Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

[Mahshid Fouladivanda]

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Dear Doug,



Here is the emails:



Message: 6
Date: Fri, 2 Aug 2019 01:55:34 +
From: "Greve, Douglas N.,Ph.D." 
Subject: Re: [Freesurfer] How to Create Cortex Parcellation Using
   "mri_aparc2aseg"?
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: <183e8a60-1cc2-1680-26a7-bce8a1d03...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

If you look in the recon-all.log file for any subject, you will see a 
mri_aparc2aseg command line. YOu can use that specifying your annot and the 
new output name.

On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote:

External Email - Use Caution

Dear experts,

I have a segmentation file of all the tissues in the brain and the ribbon 
file which were extracted by another toolbox rather than freesurfer. Also, I 
have created the annotation file using "write_annotation.m". Now, I wanna 
create a parcellation file based on the segmentation and annotation files 
using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the 
terminal and extract the parcels:
mri_aparc2aseg --s subject name --annot annotation name --o output name

and I used the segmentation file as the "aseg.mgz" for the above command. 
Now, I am wondered that do I select the right aseg file or not??
Any help would be appreciated.

Regards,
Mahshid



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Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

[Greve, Douglas N.,Ph.D.]

sorry, all the previous emails did not make it into this one so I'm a 
bit lost. Can you repost with the previous correspondence?

On 8/14/19 1:51 PM, Mahshid Fouladivanda wrote:
>
> External Email - Use Caution
>
> Dear Doug,
> Thanks for your reply. I have used the same command in the 
> recon-all.log file (seen bellow), but I have a doubt for the 
> highlighted part in the command:
> "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel 
> mri/norm.mgz mri/transforms/talairach.m3z 
> */usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca* 
> mri/aseg.auto_noCCseg.label_intensities.txt"
>  which used a predefined file from freesurfer folder. Actually, I used 
> the mri_aparc2aseg command with some changes, seen bellow:
> mri_aparc2aseg --s mysubj --annot aparc --o 
> $SUBJECTS_DIR/mysubj/mri/parc.mgz
> so, I am wondered if it reads the ' 
> */usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca*' 
> automatically. I would appreciate it of you could help on.
> Regards,
> Mahshid
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

[Mahshid Fouladivanda]

External Email - Use Caution

Dear Doug,

Thanks for your reply. I have used the same command in the recon-all.log 
file (seen bellow), but I have a doubt for the highlighted part in the 
command:

"mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt"

 which used a predefined file from freesurfer folder. Actually, I used the 
mri_aparc2aseg command with some changes, seen bellow:

mri_aparc2aseg --s mysubj --annot aparc --o 
$SUBJECTS_DIR/mysubj/mri/parc.mgz

so, I am wondered if it reads the ' 
/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I 
would appreciate it of you could help on.

Regards,
Mahshid
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Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

[Greve, Douglas N.,Ph.D.]

If you look in the recon-all.log file for any subject, you will see a 
mri_aparc2aseg command line. YOu can use that specifying your annot and the new 
output name.

On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote:

External Email - Use Caution

Dear experts,

I have a segmentation file of all the tissues in the brain and the ribbon file 
which were extracted by another toolbox rather than freesurfer. Also, I have 
created the annotation file using "write_annotation.m". Now, I wanna create a 
parcellation file based on the segmentation and annotation files using 
"mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal 
and extract the parcels:
mri_aparc2aseg --s subject name --annot annotation name --o output name

and I used the segmentation file as the "aseg.mgz" for the above command. Now, 
I am wondered that do I select the right aseg file or not??
Any help would be appreciated.

Regards,
Mahshid





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