[caret-users] caret5 - (winxp and vista) - open data file / hanging ... /out of memory/ By Kure
kaiwu
kaiwu at idac.tohoku.ac.jp
Sun Jun 21 04:25:53 CDT 2009
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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> 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>
>>
>> _______________________________________________
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>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
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>>
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