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Dear Bruce,

All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation file? I mean what information, it needs?

Regards Mahshid

From: freesurfer-request@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 08 Jul 2019 11:34:24 -0400 Subject: Freesurfer Digest, Vol 185, Issue 11

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Today's Topics:

1. Re: Skull Strip (Bruce Fischl) 2. How to Divide the Surface Parcellations of the Brain (Mahshid Fouladivanda) 3. Re: How to Divide the Surface Parcellations of the Brain (Bruce Fischl) 4. Assigning voxels different intensity values (Fotiadis, Panagiotis) 5. Re: Assigning voxels different intensity values (Bruce Fischl) 6. Re: Assigning voxels different intensity values (Fotiadis, Panagiotis) 7. Re: Assigning voxels different intensity values (Bruce Fischl) 8. Re: Assigning voxels different intensity values (Fotiadis, Panagiotis) 9. how to map regional t values on surface (fengmei fan) 10. Skull Strip (Admin) 11. Error in analyze (Qdec) (Abby tang) 12. Re: Freesurfer Digest, Vol 185, Issue 9 (vittal korann) 13. Postdoctoral Position opening at the University of Pittsburgh in neuroimaging of mood disorders (Anna Manelis) 14. Re: make_average_subject error: could not load norm volume from (null) (Greve, Douglas N.,Ph.D.) 15. Re: Skull Strip (Hoopes, Andrew) 16. Re: recon-all error: Correcting defect (Diamond, Bram Ryder) 17. Re: recon-all error: Correcting defect (Miguel ?ngel Rivas Fern?ndez)

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Message: 1 Date: Sun, 7 Jul 2019 13:33:35 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull Strip To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1907071333050.916@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

I believe I already answered this. I don't understand what amplified noise you mean. The brainmask.mgz can be used with mri_mask to apply to any input volume you want.

cheers Bruce On Sun, 7 Jul 2019, Admin wrote:

????????External Email - Use Caution????????

Dear Freesurfer group? Now,I want ?generated a brain mask including the

brain but excluding the

amplified noise regions after skull strip, but I can't find the

corresponding command line, so I

send this email to you,?hoping to get your help.? My English is poor, if?I make mistakes ,?I hope you can understand me.

Thanks for your help?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

? ? ? ? ? ? ? ? ? ? ? ? ?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

? Sincerely: Meng Nan Lin

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

? ? ? ? ? ? ? ? ? ? ? ? ?

? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

? Date: 07/04/2019

?

?

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Message: 2 Date: Mon, 08 Jul 2019 01:06:44 +0430 From: "Mahshid Fouladivanda" M.Fouladivanda@sutech.ac.ir Subject: [Freesurfer] How to Divide the Surface Parcellations of the Brain To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: WC20190707203644.661057@sutech.ac.ir Content-Type: text/plain; charset="us-ascii"

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Dear Freesurfer Experts,

I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical and sub-cortical. As I understand from help comments, mris_divide_parcellation would help, but it needs annotation file to be imported as input. I do not have the annotation file. I would appreciate it if you could help me how to divide my parcells in more regions?

Regards, Mahshid