How was H-O_subcortical_parcellation_thr50.nii created? Those
instructions are for when you have a segmentation in the FS conformed
space and you want to get them back to the native space. So your
segmentation must be in FS conformed space of the individual
On 6/10/2022 6:49 PM, Christopher Pirrung wrote:
External Email - Use Caution
Hi Freesurfer Devs,
I’m attempting to transform the Harvard-Oxford subcortical atlas
(obtained from https://neurovault.org/collections/262/) to my
subjects’ native anatomical space to create individualized versions of
this atlas. To do so I used the line:
mri_label2vol --seg H-O_subcortical_parcellation_thr50.nii --temp
rawavg.mgz --o HO-subcort.mgz --regheader
H-O_subcortical_parcellation_thr50.nii
based on the recommendation from *MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
<https://secure-web.cisco.com/1bcvHE7fWzSmfgBGxlww4NvvAmOJRlTofNlaCk_OCSbG9ANgzz4e3XBBmPopN_948C7sv6lLJ1es2DsjHPbWpoQJLkukB9UacF4p_8SO6NaCMPnpiOSQ2hCcBGbnbg2q7YjuocpFXj8-b1cDDAzWqtqBVAn__Xv_7pdr93NPAl_knSgBECp5_q19itTq2Gbfz5EvzoJ6eLPCwpk7aBdt_lZwd0CQRjlkEj3knSpQzmFdfI933JQiMWTvsoBFmxEAO2xBDX6JByBvLN557dPriErmskr_ZkAnVzAdfd9JPbMLN67rLH2tKGtoDVDU95L6OX66uDsgYosdo5yCA_tbsmw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat>.
However, when I load the rawavg.mgz and individualized atlas in
freeview, the atlas is ~30 mm away from being aligned. Do you have
any idea why this might be the case or recommendations to get a better
alignment?
Thanks!
Chris
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