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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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

In freeview I believe you can right click on a given label in the list in the left-hand pane and “go to centroid” or something is an option

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, June 28, 2024 9:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer atlases

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Thursday, June 27, 2024 12:36 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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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