
I confess I'm reaching for an idea here. I'm out of good ones.
>
> Thanks for these kind suggestions.
>
> .Midoli. :-)
>
>
>
>
> On Wed, Jun 17, 2009 at 3:09 AM, John Harwell <john at brainvis.wustl.edu
> <mailto:john at brainvis.wustl.edu>> wrote:
>
> Midoli,
>
> Which version of OS X is installed on your Mac (Apple Menu->About this
> Mac will tell you)? We know that Caret will not run on versions prior
> to 10.4.
>
> John
>
>
>
> On Jun 12, 2009, at 8:57 PM, midoli wrote:
>
> > Thanks for these kind suggestions.
> >
> > In fact, my Carot was broken down after my stupid operation.
> > Everytime I open it, it seems to do the wrong process automatically
> > then crashes. I have tried to reinstall it and it still keeps
> > crashing.
> > How could I kill the fail process clearly?
> > If I can't kill it clearly, I will reinstall the MacOSX to repair
> > the Carot and then follow suggestions.
> >
> > Thanks,
> > Midoli :-)
> >
> >
> > On Sat, Jun 13, 2009 at 2:03 AM, Donna Dierker
> <donna at brainvis.wustl.edu <mailto:donna at brainvis.wustl.edu>
> > > wrote:
> > If you don't have AFNI installed, you can upload your .hdr here,
> and I
> > can try mayo_analyze on my end:
> >
> > http://pulvinar.wustl.edu/cgi-bin/upload.cgi
> >
> > If you upload the .img file, too, I can try opening it in Caret.
> >
> > On 06/12/2009 11:43 AM, John Harwell wrote:
> > > If you tried to load the "img" file, caret will ask the user
> for the
> > > type of file. Do not select the img file.
> > >
> > > Try selecting and loading the "hdr" file. If caret is getting
> stuck
> > > loading the file, then there is probably a problem the with
> hdr/img
> > > files, most likely the byte order is incorrect so that dimensions
> > > appear enormous to Caret.
> > >
> > > How were the hdr/img files created?
> > >
> > > If you have AFNI installed, try running "mayo_analyze
> <name-of-hdr-
> > > file>". What is the output?
> > >
> > > On Jun 12, 2009, at 9:37 AM, midoli wrote:
> > >
> > >
> > >> Hi, All
> > >>
> > >> I'm just beginning to use Caret.
> > >>
> > >> I installed Caret5 in Mac OS.
> > >> I used "File/Open Data File" to upload .hdr or .img file
> (sorry, I
> > >> forgot which one I chose.) and it was hanging.
> > >> The cursor kept on showing "processing" status, I waited for
> a long
> > >> time... finally I used Ctrl+C to terminate Caret.
> > >> I reopened Caret, it still showed "processing" status at the
> > opening
> > >> time, I had no chance to do anything.
> > >> I tried to restart OS, even reinstall Caret in a different
> > >> directory.... these efforts were in vain.
> > >>
> > >> Did Caret hide something outside Caret's directory?
> > >> How could I kill this fail process clearly and use Caret again?
> > >>
> > >> Thank you. :-)
> > >>
> > >> Shih-Chuan Chen.
> >
> > _______________________________________________
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> >
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