I am trying to run McFlirt and am getting the following error…
No such file or directory ‘/scratch/06953/jes6785/CPT/output/preproc_ses2_scan1/mcflirt/20200207.005.2_func_task-CPTPNND_run-01_dir-AP_20200207181451_15_brain_mcf_mean_reg.nii.gz’ for output ‘mean_img’ of a MCFLIRT interface
I noticed that the discussion above, but I noticed that the code (including the version that I am using has been fixed). I am using python 6 and am calling for a mean image output, but it looks like the problem was “fixed” in the code. The source code that I am running for Mcflirt appears to contain the fix. I am running FSL 6.03. I can’t currently install FSL 5.0 and I would rather not go back to an old version. I also get the same error message when I gunzip the functional file and specify the output type for each node to NIFTI (and also if I don’t do this).
I am at the testing phase of running my script and I would like to be able to run this file on our test scan. Could someone help on what is going wrong and what I can do to fix this? Surely someone else must have come across this problem too? I am pretty new to nipype, but have been researching this for a few days now and it is very frustrating.
Does anyone have any idea why I might STILL be getting this error?
Also, what is the trick to output the command line from a node, having trouble finding this online?
Here is actual code…
#Initiate Gunzip node
gunzip_func = Node(Gunzip(in_file = func_file),
bet = Node(BET(args="-F",
This is currently working but it is throwing an error
mcflirt = Node(MCFLIRT(mean_vol=True,
output_type = ‘NIFTI’),
preproc_ses2_scan1_test.connect([(gunzip_func, bet, [(‘out_file’, ‘in_file’)])])
preproc_ses2_scan1_test.connect([(bet, mcflirt, [(‘out_file’, ‘in_file’)])])
except(RuntimeError) as err: