opps sorry one last question. Will segstats get me LGI estimates of the pial
surface?
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 2:15:33 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf
mc-z.abs.th13.sig.ocn.dat --excludeid 0
where y.mgh is the file created by qdec to be used in the glm analysis
doug
On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote:
> 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
Phone Number: 617-724-2358
Fax: 617-726-7422
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