External Email - Use Caution Dear Douglas,
how should the input for mri_mergelabels be? Should I use the name of the file, or the number of the label (from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT )? Thank you very much, Fernanda On Tue, Aug 7, 2018 at 4:32 PM Fernanda Hansen P. de Moraes < fernandahmor...@gmail.com> wrote: > 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 <dgr...@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 >> > <dgr...@mgh.harvard.edu <mailto:dgr...@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 >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto: >> Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > 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. >> > >> > -- >> > Fernanda Hansen P. de Moraes >> > Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > Fernanda Hansen P. de Moraes > > Física Médica | Rede D'Or São Luiz > + 55 (21) 3461-3630 <+55%2021%203461-3630> - Engenharia Clínica > Corporativa > -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz
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