I see. Thank you so much for everything!
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 2:42:36 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
it gives you estimates of whatever you give it. If the y.mgh file are
pial estimates, then that is what you will get
doug
On 10/08/2013 03:40 PM, Tara Ann Miskovich wrote:
> 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
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Fax: 617-726-7422
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