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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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 CautionDear 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 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
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.
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 > > > _______________________________________________ > 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
External Email - Use Caution
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:
External Email - Use CautionDear 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 eEnsino
> > > _______________________________________________ > 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
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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/FreeSurfe... )?
Thank you very much, Fernanda
On Tue, Aug 7, 2018 at 4:32 PM Fernanda Hansen P. de Moraes < fernandahmoraes@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 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 CautionDear 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 eEnsino
> > > _______________________________________________ > 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
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-- Fernanda Hansen P. de Moraes
Física Médica | Rede D'Or São Luiz
- 55 (21) 3461-3630 <+55%2021%203461-3630> - Engenharia Clínica
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