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help > RE: Help with adult brain/atlas
Feb 24, 2020 04:02 PM | Martin Styner
RE: Help with adult brain/atlas
Based on the first call with an error, the likely source for your
problem is that the format of your brain mask is off/unknown to
ImageMath. I can see that it's stored in .mgz (likely from
FreeSurfer) and there is no "mgz" reader for ITK and thus not for
our tool.
You would need to first convert the brain mask to an ITK compatible format (e.g. Analyze, NIFTI, or NRRD). FreeSurfer has mri_convert to do that for you.
Martin
Originally posted by Pearlynne C:
You would need to first convert the brain mask to an ITK compatible format (e.g. Analyze, NIFTI, or NRRD). FreeSurfer has mri_convert to do that for you.
Martin
Originally posted by Pearlynne C:
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 | |