Try looking at it in freeview first. Some of the regions may be small,
so you may have to hunt to get them. FYI you can specify nii as the
output of mri_binarize
On 6/28/2024 5:30 AM, Savoia, Alice (Stud. FPN) wrote:
External Email - Use Caution
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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