[caret-users] caret_map_fmri

John Harwell john at brainvis.wustl.edu
Mon Mar 29 11:12:33 CDT 2010


Hi Julie,

"-surface-deformation-apply" is now "-deformation-map-apply".

If you are searching for a command, try "caret_command  -help-search <search-text>".  For example "caret_command   -help-search   deformation".

John


On Mar 29, 2010, at 10:50 AM, Julia Bender wrote:

> Hi John,
> 
> everything worked well with the script you sent me, thanks! I have another
> question: Has the caret_command "-surface-deformation-apply" also been
> replaced? I'm trying to run an older script that's calling this line, but
> I get "command not found" when I run it now. I also could'nt find it when
> I looked up all arguments under 'caret_commands -help'
> 
> thanks a lot!
> 
> Julia
> 
>> Hi Julie,
>> 
>> "caret_map_fmri" is a program that was eliminated several years ago.  Make
>> sure you have the latest version of Caret, 5.613.
>> 
>> In place of "caret_map_fmri" use "caret_command   -volume-map-to-surface".
>> 
>> Try:
>> 
>> caret_command  -volume-map-to-surface   \
>>   /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.Fiducial.65366.coord   \
>>   /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.CLOSED.65366.topo   \
>>   ""   \              <== This is the name of an input metric file to
>> which data is appended.  An empty name (two double quotes) means create
>> a new metric file.
>>   Rtest.metric   \
>>   METRIC_ENCLOSING_VOXEL  \
>>   cCue_EndoLeft.hdr
>> 
>> 
>> John Harwell
>> 
>> 
>> On Mar 26, 2010, at 9:28 AM, Julia Bender wrote:
>> 
>>> 
>>> 
>>> Hi,
>>> 
>>> I'm having trouble using caret_map_fmri. I'm running:
>>> 
>>> caret_map_fmri -m Rtest.metric -s
>>> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.spec
>>> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.CLOSED.65366.topo
>>> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.Fiducial.65366.coord -v
>>> cCue_EndoLeft.hdr
>>> 
>>> I get:
>>> Unrecognized preferences data type
>>> BINARY:BINARY:BINARY:BINARY:BINARY:BINARY:BINARY
>>> ERROR: Error  cCue_EndoLeft.hdr: No such file or directory
>>> 
>>> I'm running the command in the directory where my statistical maps (e.g.
>>> cCue_EndoLeft.hdr) for this subject are and I have full permission on
>>> all
>>> files.
>>> 
>>> I'm using caret (current release) on a linux machine (openSUSE
>>> 11.2).Does
>>> anyone have an idea what could be wrong?
>>> 
>>> 
>>> Thanks a lot!
>>> 
>>> Julia
>>> 
>>> 
>>> 
>>> Dipl. Psych. Julia Bender
>>> Humboldt Universität zu Berlin
>>> Mathematisch - Naturwissenschaftliche Fakultät II
>>> Institut für Psychologie, Abt. Klinische Psychologie
>>> Unter den Linden 6
>>> D-10099 Berlin
>>> 
>>> 
>>> 
>>> Dipl. Psych. Julia Bender
>>> Humboldt Universität zu Berlin
>>> Mathematisch - Naturwissenschaftliche Fakultät II
>>> Institut für Psychologie, Abt. Klinische Psychologie
>>> Unter den Linden 6
>>> D-10099 Berlin
>>> 
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>> 
>> 
>> 
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>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
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>> 
> 
> 
> Dipl. Psych. Julia Bender
> Humboldt Universität zu Berlin
> Mathematisch - Naturwissenschaftliche Fakultät II
> Institut für Psychologie, Abt. Klinische Psychologie
> Unter den Linden 6
> D-10099 Berlin
> 
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> 





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