[caret-users] Error creating BrainSet for mapping data

Peng, Huiling pengh at missouri.edu
Thu Nov 15 12:23:55 CST 2012


Hi Donna,

Thank you for all your patience. I realized I clicked the "single file action" on the website to download the spec file and that is the reason it didn't work. Now I click the "save" symbol and it works now.

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: Thursday, November 15, 2012 9:04 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Error creating BrainSet for mapping data

Hi Huiling,

No, there is no script like that, because Caret isn't designed to use pathnames in the spec files, though we do that when it makes sense (which isn't often).

Here is how it's supposed to work:

* You download caret somewhere like /usr/local/caret, and there are many subdirectories that contain files Caret needs to do the right thing.  If you solve this specific problem, but your distribution is incomplete, ten more problems will take its place -- until you use a complete distribution.
* It's a little too easy to download multiple versions, maybe stick one somewhere like your home directory, that doesn't need root write privileges, and then either put a shortcut to it on your dock/desktop.  But if any of these are in incomplete distribution directories, then trouble will keep following you until you use a complete distribution.
* When you launch caret from a dock/desktop shortcut, rather than from a terminal directory where you have already cd'd to the directory where your data lives, then you'll need to change the current working director (File menu).  Many of us launch caret from the command line, from within the directory where our data is located, so we don't have to do this.  But you can do it either way.
* But even if I cd /directory/where/my/func/data/lives and launch caret, then caret will still let me map to ATLAS spec file and find the right topo/coord files, because it looks in /usr/local/caret/data_files/fmri_mapping_files -- which is complete on my distribution.

Adding absolute paths to your spec file is not the answer.

I still worry you have an incomplete distribution.  Or, you have a complete distribution, but your shortcut is pointing somewhere OTHER than /usr/local/caret/[platform-specific-bin-directory]/caret5[optional-platform-specific-extension] .

Donna


On Nov 14, 2012, at 4:56 PM, "Peng, Huiling" <pengh at missouri.edu> wrote:

> 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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>>
>>
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