[Freesurfer] Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)

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Hi,

I spoke too soon - using the developmental version of freesurfer did not work. A reminder of the issue below:

I have a script that utilizes the -ss flag on the freeview command to take axial, sagittal, and coronal screenshots iteratively. I have multiple images loaded into freeview at a time for each screenshot, and most of the loaded images are the same across all the screenshots, except for one spherical ROI that is only the same within a given sagittal/axial/coronal set.

I have been encountering a problem where some of the screenshots are horizontally mirrored (left-hemisphere/right hemisphere flipped) in comparison to the rest of the images. This happens the most often for the coronal screenshot, but has also occurred for the axial screenshot. The spherical ROIs for which this mirroring occurs is not consistent - every time I run the script, it's a different set that's horizontally mirrored.

*Ania Holubecki*

On Tue, Jun 3, 2025 at 11:10 AM Ania Holubecki ania.holubecki@gmail.com wrote:

Hi Ruopeng,

I tried the two latest versions installed on our computing cluster:

freesurfer/7.3.2 freesurfer/8.1

The most recent development version worked - thanks so much!

*Ania Holubecki*

On Thu, May 15, 2025 at 9:10 AM freesurfer-request@nmr.mgh.harvard.edu wrote:

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Message: 1 Date: Tue, 13 May 2025 15:23:26 -0500 From: Ania Holubecki ania.holubecki@gmail.com Subject: [Freesurfer] freeview -ss orientation inconsistencies To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CADR7LJVJ1hFA0tPR-W2uXnKwY4GGQoW= vP983k6hL4uaqAr0wg@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

    External Email - Use Caution

Hi,

I have a script that utilizes the -ss flag on the freeview command to take axial, sagittal, and coronal screenshots iteratively. I have multiple images loaded into freeview at a time for each screenshot, and most of the loaded images are the same across all the screenshots, except for one spherical ROI that is only the same within a given sagittal/axial/coronal set.

I have been encountering a problem where some of the screenshots are horizontally mirrored (left-hemisphere/right hemisphere flipped) in comparison to the rest of the images. This happens the most often for the coronal screenshot, but has also occurred for the axial screenshot. The spherical ROIs for which this mirroring occurs is not consistent - every time I run the script, it's a different set that's horizontally mirrored.

Has anyone encountered this issue and has a way to guarantee the orientation of the screenshot? Any tips are greatly appreciated!

Best,

*Ania Holubecki*