Error message displayed as shown in Fig left .
The format of the input data directory is as shown in Fig right.
Despite the presence of the “T1w” folder in the directory, an error is still being reported.
Thanks
XCP-D version latest
Hi, is your dataset into BIDS format? I think XCP_D is expected BIDS formatted datasets.
Also you should have you preprocessed data with the same naming convention as FMRIPREP outputs. I quote the sentence below from the XCP_D documentation:
XCP-D picks up right where fMRIprep ends, directly consuming the outputs of fMRIPrep.
Could you perhaps share you dataset tree? (The one which is in /wd/dset_bids/derivatives/hcp/sub-100307). Thanks!
Hi,
When the –input-type hcp flag is added to the command, isn’t it specifically designed to handle HCP datasets?I suppose that way there is no need to convert the data format to BIDS , right?
oh, I didn’t know about that option! Well I don’t know then what kind of formatting is expected from the HCP data when you use this flag. I hope you can get help from other users/developpers of XCP_D.
Hi @Donggua, we will need more info to help, mainly knowing your full command you used to run XCP_D.
Thank you very much for responding to my questions.
docker run --rm -v F:/temp:/wd -v E:/HCP_Resting_State_fMRI1_Preprocessed_test:/data -v F:/hcpout:/out -v D:/fantest/:/freesurfer_license pennlinc/xcp_d:latest /data /out participant -w /wd --input_type hcp -p 36P --despike --lower-bpf 0.01 --upper-bpf 0.1 --smoothing 6 --cifti
Thank you, can you show us the contents of the MNINonLinear folder?
Fig2 show the contents of the **MNINonLinear** folder
Are you on a Windows machine? If so, the way you put in paths (that is, with / separating the folders) might not be correct. I do not have much experience with Windows but I think using Cygwin or WSL will allow you to use syntax closer to what other users use.
Yes, I am using a Windows system, but I have installed the Docker version of XCP-D. And the command line uses “/” as the path separator, which is correct.
Moreover, I am using Docker commands, and the syntax and specifications are the same. docker run --rm -v F:/temp:/wd -v E:/HCP_Resting_State_fMRI1_Preprocessed_test:/data -v F:/hcpout:/out -v D:/fantest/:/freesurfer_license pennlinc/xcp_d:latest /data /out participant -w /wd --input_type hcp -p 36P --despike --lower-bpf 0.01 --upper-bpf 0.1 --smoothing 6 --cifti
I haven’t been able to identify where the issue lies either.