External Email - Use Caution
Hello FreeSurfer experts,
I'm attempting to obtain volume values for the ROIs, each corresponding to a specific network based on Yeo's 17 Network atlas.
Here are the steps I've done so far:
1. Transform from fsaverage to subject's surface (LH, RH) mri_surf2surf --srcsubject fsaverage5 --trgsubject sdas/sub052 --hemi lh --sval-annot 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/sub052/label/lh.Yeo_17Network_native.annot
2. Transform from subject's surface into my subject's volume mri_aparc2aseg --s sub052 --o $SUBJECTS_DIR/sub052/mri/Yeo17.mgz --annot Yeo_17Network_native --annot-table Downloads/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
Upon inspecting the output file (Yeo17.mgz) overlaid with 17Networks_ColorLUT_freeview.txt before extracting the volume values, I observed that the actual ROI doesn't match the label. ex) The label indicates "DefaultB_IPL" when I point the caudate nucleus
Is there something I might be missing?
And would you let me know how to extract the volumes of the ROIs for each of the 17 Networks? So I would be getting volumes for 114 ROIs in total.
I would greatly appreciate your help.
Jihye
상기 메일은 지정된 수신인 만을 위한 것이며 부정경쟁 방지 및 영업비밀보호에 관한 법률을 포함하여 관련 법령에 따라 보호의 대상이 되는 영업비밀, 산업기술 등을 포함하고 있을 수 있습니다. 본 문서에 포함된 정보의 전부 또는 일부를 무단으로 제3자에게 공개, 배포, 복사 또는 사용하는 것은 엄격히 금지됩니다. 본 메일이 잘못 전송된 경우, 발신인에게 알려주시고 즉시 삭제하여 주시기 바랍니다. The above message is intended solely for the named addressee and may contain trade secret, industrial technology or privileged and confidential information otherwise protected under applicable law including the Unfair Competition Prevention and Trade Secret protection act. Any unauthorized dissemination, distribution, copying or use of the information contained in this communication is strictly prohibited. If you have received this communication in error, please notify the sender by email and delete this communication immediately.
‘mri_aparc2aseg’ adjusts Yeo’s 17 Network segmentation value to 1000+ for lh, and 2000+ for rh. I don’t think you can use Freeview with ‘1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt’, which labels from 1-114.
You may find it helpful https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce...
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ???(?????) Sent: Friday, November 24, 2023 1:30 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Yeo's 17 Network atlas: label mismatch and volume stats extraction
External Email - Use Caution Hello FreeSurfer experts,
I'm attempting to obtain volume values for the ROIs, each corresponding to a specific network based on Yeo's 17 Network atlas.
Here are the steps I've done so far:
1. Transform from fsaverage to subject's surface (LH, RH) mri_surf2surf --srcsubject fsaverage5 --trgsubject sdas/sub052 --hemi lh --sval-annot 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/sub052/label/lh.Yeo_17Network_native.annot
2. Transform from subject's surface into my subject's volume mri_aparc2aseg --s sub052 --o $SUBJECTS_DIR/sub052/mri/Yeo17.mgz --annot Yeo_17Network_native --annot-table Downloads/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
Upon inspecting the output file (Yeo17.mgz) overlaid with 17Networks_ColorLUT_freeview.txt before extracting the volume values, I observed that the actual ROI doesn't match the label. ex) The label indicates "DefaultB_IPL" when I point the caudate nucleus
Is there something I might be missing?
And would you let me know how to extract the volumes of the ROIs for each of the 17 Networks? So I would be getting volumes for 114 ROIs in total.
I would greatly appreciate your help.
Jihye
상기 메일은 지정된 수신인 만을 위한 것이며 부정경쟁 방지 및 영업비밀보호에 관한 법률을 포함하여 관련 법령에 따라 보호의 대상이 되는 영업비밀, 산업기술 등을 포함하고 있을 수 있습니다. 본 문서에 포함된 정보의 전부 또는 일부를 무단으로 제3자에게 공개, 배포, 복사 또는 사용하는 것은 엄격히 금지됩니다. 본 메일이 잘못 전송된 경우, 발신인에게 알려주시고 즉시 삭제하여 주시기 바랍니다. The above message is intended solely for the named addressee and may contain trade secret, industrial technology or privileged and confidential information otherwise protected under applicable law including the Unfair Competition Prevention and Trade Secret protection act. Any unauthorized dissemination, distribution, copying or use of the information contained in this communication is strictly prohibited. If you have received this communication in error, please notify the sender by email and delete this communication immediately.
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
최지혜(영상의학과)