Dear Douglas,

thank you very much. I've already done the first  mri_annotation2label. Now I should go to the mri_mergelabels step, which I am trying to do with the following code:

mri_mergelabels -i PRI002/label/lh.superiorfrontal -i PRI002/label/lh.rostralmiddlefrontal -i PRI002/label/lh.caudalmiddlefrontal -i PRI002/label/lh.parsopercularis -i PRI002/label/lh.parsorbitalis -i PRI002/label/lh.parstriangularis -i PRI002/label/lh.precentral -i PRI002/label/lh.paracentral -i PRI002/label/lh.frontalpole -o PRI002/label/lh.frontal.IDOR

It returns this error: 

ERROR: PRI002/label/lh.superiorfrontal does not exist

I do not understand how to use mri_mergelabels, since it always returns to me " ERROR: SUBJxxx/label/lh.xxxx does not exist"

Could you please send me an example? Maybe it could be helpful.

Thank you very much in advance again,

Fernanda

2018-08-06 14:22 GMT-03:00 Douglas N. Greve <dgreve@mgh.harvard.edu>:

If you want custom lobes, then the easiest thing to do is to break up
the aparc annotation into labels (mri_annotation2label) and then merge
each lobe into a single label (mri_mergelabels), then combined the
merged labels back into an annotation (mris_label2annot).

On 08/06/2018 12:38 PM, Fernanda Hansen P. de Moraes wrote:
>
>         External Email - Use Caution
>

> Dear Douglas,
>
> thank you for your response.
> Sorry if I've been misunderstood.
> I want to have the following parcellation of lobes:
> Frontal
> • Superior Frontal
> • Rostral and Caudal Middle Frontal
> • Pars Opercularis, Pars Triangularis, and Pars Orbitalis
> • Lateral and Medial Orbitofrontal
> • Precentral
> • Paracentral
> • Frontal Pole
> • Rostral Anterior Cingulate
> • Caudal Anterior Cingulate
> Parietal
> • Superior Parietal
> • Inferior Parietal
> • Supramarginal
> • Postcentral
> • Precuneus
> • Posterior Cingulate
> • Isthmus
> Temporal
> • Superior, Middle, and Inferior Temporal
> • Banks of the Superior Temporal Sulcus
> • Fusiform
> • Transverse Temporal
> • Entorhinal
> • Temporal Pole
> • Parahippocampal
> Occipital
> • Lateral Occipital
> • Lingual
> • Cuneus
> • Pericalcarine
>
> After the
> mri_annotation2label --subject PRI002 --hemi lh --lobesStrict
> lh.lobesStrict.annot
> how can I merge the labels originally assigned to the Cingulate
> (Rostral Anterior (Frontal), Caudal Anterior (Frontal), Posterior
> (Parietal) e Isthmus (Parietal)), at the lobes?
>
> Thank you very much in advance,
> Fernanda H. P. de Moraes
>
>
>
>
> On Mon, Aug 6, 2018 at 1:10 PM Douglas N. Greve

> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>
>     Sorry, I'm not sure I understand. You want the lobes annotation
>     but you
>     want to merge the cingulate with the frontal? After you run the 1st
>     mri_annotation2label, run it again with the lobes as the input
>     annotation and specifying --outdir to break up the annotation into
>     labels. Then run your mergelabels command to merge cingulate with
>     frontal. Then run mris_label2annot to create a new annotation with
>     the
>     merged labels.
>
>     On 08/03/2018 05:40 PM, Fernanda Hansen P. de Moraes wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Dear FreeSurfer experts,
>     >
>     > I want to get with mris_anatomical_stats the stats from the four
>     > lobes, Frontal, Parietal, Temporal and Occipital as suggest here
>     >
>     (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), but
>     > without the cingulate.
>     >
>     > I am trying to use the mri_mergelabels to merge that labels:
>     > Rostral Anterior (Frontal)
>     > Caudal Anterior (Frontal)
>     > Posterior (Parietal)
>     > Isthmus (Parietal)
>     > in their lobes, but I am facing some difficulties. I am sorry if
>     this
>     > is a basic question, but I couldn't find an example that worked
>     for me
>     > in the mail archive.
>     >
>     > I am following these steps:
>     >
>     > mri_annotation2label --subject PRI002 --hemi lh --lobesStrict
>     > lh.lobesStrict.annot
>     > mri_mergelabels -i lh.frontal -i lh.rostralanteriorcingulate -i
>     > lh.caudalanteriorcingulate -o lh.frontal
>     >
>     > Is there an easier way to do it?
>     >
>     > Thank you very much in advance,
>     > Fernanda Hansen P. de Moraes
>     >
>     > --
>     > Fernanda Hansen P. de Moraes
>     >
>     > Física Médica | Rede D'Or São Luiz
>     > Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
>     >
>     >
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> Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz
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