I see, could you help me go about this. I have not been able to figure out how
to do this with an annotation file. And I believe I already mapped my lgi to
fsaverage space before group level through recon-all -qcache. Is this what you
mean?
Thank you again for the help!
Tara
----- Original Message -----
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: "Tara Ann Miskovich" <misko...@uwm.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, October 7, 2013 1:59:37 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Oh, you'll need to map the annotation into the individual space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
> Thank you Doug, this did work. However, for every subject I get this line
> repeated over and over before it outputs the stats. I still get a stats file
> that seems to make sense but I am not sure if this is an issue.
>
> MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=00000000,
> in_array_size=136201
> annot file:
> ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
>
> Thank you for the help!
> Tara
>
>
>
> ----- Original Message -----
> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, October 4, 2013 6:29:49 PM
> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>
>
> This may sound incredibly trivial, but try putting a "./" infront of
> qdec, ie, "-a ./qdec/..."
>
> doug
>
>
> On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
>> Hi Everyone,
>>
>> I am having trouble running mris_anatomical_stats on an annotation file
>> produced from my group analysis in qdec.
>>
>> This is my code, but it seems to want to pull the annotation file from the
>> subject/label directory. Should I just make a copy into everyone's label
>> file?
>>
>> mris_anatomical_stats -a
>> qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
>> -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
>> ${subject} lh
>>
>> Thank you!
>> Tara
>> _______________________________________________
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>>
>>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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