[caret-users] Error creating BrainSet for mapping data

Peng, Huiling pengh at missouri.edu
Wed Nov 14 16:56:59 CST 2012


I think I figured out the problem. The spec file I downloaded from website contains information like the following:

CLOSEDtopo_file Human.sphere_6.LEFT_HEM.73730.topo 
CLOSEDtopo_file Human.sphere_6.RIGHT_HEM.73730.topo 

It doesn''t include the path to reach these files. So the system automatically search around under the directory where the spec file was saved (in my case it is /home/pengh/Template). Is there any script to add path for each file since I think these files may be saved under different directories, not only /usr/local/caret/data_files/fmri_mapping_files/. 

Thanks,
Huiling 
________________________________________
From: caret-users-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker [donna at brainvis.wustl.edu]
Sent: Wednesday, November 14, 2012 12:03 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Error creating BrainSet for mapping data

I'd tweak your path so it finds /usr/local/caret/bin before /home/pengh/Templates (or some subdirectory below it that contains the caret5 executable).

It sounds like you have caret5 (the executable -- not the distribution) installed in multiple places, and when you enter caret5, it finds the one under /home/pengh/Templates first.  But I worry there are other files missing from that directory you might need later.

Put more simply, make sure you use caret5 from a complete installation directory.


On Nov 14, 2012, at 11:07 AM, "Peng, Huiling" <pengh at missouri.edu> wrote:

> There is only English installed. Here is some updates. I saved caret in /usr/local/caret, and save the spec file in /home/pengh/Templates. Meanwhile, I set path in .bashrc as /usr/local/caret/bin_linux64. It looks like caret is trying to find those cood and topo files under /home/pengh/Templates and couldn't find them. So I copied all files under /usr/local/caret/data_files/fmri_mapping_files/ to /home/pengh/Templates. Now the error window not show up any more. But I am wondering whether it is correct way to save those files. Any suggestion?
>
> Thanks,
> Huiling
>
> -----Original Message-----
> From: caret-users-bounces at brainvis.wustl.edu [mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Wednesday, November 14, 2012 10:07 AM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] Error creating BrainSet for mapping data
>
> Do you have a non-English character set installed, by any chance?
>
> This is something that varies by platform and window system, but is usually controlled by a personal language setting.  Make sure it's just English.  Log out and back in, if needed, before restarting caret.
>
>
> On Nov 14, 2012, at 9:32 AM, "Peng, Huiling" <pengh at missouri.edu> wrote:
>
>> I checked the directory and the file: Human.PALS_B12.LEFT (RIGHT)_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord did exist. Could it be any other reason?
>>
>> Thanks,
>> Huiling
>> ________________________________________
>> From: caret-users-bounces at brainvis.wustl.edu [caret-users-bounces at brainvis.wustl.edu] on behalf of Donna Dierker [donna.dierker at sbcglobal.net]
>> Sent: Tuesday, November 13, 2012 5:22 PM
>> To: Caret, SureFit, and SuMS software users
>> Subject: Re: [caret-users] Error creating BrainSet for mapping data
>>
>> This could happen if your distribution didn't unzip completely, or some files got inadvertently removed.
>>
>> Suppose your caret distribution is in /usr/local/caret.  Then do this:
>>
>> cd /usr/local/caret/data_files/fmri_mapping_files
>>
>> Then do:
>>
>> ls *FLIRT*coord
>>
>> If you really don't see the coord file it is complaining about below, then your distribution got corrupted somehow.
>>
>>
>> On Nov 13, 2012, at 4:50 PM, "Peng, Huiling" <pengh at missouri.edu> wrote:
>>
>>> Hi all,
>>>
>>> I am pretty new to caret. I only run caret for resting fMRI data. I was able to run it month ago before my linux computer crashed. After I installed a new version of CentOS 6.3 x86_64, it doesn't work correctly any more. I downloaded Caret 5.65 and spec file:
>>> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730
>>>
>>> After I add data volume, map to Spec file, select all coord files, and finally name data file, it popped out an error window:
>>> Error creating BrainSet for mapping data.
>>> Human.sphere_6.LEFT_HEM.73730.topo does not exist.
>>> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord does not exist.
>>>
>>>
>>>
>>>
>>> Any suggestion is greatly appreciated!
>>>
>>>
>>> Thanks,
>>> Huiling
>>
>>
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