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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
