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help > Help with adult brain/atlas
Feb 23, 2020 03:02 AM | pearlynne
Help with adult brain/atlas
I am trying to process using a T1
image of an adult brain. However when I tried using an adult atlas,
multiple errors occurred.
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_MID00.nrrd -mask /home/chong30/UZ/BMS_103/brainmask.auto.mgz
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details >>> main_script.py : Cutting below AC-PC line
>>> main_script.py : Creating coronal mask
>>> main_script.py : Coronal mask created
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_MID00.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID01.nrrd -mask coronal_mask_70.nrrd
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details >>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID01.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID02.nrrd -extractLabel 3
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details >>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID02.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID03.nrrd -conComp 1
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details
I am not sure if I am missing anything else. I have attached the error log as well.
Any help is appreciated - thank you!
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_MID00.nrrd -mask /home/chong30/UZ/BMS_103/brainmask.auto.mgz
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details >>> main_script.py : Cutting below AC-PC line
>>> main_script.py : Creating coronal mask
>>> main_script.py : Coronal mask created
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_MID00.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID01.nrrd -mask coronal_mask_70.nrrd
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details >>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID01.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID02.nrrd -extractLabel 3
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details >>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID02.nrrd -outfile /home/chong30/UZ/Output/BMS_103/Output2 -nrrd with adult/T1_stripped_labels_EMS_MID03.nrrd -conComp 1
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath : errors occured, see errors log for more details
I am not sure if I am missing anything else. I have attached the error log as well.
Any help is appreciated - thank you!
Threaded View
| Title | Author | Date |
|---|---|---|
| pearlynne | Feb 23, 2020 | |
| Martin Styner | Feb 24, 2020 | |
| pearlynne | Mar 2, 2020 | |
| pearlynne | Feb 25, 2020 | |