antsMultivariateTemplateConstruction: cannot read file

[jskim628]

I am not sure why the input file cannot be read. Everything is in the same directory and the file can be opened to view on other software. Appreciate any help.

antsMultivariateTemplateConstruction.sh -d 3 -m 50x90x50 -g 0.15 -r 1 -t GR -s CC -c 2 -i 4 -k 4 -j 11 -o Multi SCAN_scanlist.csv

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 Multivariate template construction using the following 4-tuples:  
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Subj10265_anat-T1w_acq-mprage.nii.gz Subj10265_anat_PDw_Warped.nii.gz Subj10265_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj10265_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj10266_anat-T1w_acq-mprage.nii.gz Subj10266_anat_PDw_Warped.nii.gz Subj10266_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj10266_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj2_anat-T1w_acq-mprage.nii.gz Subj2_anat_PDw_Warped.nii.gz Subj2_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj2_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj3_anat-T1w_acq-mprage.nii.gz Subj3_anat_PDw_Warped.nii.gz Subj3_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj3_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj4_anat-T1w_acq-mprage.nii.gz Subj4_anat_PDw_Warped.nii.gz Subj4_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj4_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj5_anat-T1w_acq-mprage.nii.gz Subj5_anat_PDw_Warped.nii.gz Subj5_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj5_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj6_anat-T1w_acq-mprage.nii.gz Subj6_anat_PDw_Warped.nii.gz Subj6_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj6_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj8_anat-T1w_acq-mprage.nii.gz Subj8_anat_PDw_Warped.nii.gz Subj8_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj8_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj10_anat-T1w_acq-mprage.nii.gz Subj10_anat_PDw_Warped.nii.gz Subj10_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj10_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj11_anat-T1w_acq-mprage.nii.gz Subj11_anat_PDw_Warped.nii.gz Subj11_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj11_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj12_anat-T1w_acq-mprage.nii.gz Subj12_anat_PDw_Warped.nii.gz Subj12_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj12_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj15_anat-T1w_acq-mprage.nii.gz Subj15_anat_PDw_Warped.nii.gz Subj15_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj15_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj16_anat-T1w_acq-mprage.nii.gz Subj16_anat_PDw_Warped.nii.gz Subj16_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj16_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj19_anat-T1w_acq-mprage.nii.gz Subj19_anat_PDw_Warped.nii.gz Subj19_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj19_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj20_anat-T1w_acq-mprage.nii.gz Subj20_anat_PDw_Warped.nii.gz Subj20_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj20_anat-T1w_acq-FSE_run-02_Warped.nii.gz
Subj21_anat-T1w_acq-mprage.nii.gz Subj21_anat_PDw_Warped.nii.gz Subj21_anat-T1w_acq-FSE_run-01_Warped.nii.gz Subj21_anat-T1w_acq-FSE_run-02_Warped.nii.gz
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 Creating template Multitemplate0.nii.gz from a population average image from the inputs.
   Subj10265_anat-T1w_acq-mprage.nii.gz Subj10266_anat-T1w_acq-mprage.nii.gz Subj2_anat-T1w_acq-mprage.nii.gz Subj3_anat-T1w_acq-mprage.nii.gz Subj4_anat-T1w_acq-mprage.nii.gz Subj5_anat-T1w_acq-mprage.nii.gz Subj6_anat-T1w_acq-mprage.nii.gz Subj8_anat-T1w_acq-mprage.nii.gz Subj10_anat-T1w_acq-mprage.nii.gz Subj11_anat-T1w_acq-mprage.nii.gz Subj12_anat-T1w_acq-mprage.nii.gz Subj15_anat-T1w_acq-mprage.nii.gz Subj16_anat-T1w_acq-mprage.nii.gz Subj19_anat-T1w_acq-mprage.nii.gz Subj20_anat-T1w_acq-mprage.nii.gz Subj21_anat-T1w_acq-mprage.nii.gz
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 Cannot read input file: Subj10265_anat-T1w_acq-mprage.nii.gz
summarizeimageset: ERROR - output file Multitemplate0.nii.gz could not be created

[cookpa]

Is there any chance your SCAN_scanlist.csv contains Windows new lines? If it was written by Python or Excel, it might. You can check with

file SCAN_scanlist.csv

[jskim628]

This was the issue. Thanks a lot! It is working now.

[cookpa]

Fixed via #1845