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Thank you for the reply,

I need to create a mask of each segmented subfield (segmented with freesufer) and then I need to use the obtained mask in FSL to do a DTI. However, I am not sure about the pipeline I have to follow to do so. So far I have been following this one:

mri_label2vol --seg <> --temp rawavg.mgz --regheader <> --o "".mgz
mri_binarize --i --o --match "17"

mri_convert --in_type mgz --out_type nii

flirt -in -out -init -applyxfm

fslmaths -bin

But when I try to open the mask in FSL I cannot visualize them. Does anyone have suggestions?

Thanks,

Alice

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: Thursday, June 27, 2024 12:36 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer atlases

I'm not sure what you mean. We don't have an image of the subfields in, eg, mni space. Usually, you just run the subfield seg on the data that you want subfields for

On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:

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Hello,

I am looking for a freesufer standard atlas for hippocampal subfields (to be used for a DTI pipeline in FSL) but I cannot find it in fsaversage/label.

Does anyone have any suggestion?

Thank for the help,

Alice
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