help > Help with adult brain/atlas
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Feb 23, 2020  03:02 AM | Pearlynne C
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!
Attachment: errors_log.txt
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:
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!
Feb 25, 2020  03:02 PM | Pearlynne C
RE: Help with adult/adolescent brain/atlas
Thank you for that! I converted the files to nrrd but I still encountered a few errors. I have attached the error log again.

This is the first thread of two:
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ABC_CLI : errors occured, see errors log for more details
/home/chong30/UZ/BMS_102/Output_102_adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd
/home/chong30/UZ/BMS_102/Output_102_adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd doesnt exist
>>> main_script.py : Finished running tissue_seg_script.py

>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/BMS_102/Output_102_adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_adult/T1_MID00.nrrd -mask /home/chong30/UZ/BMS_102/brainmask.auto.nrrd
/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/BMS_102/Output_102_adult/T1_MID00.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_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/BMS_102/Output_102_adult/T1_stripped_labels_EMS_MID01.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_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/BMS_102/Output_102_adult/T1_stripped_labels_EMS_MID02.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_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
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/BMS_102/brainmask.auto.nrrd -erode 1,1 -outfile brainmask.auto_Erosion00.nrrd


Thank you again.
Attachment: errors_log.txt
Mar 2, 2020  03:03 PM | Pearlynne C
RE: Help with adult brain/atlas
Thank you for that! I converted the files to nrrd but I still encountered a few errors. I have attached the error log again.

This is the first thread of two:
/home/chong30/Auto_EACSF-release-v1.3/usr/bin/ABC_CLI : errors occured, see errors log for more details
/home/chong30/UZ/BMS_102/Output_102_adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd
/home/chong30/UZ/BMS_102/Output_102_adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd doesnt exist
>>> main_script.py : Finished running tissue_seg_script.py
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/BMS_102/Output_102_adult/ABC_Segmentation/T1_stripped_labels_EMS.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_adult/T1_MID00.nrrd -mask /home/chong30/UZ/BMS_102/brainmask.auto.nrrd
/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/BMS_102/Output_102_adult/T1_MID00.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_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/BMS_102/Output_102_adult/T1_stripped_labels_EMS_MID01.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_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/BMS_102/Output_102_adult/T1_stripped_labels_EMS_MID02.nrrd -outfile /home/chong30/UZ/BMS_102/Output_102_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
>>> main_script.py : Running: /home/chong30/Auto_EACSF-release-v1.3/usr/bin/ImageMath /home/chong30/UZ/BMS_102/brainmask.auto.nrrd -erode 1,1 -outfile brainmask.auto_Erosion00.nrrd

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![/quote][/quote]
Attachment: errors_log (1).txt