can you send the qdec file with variables?


On 11/09/2016 11:51 AM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> Somehow even after adding variables, it's not working, although same
> qdec file works fine when I perform GLM in qdec.
> So I replaced the flag with subjectsfile and provided subject list.txt
> file. So in that way, it's working fine now.
>
> I was also wondering (a) how can I average these thickness stats (b)
> are these in fsaverage (standard) space and (c) how can I display it
> on standard fsaverage for publications purpose?
>
> Thanks a lot.
>
> On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     Appears to be having problems reading the qdec table. It might be
>     expecting the qdec table to actually variables in it. Can you try
>     adding variables? Also, try it without the --qdec flag instead
>     specifying the subjects with --subjects HC003_1 HC004_1 ...
>
>
>     On 11/8/16 8:09 PM, Martin Juneja wrote:
>>     Hi everyone,
>>
>>     I am trying to use following command to save stats from a set of
>>     subjects in a table format:
>>
>>     aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t
>>     zzz.txt
>>
>>     But after I run this, I get following error:
>>
>>     Traceback (most recent call last):
>>
>>       File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in
>>     <module>
>>
>>     subj_listoftuples = assemble_inputs(options)
>>
>>       File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in
>>     assemble_inputs
>>
>>     fsid=row['fsid'].strip()
>>
>>     KeyError: 'fsid'
>>
>>     My qdec.dat file looks like below:
>>
>>     fsidHC003_1
>>     HC004_1
>>     HC006_1
>>     HC015_1
>>
>>     This command works fine if I use subject IDs individually here e.g.
>>     aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1
>>     HC015_1 --hemi lh --meas thickness -t zzz.txt
>>
>>     Another question I have here is: How can I average these
>>     thickness stats and display it on standard fsaverage?
>>
>>     Any help would be really appreciated.
>>
>>
>>
>>
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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