[Freesurfer] RES: Running autorecon2-wm after wm edits

again and send to you. Best,Fernanda Hansen P. de Moraes  fernandamor...@if.ufrj.brFísica Médica e Doutora em Ciências MédicasmetaBIO - IF UFRJ e Brain Connectivity Unit - Instituto D'Or de Pesquisa e Ensino De: Huang, YujingEnviado:Tuesday, November 7, 2023 10:27 AMPara: Freesurfer support listAssunto

[Freesurfer] Running autorecon2-wm after wm edits

file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências

Re: [Freesurfer] Fwd: average lobar cortical thickness

! Best, Fernanda Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutora em Ciências Médicas | metaBIO (IF-UFRJ) e Instituto D'Or de Pesquisa e Ensino On Wed, Nov 9, 2022 at 11:35 AM Douglas N. Greve wrote: > I would weight by the number of vertices in each ROI > > On 11/8/2022

[Freesurfer] infantFS surface stats file

you very much in advance, Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino e metaBIO (IF-UFRJ) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] REtrieve perimeter from generated surfaces

External Email - Use Caution Dear FreeSurfer experts, Is there a way to estimate the perimeter from a surface (e.g. ?h.pial) for each slice in an automated manner at any orientation? Thank you very much, Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutoranda em

Re: [Freesurfer] InfantFS witg segfile exiting with errors

--i > /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.nii.gz > --noverbose > ``` > > -Paul > > On Thu, Jul 1, 2021 at 11:41 AM Fernanda Hansen P. de Moraes < > fernandahmor...@gmail.com> wrote: > >> External Email - Us

[Freesurfer] InfantFS witg segfile exiting with errors

this? Thank you very much. Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino sub-CC00060XX03_infant_recon_all.2106221156.log Description: Binary data ___ Freesurfer mailing list

[Freesurfer] InfantFS witg segfile exiting with errors

this? Thank you very much. Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino Logfile for infant_recon_all ter jun 22 11:56:53 -03 2021 --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc

Re: [Freesurfer] Installing anither Freesurfer version - lincese not working

-1_acq-wb_mod-t1w_orient-std_brain.nii.gz /home/fernanda/Documentos/AHEAD/freesurferv5/sub-0002/mri/orig/001.mgz Em qui., 11 de fev. de 2021 às 11:45, Fernanda Hansen P. de Moraes < fernandahmor...@gmail.com> escreveu: > Dear Freesurfer experts, > I installed another Freesurfer v

[Freesurfer] Installing anither Freesurfer version - lincese not working

External Email - Use Caution Dear Freesurfer experts, I installed another Freesurfer version on my computer and used the same license of the version installed before. But, it is not working. How should I proceed? Best regards, Fernanda Hansen P. de Moraes fernandahmor

Re: [Freesurfer] Corpus Callosum area

dgr...@mgh.harvard.edu> escreveu: > We don't output or have tools to compute it. I can tell you how you can > get a number for it, but it would not be with a validated method. Let me > know. > > On 9/24/2019 5:37 AM, Fernanda Hansen P. de Moraes wrote: > > External Email - Us

[Freesurfer] Corpus Callosum area

External Email - Use Caution Dear Freesurfer experts, how can I extract the corpus callosum cross sectional area for each hemisphere? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências

Re: [Freesurfer] asegstats2table error - measure 63 expected 66

, but it is the first time I get this error message for all of my subjects. Do you have any suggestion on what to do? Thank you very much in advance, Fernanda Em sex, 9 de ago de 2019 às 17:51, Fernanda Hansen P. de Moraes < fernandahmor...@gmail.com> escreveu: > Dear Freesurfer experts,

[Freesurfer] asegstats2table error - measure 63 expected 66

suggestion on how can we trespass this error? Regards, -- Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino ___ Freesurfer mailing list Freesurfer

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

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 &g

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

gt; 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

[Freesurfer] Lobe parcellation without cingulate from --lobesStrict

, 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

Re: [Freesurfer] TotalGrayVol and SubCortGrayVol for multiple subjects

External Email - Use Caution Sorry, it is indeed. Thank you very much! On Fri, Jun 15, 2018 at 11:30 AM Douglas Greve wrote: > It should auotmatically be included in the output asegstats2table. is it > not? > > On 6/15/18 10:23 AM, Fernanda Hansen P. de

[Freesurfer] TotalGrayVol and SubCortGrayVol for multiple subjects

should I define the output file from mri_segstats so asegstats2table can read it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

Re: [Freesurfer] ERROR: mpr2mni305 failed

ked at > the image to make sure that there are no obvious problems? Is the voxel > size about 1mm? Is it T1 weighted? > > > On 05/21/2018 05:31 PM, Fernanda Hansen P. de Moraes wrote: > > > > Dear FreeSurfer experts, > > > > I am having some trouble to understand this

[Freesurfer] ERROR: mpr2mni305 failed

es. We are already doing this. Do you have any tip on what to do to solve it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz ___ Freesurfer mailin

Re: [Freesurfer] Differences in aseg.stats automatic results

rent results. Why not just > use one version? > > > On 05/02/2018 01:24 PM, Fernanda Hansen P. de Moraes wrote: > > > > > > Good afternoon, > > > > I've got two types of aseg.stats results from the file automatically > > created from the reg

[Freesurfer] Differences in aseg.stats automatic results

, Estimated Total Intracranial Volume, 1416319.091398, mm^3# SegVolFile mri/aseg.mgz * How can I have the aseg.stats files all the same, with the SupraTentorialVolNotVent? Thank you in advance! -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

Re: [Freesurfer] Starting with Neuroimaging

> 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

Re: [Freesurfer] LGI for the lobar annotation

External Email - Use Caution Thank you!! :D On Thu, Apr 19, 2018 at 12:57 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > yes > > > On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote: > > Douglas, thank you very much again. > >

Re: [Freesurfer] LGI for the lobar annotation

se) > averaged over vertices. If you wan the total number, multiply it by the > number of vertices or re-run with --accumulate. The area is the surface > area of the entire lobe. > > On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes wrote: > > Sorry, my mistake. > > mri_segsta

Re: [Freesurfer] LGI for the lobar annotation

t; > > On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote: > > Dear Douglas, > > > > thank you. > > > > The code worked, but I didn't understand the result very well. What > > means intensity? The area, is the ara from the piall_lgi surface > >

Re: [Freesurfer] mri_anatomical_stats with lobeStrict annot for multiple subjects

t got how to insert the > lobeStrict annot there. > > Thank you very much, > Fernanda Moraes > > -- > Fernanda Hansen P. de Moraes > Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz > > > ___ > Freesurfer mailing

Re: [Freesurfer] LGI for the lobar annotation

Thank you, Douglas, do you have any suggestions on how to make you work? Fernanda On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve <dgr...@mgh.harvard.edu> wrote: > that should work, except the command line is not quite right > > On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes

[Freesurfer] mri_anatomical_stats with lobeStrict annot for multiple subjects

Moraes -- 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 The information

[Freesurfer] LGI for the lobar annotation

lh.lobesStrict.annot.pial_lgi.stats* Thank you! -- 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