I definitely would NOT write to the caret/data_files directory. You can copy
from it, but messing with those files is not a good idea, even if the
permissions allow you to do so. Caret uses files in that directory to do its
job, so if you modify them, things will break.
Under Attributes: Metric there are many smoothing options, but caret_command
has this feature:
caret_command -metric-smoothing
<coordinate-file-name>
<topology-file-name>
<input-metric-file-name>
<output-metric-file-name>
<smoothing-algorithm>
<smoothing-number-of-iterations>
<smoothing-strength>
[-geo-gauss sigma]
[-fwhm desired-full-width-half-maximum]
[-gauss spherical-coordinate-file-name
sigma-norm
sigma-tang
norm below cutoff (mm)
norm above cutoff (mm)
tang-cutoff (mm)]
[-parallel]
Smooth metric data.
"smoothing-algorithm" is one of:
AN Average Neighbors
DILATE Dilation
FWHM Full-Width Half-Maximum
GAUSS Gaussian, requires -gauss
GEOGAUSS Geodesic Gaussian, uses -geo-gauss, default 2.0
WAN Weighted Average Neighbors
NOTE: Geodesic Gaussian IGNORES the strength parameter,
amount of smoothing is controlled solely by sigma and
iterations. The intent is to do one iteration of
smoothing, with the sigma specifying how much smoother
the metric is desired to be.
I suspect wb_command has even better smoothing (seem to recall Tim C saying
something along those lines, but I can't recall the details). This command
line utility is part of Caret Workbench and needs a different format -- GIFTI
or CIFTI. You can convert caret5 metric to GIFTI by doing:
caret_command -file-convert -format-convert XML_BASE64_GZIP my_file.metric
At least I think that is what Tim C. told me. ;-)
On Mar 31, 2014, at 10:38 AM, "Cheng, Hu" <[email protected]> wrote:
> Hi Donna,
>
> I loaded the atlas first, then I was able to see the mapping using "Map to
> Caret". In the software it shows the metric file is added to the spec file if
> using "Map to Spec File With Atlas", maybe it's forbidden to add file to
> caret/data_files/standard_mesh_atlases/Human.PALS.LEFT?
> Now I have the metric file, could you tell me how to smooth it or is there
> any way to convert it back to freesurfer which I know how to do smoothing?
> Many thanks!
>
> Regards,
>
> Hu
>
>
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Donna Dierker
> Sent: Monday, March 31, 2014 11:07 AM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] mapping fMRI data to surface
>
> Hi Hu,
>
> No, there's no log file, but if you check Debug Enabled (File: Preferences),
> all sorts of stuff will scroll to the terminal window from which Caret was
> launched.
>
> I assume you have made sure your working directory is writable by the user
> running Caret. File: Set Working Directory can show you what Caret thinks
> the working directory is.
>
> Donna
>
>
> On Mar 31, 2014, at 9:54 AM, "Cheng, Hu" <[email protected]> wrote:
>
>> Hi Donna,
>>
>> Thank you! There is no non-English character set on the mac. I just wonder
>> if there is a log file so that I can see what's wrong.
>>
>> Regards,
>>
>> Hu
>>
>>
>> -----Original Message-----
>> From: [email protected]
>> [mailto:[email protected]] On Behalf Of Donna Dierker
>> Sent: Friday, March 28, 2014 5:07 PM
>> To: Caret, SureFit, and SuMS software users
>> Subject: Re: [caret-users] mapping fMRI data to surface
>>
>> Do you have a non-English character set installed on this computer? We have
>> had issues with writing metric files when a non-English character set was
>> installed, but the error I recall was worded slightly different.
>>
>>
>> On Mar 28, 2014, at 1:22 PM, Cheng, Hu wrote:
>>
>>> Dear Caret users,
>>>
>>> I'm trying to map fMRI data to surface template and do surface based
>>> smoothing. The fMRI data I used were already normalized in spm8. I ran
>>> attribute "Map Volumes(s) to Surface(s)" accordingly to
>>> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MapVolumeToSurface,
>>> I selected "Map to Spec File With Atlas" using "
>>> Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730" SPEC file and chose "SPM5"
>>> space. The program ran smoothly at the beginning but an error popped out in
>>> the end showing :Unable to save metric file ...". This was done in Windows.
>>> I repeated the same process on Mac, the program seemed to terminated
>>> without any error except a sound, there is no metric file created in the
>>> working directory.
>>> Thanks for your help.
>>>
>>> Regards,
>>>
>>> Hu
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> caret-users mailing list
>>> [email protected]
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>>
>> _______________________________________________
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>>
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>
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