Aslprep failed to generate cortical masks

Summary of what happened:


We are processing pcasl data with aslprep. The process finished successfully, however we found the following error in the log file.

We wanted to check if we are doing properly or if we are failing at any step, and check whether differences are mainly due to basil or aslprep use.
Thank you in advance!

Command used (and if a helper script was used, a link to the helper script or the command generated):

Moreover, we wanted to compare outputs from aslprep versus basil itself. We found that though data and parameters introduced are the same results does not seem to be similar. Here I show you argument lines for both:


Input file: /neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/prueba_189/aslprep_wf/single_subject_189_wf/asl_preproc_ses_1_wf/compute_cbf_wf/extract_deltam/sub-189_ses-1_asl_DeltaMOrCBF.nii.gz
Saving results in natve (ASL aquisition) space to /neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/prueba_189/aslprep_wf/single_subject_189_wf/asl_preproc_ses_1_wf/compute_cbf_wf/extract_deltam/native_space
Number of TIs in list: 9
TIs list: --ti1=2.0 --ti2=2.0 --ti3=2.5 --ti4=2.5 --ti5=3.0 --ti6=3.0 --ti7=3.5 --ti8=3.5 --ti9=3.5
Input ASL format is: diff
Input block format is: rpt
Number of voxels is:442368
Number of repeats in data is:1
Outputting ASL data mean at each TI
Label-control difference data provided: /neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/prueba_189/aslprep_wf/single_subject_189_wf/asl_preproc_ses_1_wf/compute_cbf_wf/extract_deltam/sub-189_ses-1_asl_DeltaMOrCBF.nii.gz
Number of inversion times: 9
Number of timepoints in data: 9
Number of repeats in data: 1
2.0 2.0 2.5 2.5 3.0 3.0 3.5 3.5 3.5
Defaulting to brain extracted calibration image as initial registration reference
Using brain extracted calibration image as initial registration reference
Using mask: /neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/prueba_189/aslprep_wf/single_subject_189_wf/asl_preproc_ses_1_wf/compute_cbf_wf/refine_mask/ref_bold_corrected_brain_mask_maths_refinemask.nii.gz
T1: 1.3
T1b: 1.65
Bolus duration: 1.5
Setting up BASIL
cASL model
Infer arterial component
Fixed bolus duration
Variable arterial arrival time
Setting prior/initial (tissue/gray matter) bolus arrival time to 1.3
Setting std dev of the (tissue) BAT prior to 1
Instructing BASIL to use automated spatial smoothing
(Also alpha defined as 0.7)

oxford_asl -i=/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/basilprueba/sub189/ses1/perf/sub-189_ses-1_asl.nii.gz --iaf=tc --ibf=rpt --casl --bolus=1.5 --rpts=1,1,1,1,1,1,1,1,1 --tis=2,2,2.5,2.5,3,3,3.5,3.5,3.5 --fslanat=/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/basilprueba/sub189/ses1/anat/T1w.anat -c=/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/basilprueba/sub189/ses1/perf/sub-189_ses-1_m0scan.nii.gz --cmethod=single --tr=4.3 --cgain=1 --tissref=csf --t1csf=4.3 --t2csf=750 --t2bl=150 --te=0 -o=/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/basilprueba --bat=1.3 --t1=1.3 --t1b=1.65 --alpha=0.7 --spatial=1 --fixbolus --mc --pvcorr --artoff


aslprep 0.5.0

Environment (Docker, Singularity / Apptainer, custom installation):


Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

stdout 2023-12-04T12:39:59.161239:Generating calibration image in structural space
stderr 2023-12-04T12:39:59.168147:Image Exception : #63 :: No image files match: /tmp/fsl_xu33pve6_ox_asl/struc
stderr 2023-12-04T12:39:59.168454:Error : No image files match: /tmp/fsl_xu33pve6_ox_asl/struc
stderr 2023-12-04T12:39:59.168454:Image Exception : #22 :: Failed to read volume /tmp/fsl_xu33pve6_ox_asl/struc
stderr 2023-12-04T12:39:59.168639:Error : No image files match: /tmp/fsl_xu33pve6_ox_asl/struc
stderr 2023-12-04T12:39:59.168639:Failed to read volume /tmp/fsl_xu33pve6_ox_asl/struc
stdout 2023-12-04T12:39:59.169753:Loading supplied PV images
stdout 2023-12-04T12:39:59.170369:PV GM is: /neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/prueba_189/aslprep_wf/single_subject_189_wf/asl_preproc_ses_1_wf/compute_cbf_wf/gm_tfm/sub-189_ses-1_T1w_corrected_xform_masked_pve_1_trans.nii.gz
stdout 2023-12-04T12:39:59.192364:PV WM is: /neurodesktop-storage/Agueda/BIDS/derivatives/aslprep_Lucia/prueba_189/aslprep_wf/single_subject_189_wf/asl_preproc_ses_1_wf/compute_cbf_wf/wm_tfm/sub-189_ses-1_T1w_corrected_xform_masked_pve_2_trans.nii.gz
stdout 2023-12-04T12:39:59.318393:WARNING: No structural->standard space transformation - cannot generate cortical-only GM/WM masks

Screenshots / relevant information:

Hi @lucia_sanchez_aranda,

Please use the Software Support category for software related issues like this. It provides a post template you an use that helps us better address your problems. I have relabeled your issue and tried to reorganize your post to that template.

Of note, you can see that there is some information missing that we typically like to see.

  1. The command you used to run ASLPrep
  2. The version of ASLPrep
  3. The environment you are running ASLPrep in
  4. BIDS validation report on your data

You can edit your post to add this in.


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Hi! Thank for your answer, hope I have now indicated all the information.

Hi @lucia_sanchez_aranda,

I still don’t see the command you used to run aslprep. Also it looks like maybe some of the BIDS validation was cut off. You can just copy and paste all of it into the text box instead of using screenshots.

I’ll ping @tsalo who currently develops the software.


1 Like

It seems to just be a limitation in how ASLPrep calls BASIL. BASIL is run on native-space data just to calculate CBF (and partial volume-corrected CBF) and ATT, so many of the other features BASIL supports (e.g., normalizing the maps to standard space) are not leveraged by ASLPrep.