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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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:
External Email - Use Caution
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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