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Hi Yujing,

Thanks for the response.

We addressed the issues by modifying the labels of the vertices that represent specific areas. To do this, we employed the 'write_annotation' function in FS (MATLAB-based). Anyway, It's worth noting that the PALS_B12 annotation files in FreeSurfer may require further refinement.

Best, Xinjie ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: Tuesday, November 14, 2023 4:46:42 PM To: Freesurfer support list Subject: [EXTERN] Re: [Freesurfer] Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer

Sorry, I take my suggestion back. Annotation values are saved in .annot file, not the label id. Different colortable won’t work.

Yujing

From: Huang, Yujing Sent: Tuesday, November 14, 2023 9:24 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: RE: Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer

Hi Xinjie,

?h.PALS_B12.labels.gii in fsaverage/label/ seem to have duplicated color schemes assigned to the labels you mentioned. I’m assuming ?h.PALS_B12_Brodmann.annot is generated from the GIFTI https://secure-web.cisco.com/1T831HwdcEs9uXAG2x-7aldFZHZ4KU-2yr3C9R4WJCtuy80...

Maybe a different colortable will help the visualization?

Best,

Yujing

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 Xinjie Chen Sent: Tuesday, November 14, 2023 6:59 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer

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Dear FreeSurfer Team,

I am writing to report a significant issue I have encountered while using the PALS_B12_Brodmann.annot files in FreeSurfer. I have noticed a critical error concerning labeling certain Brodmann areas.

Specifically, in the left hemisphere, labels such as Brodmann area 33, CON_deeper_than_WS_t_2', and ASP deeper' appear to share the same label ID. Similarly, in the right hemisphere, the label for Brodmann area 3 seems to be merged with Brodmann area 33. This overlap of labels and the lack of unique IDs for distinct Brodmann areas like Brodmann 3 and Brodmann 33 are causing significant confusion and potential errors in analysis. For instance, this issue complicates tasks such as calculating variables for individual Brodmann areas, leading to inaccurate results.

I am keenly interested in any solutions or methods you could suggest for resolving this problem. Thank you in advance for your assistance and I am looking forward to a resolution.

Best regards, Xinjie