Ok, I think I got it, the unknow which is correspondent to the black area and actually desikan atlas has 34 labels to use, unknow and corpuscallosum from annot are not used, and i can just set the z-score for these two areas to be zero.

If i misunderstood it, please correct me

Thanks



De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Hao wen <hao.freesurfer@hotmail.com>
Envoyé : mardi 6 décembre 2016 11:02
À : Freesurfer support list
Objet : Re: [Freesurfer] aparcstat2label command result does not include corpuscallosum label
 

Thanks for your reply, good to know that, but when I use tksurfer to read the aparc.annot file, and in the label names, they include corpuscallosum, and when I make the z-score map, I can make this label to be 0, but if it is not the parcellation label, why it should be here???( in tksurfer: windows/label/ no.4)

Alos, inside the label names, the first one is 'unknown( in tksurfer: windows/label/ no.0)', can you explain this a little for me???


Here is the snapshot for the tksurfer:



Any idea will be appreciated

Thanks in advance

 



De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Juergen Haenggi <j.haenggi@psychologie.uzh.ch>
Envoyé : mardi 6 décembre 2016 08:29
À : Freesurfer support list
Objet : Re: [Freesurfer] aparcstat2label command result does not include corpuscallosum label
 
Dear Hao Wen

the corpus callosum is a subcortical structure and therefore not included in the parcellations. 
but there are volumetric segmentations of the corpus callosum that can be obtained by using the
asegstats2table command.

Hope this helps
Regards
Jürgen


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Am 06.12.2016 um 08:20 schrieb Hao wen:

Yes, sorry, it is 
aparcstats2tabel:)
Do you have any idea where is the corpuscallosum information???

Thanks in advance

De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Douglas N Greve <greve@nmr.mgh.harvard.edu>
Envoyé : lundi 5 décembre 2016 18:05
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] aparcstat2label command result does not include corpuscallosum label
 
Do you mean aparcstats2table?


On 12/05/2016 10:15 AM, Hao wen wrote:
>
> Hello, freesurfer experts:
>
> I have a question, recently, I use the aparcstats2label comamnd, and 
> get the result file, and I use tksurfer to display the desikan 
> atlas(?h.aparc.annot), and I want to corresponds the labels between 
> this two, but in my aparcstats2label result file, i can not find the 
> corpuscallosum which is the No.4 label in tksurfer, to bespecific, 
> here is the label ID in desikan atlas in tksurfer:
>
>
> aparc_lables= ['unknown', 'bankssts', 'caudalanteriorcingulate', 
> 'caudalmiddlefrontal', 'corpuscallosum', 'cuneus', 'entorhinal', 
> 'fusiform', 'inferiorparietal', 'inferiortemporal', 
> 'isthmuscingulate', 'lateraloccipital', 'lateralorbitofrontal', 
> 'lingual', 'medialorbitofrontal', 'middletemporal', 'parahippocampal', 
> 'paracentral', 'parsopercularis', 'parsorbitalis', 'parstriangularis', 
> 'pericalcarine', 'postcentral', 'posteriorcingulate', 'precentral', 
> 'precuneus', 'rostralanteriorcingulate', 'rostralmiddlefrontal', 
> 'superiorfrontal', 'superiorparietal', 'superiortemporal', 
> 'supramarginal', 'frontalpole', 'temporalpole', 'transversetemporal', 
> 'insula']
> which has 36 labels, and I dont understand which label is unknow....
> on the contrary, the result from aparcstat2table have 36 
> columns(includint subject_id and meanthickness),
> so bacially, they have just 34 labels add one 'unknown', it should 
> have 35 labels, but I did not find the lable
> 'corpuscallosum', Can someone help me???
> The result file for aparcstat2table file is attached:)
> Thanks in advance
>
>
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