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Dear Freesurfer Developers,
I have scrutinized the Freesurfer source code from github, found that this might be a bug in Freesurfer.
Basically, the string "Orientation : ???" comes from the function MRIdircosToOrientationString defined in mri.cpp, which depends on the MRI structure's member ras_good_flag. However, when reading a dicom file using the function DICOMRead2 defined in DICOMRead.cpp, the member ras_good_flag seems to be never been assigned a "ras good flag" value 1. That's why I got the orientation string value of "???".
Would anyone correct or confirm my finding?
Thank you!
John
Xiaojiang Yang https://secure-web.cisco.com/1z35I78V94iRbbYPmh53mt00toQQUpCtob0Flq38T-DIF4eyYbMf_bMQ3sEmfHiyZWKybvM4YKjdzOzLJ9CYVa7B82DjIMljR_9yUKIr7uKGb8S4oCzCAmCmy7QYcYZLZZ-7xiq5cY6dhd3w4WwHj6l3BxOEo3cjs7YOdqBTw94k8FpYHiJZ0Hz-Q3Bn3jbuiC5Rmta6K4Z4O4o1Fy0XTCWRk-K_ozt5-4xs3qhbOElCzwuXqphIYgA3xmDK5YYPIxd8ctYtXyInm8yn-xvo-g_8iVfDuXA329Ebxp5JvBk__fmd2Lk1zSTtJPWDo6lKrmHEkeTBFUXoH7NCBc52RKw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Xiaojiang%2BYang%2522 Mon, 10 Jan 2022 09:23:09 -0800 https://secure-web.cisco.com/1xlKT8odwFmJHyltnD83Zsoh2rGvmR8Hww2q4lAdH_dB7qbBbJz0Z0bpHIwjP_bIxwdI1vVZqr2_RUXaXfkz2G6qJSYUhRTjX7rE6xAHdzdLnyxpJiUR0nCE-tKk88v-8uUoo3k6xNW_Ja85YayGYCTkSpL0J7hAIvfTQyTtP_RBeXfxwAS5j25qOPQyRd6QyrkP2KKmxQTiRjYiVtZgj5S333AFJuO31ZlenbN6HDXZBLAhRWYXYOQKjkwKj0ga8xEPsdZDKPpdJOUJYGJPw48aoGYWwYtoAVgvfLF9vUtMiejWUPbuB4GDkaBhabQBw9z33j7rWg1WMH1dC5UjNgA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220110
External Email - Use Caution
Dear Freesurfer Experts,
I have a question regarding the orientation string gotten from mri_info. When I apply mri_info command to a DIOM series I generated programmatically, I get the "???" result, and hence primary slice direction is also unknown:
...... Orientation : ??? Primary Slice Direction: unknown ......
I already had the " Image Position Patient" and "Image Orientation Patient" written in the DICOM header. Don't know what other important info is missing.
Could you tell me what key information is used in DICOM header to determine this orientation when using mri_info?
Thanks! John
what happens if you convert it to an mgz file and then use mri_info to look at the orientation string?
On 1/11/2022 11:52 AM, Xiaojiang Yang wrote:
External Email - Use Caution
Dear Freesurfer Developers, I have scrutinized the Freesurfer source code from github, found that this might be a bug in Freesurfer. Basically, the string "Orientation : ???" comes from the function MRIdircosToOrientationString defined in mri.cpp, which depends on the MRI structure's member ras_good_flag. However, when reading a dicom file using the function DICOMRead2 defined in DICOMRead.cpp, the member ras_good_flag seems to be never been assigned a "ras good flag" value 1. That's why I got the orientation string value of "???". Would anyone correct or confirm my finding? Thank you! John
Xiaojiang Yang https://secure-web.cisco.com/1z35I78V94iRbbYPmh53mt00toQQUpCtob0Flq38T-DIF4eyYbMf_bMQ3sEmfHiyZWKybvM4YKjdzOzLJ9CYVa7B82DjIMljR_9yUKIr7uKGb8S4oCzCAmCmy7QYcYZLZZ-7xiq5cY6dhd3w4WwHj6l3BxOEo3cjs7YOdqBTw94k8FpYHiJZ0Hz-Q3Bn3jbuiC5Rmta6K4Z4O4o1Fy0XTCWRk-K_ozt5-4xs3qhbOElCzwuXqphIYgA3xmDK5YYPIxd8ctYtXyInm8yn-xvo-g_8iVfDuXA329Ebxp5JvBk__fmd2Lk1zSTtJPWDo6lKrmHEkeTBFUXoH7NCBc52RKw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Xiaojiang%2BYang%2522 Mon, 10 Jan 2022 09:23:09 -0800 https://secure-web.cisco.com/1xlKT8odwFmJHyltnD83Zsoh2rGvmR8Hww2q4lAdH_dB7qbBbJz0Z0bpHIwjP_bIxwdI1vVZqr2_RUXaXfkz2G6qJSYUhRTjX7rE6xAHdzdLnyxpJiUR0nCE-tKk88v-8uUoo3k6xNW_Ja85YayGYCTkSpL0J7hAIvfTQyTtP_RBeXfxwAS5j25qOPQyRd6QyrkP2KKmxQTiRjYiVtZgj5S333AFJuO31ZlenbN6HDXZBLAhRWYXYOQKjkwKj0ga8xEPsdZDKPpdJOUJYGJPw48aoGYWwYtoAVgvfLF9vUtMiejWUPbuB4GDkaBhabQBw9z33j7rWg1WMH1dC5UjNgA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220110
External Email - Use CautionDear Freesurfer Experts, I have a question regarding the orientation string gotten from mri_info. When I apply mri_info command to a DIOM series I generated programmatically, I get the "???" result, and hence primary slice direction is also unknown:
...... Orientation : ??? Primary Slice Direction: unknown ......
I already had the " Image Position Patient" and "Image Orientation Patient" written in the DICOM header. Don't know what other important info is missing.
Could you tell me what key information is used in DICOM header to determine this orientation when using mri_info?
Thanks! John
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Xiaojiang Yang