LUT ./kernels permissions

[ucigrangers]

Hello,

I am trying to trouble shoot an error I am getting:

-> Creating LUT for "NODDI" model:
Traceback (most recent call last):
File "/data/Diffusion_Processing/NODDI.py", line 48, in
ae.generate_kernels(regenerate=True)
File "/home/miniforge3/envs/AMICO/lib/python3.11/site-packages/amico/core.py", line 364, in generate_kernels
makedirs( self.get_config('ATOMS_path') )
File "", line 215, in makedirs
File "", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: './kernels'

I am wondering if this is an error in either my use amico.setup() or ae.set_config to enable the LUT to write to this directory somehow? I am happy to send my python code but I largely followed the NODDI tutorial.

Thank you so much in advance!

[daducci]

Hi @ucigrangers ,

Could you please post the script you used to run AMICO? Also, from which folder are you running the script?

[ucigrangers]

Hi Yes, Here is the script which I run from a directory called /data/Diffusion_Processing import os import amico import glob import nibabel as nib import sys # Check if an argument was provided if len(sys.argv) < 2: print("Usage: python myscript.py <subject_id>") sys.exit(1) # Read the first command line argument subject_id = sys.argv[1] #perform the AMICO Functions amico.setup() #amico.core.setup() ae = amico.Evaluation() #ae.set_config('ATOMS_path', '/home/danny/amico_kernels') #os.makedirs('/home/danny/amico_kernels', exist_ok=True) #build scheme file amico.util.fsl2scheme('/data/Diffusion/Conte/bval', '/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/eddy_corrected_data.eddy_rotated_bvecs',schemeFilename='/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/'+subject_id +'_amico.scheme') ae.set_config('doDebiasSignal', True) ae.set_config('DWI-SNR', 30) #load data #Eddy_Data = nib.load('/data/natelab/ATE_Study/results/dwi/'+subject_id+'/eddy_data.nii.gz') #Eddy_Data_Mask = nib.load('/data/natelab/ATE_Study/results/dwi/'+subject_id+'/hifi_b0_mask_mask.nii.gz') ae.load_data('/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/'+'/eddy_corrected_data.nii.gz','/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/'+subject_id +'_amico.scheme', mask_filename='/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/'+'my_hifi_b0_brain_mask.nii.gz', b0_thr=0) ae.set_model('NODDI') ae.generate_kernels(regenerate=True) ae.load_kernels() #fit the model ae.fit() #ae.save_results('/data/natelab/ATE_Study/results/dwi/'+subject_id+'/') os.makedirs('/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/AMICO_30', exist_ok=True) ae.set_config('OUTPUT_path', '/data/Diffusion/Conte/conte_'+subject_id+'/sub-'+subject_id+'/ses-UCSD/dwi/output/AMICO_30') ae.save_results()

…

On Tue, Apr 28, 2026 at 6:48 AM Alessandro Daducci ***@***.***> wrote: *daducci* left a comment (daducci/AMICO#218) <https://urldefense.com/v3/__https://github.com/daducci/AMICO/issues/218*issuecomment-4335817155__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!K6pGhuyf9U9vscJDM_soorRmjVuuW4SBPifXE6x0olPqirq2wpz97KnzZ7w8tY1IDoDGfWkH2Qdkae0CFVPm8yw$> Hi @ucigrangers <https://urldefense.com/v3/__https://github.com/ucigrangers__;!!CzAuKJ42GuquVTTmVmPViYEvSg!K6pGhuyf9U9vscJDM_soorRmjVuuW4SBPifXE6x0olPqirq2wpz97KnzZ7w8tY1IDoDGfWkH2Qdkae0CyOx1pp8$> , Could you please post the script you used to run AMICO? Also, from which folder are you running the script? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/daducci/AMICO/issues/218*issuecomment-4335817155__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!K6pGhuyf9U9vscJDM_soorRmjVuuW4SBPifXE6x0olPqirq2wpz97KnzZ7w8tY1IDoDGfWkH2Qdkae0CFVPm8yw$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AHAGJS5NYL5XV2OULEWNQ4L4YCZEPAVCNFSM6AAAAACYI2LNMCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DGMZVHAYTOMJVGU__;!!CzAuKJ42GuquVTTmVmPViYEvSg!K6pGhuyf9U9vscJDM_soorRmjVuuW4SBPifXE6x0olPqirq2wpz97KnzZ7w8tY1IDoDGfWkH2Qdkae0Csw4D_08$> . Triage notifications on the go with GitHub Mobile for iOS <https://urldefense.com/v3/__https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!CzAuKJ42GuquVTTmVmPViYEvSg!K6pGhuyf9U9vscJDM_soorRmjVuuW4SBPifXE6x0olPqirq2wpz97KnzZ7w8tY1IDoDGfWkH2Qdkae0CVo1-2Ss$> or Android <https://urldefense.com/v3/__https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!CzAuKJ42GuquVTTmVmPViYEvSg!K6pGhuyf9U9vscJDM_soorRmjVuuW4SBPifXE6x0olPqirq2wpz97KnzZ7w8tY1IDoDGfWkH2Qdkae0CAlzw4F8$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Steven J. Granger | Graduate Student Researcher Center for the Neurobiology of Learning and Memory Department of Neurobiology and Behavior University of California, Irvine ***@***.***