External Email - Use Caution Good afternoon,
Absolutely. Here’s the explanation of the issue in more detail. I have already recon-all’d a subject’s T1W image. Now, I’m trying to use the HCP atlas annotation files in fsaverage space (downloaded from here<https://secure-web.cisco.com/1RUlbihl_P7o4iECkLXdYd7_A71_OWggWGKTcu9o3hEd1Q-TIbJydYcpaMQ6fo6JrKecYvuag9pRj0svtM-tbZHyzOf--ziIZbRt3KZ-s273-wWXgwuWLz3_j6DIrKSiJB9xDfjO7TXoRlBY6j7PD0gZvue_aciq07dI505bqMEmXZ1uP3F-_aCwFXl914_RjYxLmyD2BW3AIYseqx3VO4-lgJJvB1qOkeqtl9XALsZFZTVmYtg3Zjfia6F0tH82nhvFtLOak0mCYm9rH0ZcvOg/https%3A%2F%2Ffigshare.com%2Farticles%2Fdataset%2FHCP-MMP1_0_projected_on_fsaverage%2F3498446>) to ultimately make the individual ROIs defined in this atlas in the subject-specific volumetric space. In order to do that, I used “mri_annotation2label” to find the label files related to the HCP atlas in the fsaverage space and then I used “mri_label2label” to transform each label to subject-specific space. Then, I used mris_label2annot to create the annotation file in subject-specific space and from there I used mri_aparc2aseg to create a volumetric .nii file in which each ROI is labeled with a different number. From here I was able to extract each ROI in the subject-specific space. Even though I was able to create my ROIs of interest at the end, I noticed that during the execution of the “mris_label2annot” I got warnings stating that some vertices mapped to multiple labels. This indicates that during the conversion in the prior step using “mri_label2label”, some vertices were assigned to multiple labels, however, I’m not sure how I could have prevented this from happening. Here’s the syntax I used for the left hemisphere as an example: mri_label2label --srcsubject fsaverage --srclabel XYZ1 --trgsubject XYZ2 --trglabel XYZ3 --regmethod surface --hemi lh Please let me know if I should have included a certain flag while executing “mri_label2label” that could have avoided the label overlaps in the new space. Thank you, Negin ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, May 8, 2023 10:47 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question about volumetric atlas ROIs overlap External Email - Use Caution I don't understand what you are referring to. Can you elaborate? On 5/5/2023 7:53 PM, Nadvar, Negin wrote: External Email - Use Caution Hello, I have a general question about handing atlas ROIs after applying recon-all on a T1W image. Could you please clarify how I can minimize/prevent atlas ROIs overlap in volumetric subject-specific space when going from surface-based space to volumetric space? Please let me know if you need more information. Thanks in advance, Negin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1kwqWQblUfJDueEJpQJL9R9IWjP8ghzLSTBe1_BqE1qpkWxI-dDgeewfZG9hyQwEp5zTC-H97SptkFmJHxGLA0zqpDbjTDSbrIEkjGzDEIEANls7YoEOCZ3h7EeS4JkP_RgTkDV6_iBZAnV1Piha1enW-Oh5a_euaeY6DZen75_Zn2kGPnaC_28qJ9ubeJqm27m1d0hXkFRNO-mG5lw7CaKWGI9fB-GkzUr5mXjbaJxW6OiADD4o052vA9SAZ72CgUmayObp4WEpAOSLF6gWdtQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1rIm3-BNXDpl2MpHP6t0EUGmhHiNoYSB2dIvepLOF2P28FHYTXmFhth-ZJeS_6emhRdM1j0eJtlz827kiuGj9hKp2eZD7_2QUWpE5uMLsu_GXlYULFE_J_4EQT9saQGLXIhOnNqAgPFOWAAOQSNEDN_4IoLQy3a3MQOhYsC1KCC6R6rBKdqlrUyGQ_V3X3rGabHnpl-EwtJtpqcB_uIwaWrvOOdmaMJkmqoTgD_Hbl2ew9ueZgnN7H-jEJ-7Wk8sfolOVyRA7fxuO5G7Fp3JYsg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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