Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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 星期六 六月 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 星期六 六月 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.eduwrote: 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
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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,
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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 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 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 ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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 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.) - 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. Thanks for these kind suggestions. .Midoli. :-) On Wed, Jun 17, 2009 at 3:09 AM, John Harwell j...@brainvis.wustl.eduwrote: 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 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 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 ___ 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
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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.eduwrote: 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 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
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
Hi Midoli, It is unlikely that opening a .hdr file or .img would cause the crashing you are seeing. And after rebooting the machine, as you did before, any hanging/rogue Caret processes would be killed off, for sure. Caret does not try to pick up where it left off when you relaunch. It might remember path locations, but that's about it. There is a Caret environment file named like .caret* (where * is replaced with some string I can't currently recall) that stores the history. In a terminal window, do cd ~ and then ls -al .caret* and see if it finds any files named like that. If it does find something named like .caret_history, then do rm .caret_history and see if Caret launches. You are welcome to try upgrading the OS, but that measure seems unwarranted. By the way, what version of MacOSX are you running? Older ones may not work. Donna 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.eduwrote: 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 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 ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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 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
Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..
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 http://brainvis.wustl.edu/mailman/listinfo/caret-users
