External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@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-2yr3C9R4WJCtuy80BemyJiH_Fq24Lc2X34QD-LDO-M6U3VN7W0sXPaym6KOncuFpxdlUX5Eqhbbe8MsPcfeayVbs54dR9NlFaJ31W7E-IhU38z5TH2-v2IeTQJksF1hsvrSuyoS2UI46fzT8jinhfP7Xf4Ri1uuOMNEVL1JlZoWZiuwZTvpLb5-sIvHnjmRlGaGOsSVGgUBdugCx5jqyJ0lmXj1pA7_RTWy_tyHGFHukcPX7YUMydMCI_K5RIpTKl5Afv8cuhT1abHMQljLYi9eMoiZq4bBWQH0geKKl6MjTLb9dJErEcW6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPALS_B12 Maybe a different colortable will help the visualization? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Xinjie Chen Sent: Tuesday, November 14, 2023 6:59 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer External Email - Use Caution 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
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