[caret-users] caret5 - (winxp and vista) - open data file / hanging ... /out of memory/ By Kure
Donna Dierker
donna at brainvis.wustl.edu
Mon Jun 22 07:44:33 CDT 2009
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 <midoli at gmail.com>
> To: "Caret, SureFit, and SuMS software users"
> <caret-users at brainvis.wustl.edu>
> Message-ID:
> <958263d50906201929r6bcc4759ya482a3cdac46a450 at 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：=======
>
>
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>> Today's Topics:
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>> 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 <midoli at gmail.com>
>> Subject: Re: [caret-users] caret5 - (macosx) - open data file /
>> hanging ... / reinstall is useless..
>> To: "Caret, SureFit, and SuMS software users"
>> <caret-users at brainvis.wustl.edu>
>> Message-ID:
>> <958263d50906201929r6bcc4759ya482a3cdac46a450 at 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 <donna at 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 <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.
>>>> >
>>>> > _______________________________________________
>>>> > caret-users mailing list
>>>> > caret-users at brainvis.wustl.edu
>>>> <mailto:caret-users at brainvis.wustl.edu>
>>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>> >
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>>>>
>>> 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 at brainvis.wustl.edu
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
>>>
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