version 5.0.0
----- 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: Tuesday, October 8, 2013 1:57:35 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
what version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
> I did. This is what I get from my group analysis in the folder. I didn't find
> the ocn.dat file. Is there something I need to do in Qdec to produce it?
>
> C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
> cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vertex.mgh
> F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh
> gamma.mgh mc-z.abs.th13.sig.cluster.summary
> gammavar.mgh mc-z.abs.th13.sig.ocn.annot
>
> 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: Tuesday, October 8, 2013 10:48:10 AM
> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>
>
> Did you generate the annotation from a qdec analysis of lgi? If so, then
> there should be a file already there called something like
> mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
> each cluster. The value will be the mean lgi for that subject and
> cluster. Is this what you need?
>
> doug
>
>
>
>
> On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
>> 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
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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