Automate for multiple .nii file (generating slices)

[ShibaPrasad]

Hi

I am trying to create slices from .nii file and automate the process in python. i am able to create slices using the below commands from Linux command prompt: (but one by one). But I would like to automate the process. But it's not working.

Command:

med2image -i '3dNewImage_mask_200.nii.gz' -d 'Downloads/NewTest/200' -o image.jpg -s -1 sliceToConvert: -1

I am trying to automate using below from jupyter notebook

---

import subprocess

file_name_list = glob.glob('/Downloads/test/*.nii.gz')
pathtosave = '/Downloads/NewTest/'

for i in range(5):
newpath = pathtosave + str(i)
print(file_name_list[i])
print(newpath)
os.system("/nfs/s-iibi54/users/skuanar/Downloads/med2image-master/med2image/med2image.py -i file_name_list[i] -d newpath -o image.jpg -s -1")

---

[rudolphpienaar]

Your python syntax in the call to os.system is incorrect. It should be something like:

os.system("/nfs/s-iibi54/users/skuanar/Downloads/med2image-master/med2image/med2image.py -i %s -d %s -o image.jpg -s -1" % (file_name_list[i], newpath))

[ShibaPrasad]

Hi,
Thank you. Updated my script. BUt it's now working ... would you please advise me

pathtosave = '/Downloads/test/Testing/testing/'

for i in range(5):
#newpath = pathtosave + str(i)
newpath = os.path.join(pathtosave, str(i), "")
print(file_name_list[i])
print(newpath)
os.mkdir(newpath)

os.system("Downloads/med2image-master/med2image/med2image.py -i %s -d %s -o image.jpg -s -1" % (file_name_list[i], newpath))

output
/Downloads/test/shiba3dNewImage_mask_1.nii.gz
/Downloads/test/Testing/testing/0/
/Downloads/test/shiba3dNewImage_mask_7.nii.gz
/Downloads/test/Testing/testing/1/
/Downloads/test/shiba3dNewImage_mask_13.nii.gz
/Downloads/test/Testing/testing/2/
/Downloads/test/shiba3dNewImage_mask_15.nii.gz
/Downloads/test/Testing/testing/3/
/Downloads/test/shiba3dNewImage_mask_20.nii.gz
/Downloads/test/Testing/testing/4/

​
But the script is not making any jpeg files ?

But I wrote a different unix script separately and it's working. But the above python script is not working. Please advice me i am making any mistake on above python script

[ShibaPrasad]

Hi,

It's working now.
I used "/Downloads/med2image-master/bin/med2image" in stead of Downloads/med2image-master/med2image/med2image.py in os.system("Downloads/med2image-master/med2image/med2image.py -i %s -d %s -o image.jpg -s -1" % (file_name_list[i], newpath))

and it worked.
Thank you