Re: [Freesurfer] Lobe parcellation without cingulate from --lobesStrict

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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 exis*t"

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:

...

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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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