Kure and Midoli, First, thank you both for the excellent detail provided below. It sheds a lot of light on the problem.
Second, I do recall another thread where language issues caused similar problems: http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01635.html Unfortunately, I don't have a solution, but I do think this information will help John understand what is going on. Donna On 06/21/2009 04:25 AM, kaiwu wrote: > Hi, I'm also a beginner of Caret, and I met almost the same problem as the > below message mentioned. > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > From: midoli <mid...@gmail.com> > To: "Caret, SureFit, and SuMS software users" > <caret-users@brainvis.wustl.edu> > Message-ID: > <958263d50906201929r6bcc4759ya482a3cdac46a...@mail.gmail.com> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > I installed the caret5.61 in both my computer with WinXp Chinese edition and > Vista Japanese edition, respectively. > When I open a spec file, i.e. the spec file > "PALS_B12.RIGHT.MCW_2008_06.73730.spec" in the > "Caret5_Quick_Start_June_2008_Data" files, it alway display "opening" and > then prompt "out of memory" finally. > I don't know how to solve this problem. > Your help would be greatly appreciated. > > Kure > > ======= 2009-06-21 14:45:36 As you wrote：======= > > >> Send caret-users mailing list submissions to >> caret-users@brainvis.wustl.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> or, via email, send a message with subject or body 'help' to >> caret-users-requ...@brainvis.wustl.edu >> >> You can reach the person managing the list at >> caret-users-ow...@brainvis.wustl.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." >> >> >> Today's Topics: >> >> 1. Re: caret5 - (macosx) - open data file / hanging ... / >> reinstall is useless.. (midoli) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 21 Jun 2009 10:29:25 +0800 >> From: midoli <mid...@gmail.com> >> Subject: Re: [caret-users] caret5 - (macosx) - open data file / >> hanging ... / reinstall is useless.. >> To: "Caret, SureFit, and SuMS software users" >> <caret-users@brainvis.wustl.edu> >> Message-ID: >> <958263d50906201929r6bcc4759ya482a3cdac46a...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-2022-jp" >> >> Thank you for the reply. The data file was on local hard disk, not accessed >> via network. >> >> Open successfully: >> [File] - [Open Data File] - choose [beta_0003.hdr] - [Would you like to >> create a Spec file] - [No] - [Volume Functional Files] - [If the volume >> being loaded an SPM volume that is left/right flipped (radiological >> orientation)] - [Yes] -- Open successfully >> >> Open fail: >> [File] - [Open Data File] - choose [beta_0003.hdr] - [Would you like to >> create a Spec file] - [Yes] - [subject: test2, structure: both] - [Name of >> Spec File that will be created .You may change the name: >> Human.test2.LR.spec] - [Volume Functional Files] - [If the volume being >> loaded an SPM volume that is left/right flipped (radiological orientation)] >> - [Yes] - crashed, and error message: "MultiByteToWideChar: Cannot convert >> multibyte text" >> >> I had a new idea last night. Did these problems come from "double-bytes >> language" Operation System? >> >> I used Window XP professional Chinese Version. >> When I created a new spec file, Caret would crash and there was a message >> showed in Caret terminal: >> "MultiByteToWideChar: Cannot convert multibyte text" >> >> I found a new spec file "Human.test2.R.spec" and opened it with Notepad++. >> In the spec file, date information was written with Chinese. I uploaded the >> spec file here ( http://midodo.net/neuro/Human.test2.LR.spec ) >> >> -------- >> BeginHeader >> Caret-Version 5.61 >> category Individual >> comment test2 >> date ??? ?? 20 15:41:05 2009 <------------ Chinese time format >> encoding ASCII >> space UNKNOWN >> species Human >> structure both >> subject test2 >> EndHeader >> -------- >> Date information was also written with Chinese in the preference file >> (preferences_file_0caret5_preferences) >> I uploaded the preference file here ( >> http://midodo.net/neuro/preferences_file_0caret5_preferences ) >> >> -------- >> BeginHeader >> Caret-Version 5.61 >> date ??? ?? 20 15:41:05 2009 <------------ Chinese time format >> encoding ASCII >> EndHeader >> >> >> I restart Caret but Caret keep hanging. After deleting "Human.test2.R.spec" >> and "preferences_file_0caret5_preferences" files, Caret could restart >> successfully. >> >> I guess.... >> When I created a spec, Caret wrote time stamp in files. I used a Chinese >> version Operation System, so the date information was written with Chinese >> automatically. The next time Caret read the files, Caret could not convert >> double bytes texts, so it crashed. >> I was very unlucky to have so many problems with Caret because I used >> "Double-byte" Operation Systems (both in Window and Mac environment)? >> >> >> .Midoli. >> >> On Thu, Jun 18, 2009 at 10:04 PM, Donna Dierker >> <do...@brainvis.wustl.edu>wrote: >> >> >>> 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 >>>> <j...@brainvis.wustl.edu<mailto: >>>> j...@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 >>>> <do...@brainvis.wustl.edu <mailto:do...@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. >>>> > >>>> > _______________________________________________ >>>> > caret-users mailing list >>>> > caret-users@brainvis.wustl.edu >>>> <mailto:caret-users@brainvis.wustl.edu> >>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> > >>>> > _______________________________________________ >>>> > caret-users mailing list >>>> > caret-users@brainvis.wustl.edu >>>> <mailto:caret-users@brainvis.wustl.edu> >>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu <mailto:caret-users@brainvis.wustl.edu> >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>>> >>> Analyze Header Dump of: </upload/beta_0003.hdr> >>> sizeof_hdr: <348> >>> data_type: <dsr > >>> db_name: <beta_0003> >>> extents: <0> >>> session_error: <0> >>> regular: <r> >>> hkey_un0: <^@> >>> dim[0]: <4> >>> dim[1]: <61> >>> dim[2]: <73> >>> dim[3]: <85> >>> dim[4]: <1> >>> dim[5]: <0> >>> dim[6]: <0> >>> dim[7]: <0> >>> datatype: <16> >>> bitpix: <32> >>> pixdim[0]: <0.0000> >>> pixdim[1]: <3.0000> >>> pixdim[2]: <3.0000> >>> pixdim[3]: <3.0000> >>> pixdim[4]: <1.0000> >>> pixdim[5]: <0.0000> >>> pixdim[6]: <0.0000> >>> pixdim[7]: <0.0000> >>> vox_offset: <0.0000> >>> funused1: <1.0000> >>> funused2: <0.0000> >>> funused3: <0.0000> >>> cal_max: <1.0000> >>> cal_min: <0.0000> >>> compressed: <0.0000> >>> verified: <0.0000> >>> glmax: <1> >>> glmin: <0> >>> descrip: <spm_spm:beta (0003) - Sn(1) nopain*bf(1)> >>> aux_file: <> >>> orient: <0> >>> SPM originator decodes to 31 43 25 >>> originator: <^_> >>> generated: <today> >>> scannum: <> >>> patient_id: <> >>> exp_date: <> >>> exp_time: <> >>> hist_un0: <> >>> views: <0> >>> vols_added: <0> >>> start_field:<0> >>> field_skip: <0> >>> omax: <0> >>> omin: <0> >>> smin: <0> >>> smin: <0> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://brainvis.wustl.edu/pipermail/caret-users/attachments/20090621/4a819a71/attachment.html >> >> >> ------------------------------ >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> End of caret-users Digest, Vol 69, Issue 9 >> ****************************************** >> >> > > > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
