ciftify
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edickie
The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
docker run -ti --rm \ -v /Users/neurolab/Desktop/Pipeline_test3/:/data:ro \ -v /Users/neurolab/Desktop/Pipeline_test4:/out \ tigrlab/fmriprep_ciftify:latest /data /out participant --participant_label 1 --fs-license /Users/neurolab/Desktop/license.txt tells me "Input /Users/neurolab/Desktop/license.txt, does not exist, or you do not...
Is it available to map non-HCP DTI data to CIFTI ?
I got an error message such as "left surface has the wrong number of vertices" when I running ciftify_peaktable to get the annotomy label of my dscalar.nii data. Does it...
https://github.com/TIGRLab/tigr_parc/blob/master/code/tigr_parc/dlabelIO.py These functions are a combination of things that work directly on dlabel.nii images and more pure pythonic ways of doing things that are already in ciftify.niio but both ciftify.niio...
there's some notebooks in tigr_parc that should probably actually go here.. notably.. https://github.com/TIGRLab/tigr_parc/blob/master/notebooks/06_playing_w_pscalars.py https://github.com/TIGRLab/tigr_parc/blob/master/notebooks/07_pscalar_plotting.py -steps 1. convert notebook to executed markdown (with jupytext) so that docify can render it? 2....
I am getting a segmentation fault error with ciftify. I am not sure where to start looking for problems. 15/160 of my subjects have this error. The freesurfer outputs look...
Hi, running: docker run -ti --rm -v /home/neurolab2/Schreibtisch/Stephan/Programmes/freesurfer/license.txt:/fslicense.txt:ro -v /home/neurolab2/Schreibtisch/Drmed/final_GSP:/data:ro -v /home/neurolab2/Schreibtisch/Drmed/final_ciftify_GSP:/out tigrlab/fmriprep_ciftify:latest /data /out/out participant --participant_label=1 --read-from-derivatives /home/neurolab2/Schreibtisch/Drmed/final_GSP/derivatives --resample-to-T1w32k --anat_only --fs-license /fslicense.txt --n_cpus 4 creates the output folder, but...
@edickie I downloaded ciftify using pip install ciftify to be run on windows subsystem for linux. I have my fmri data preprocessed using fmriprep and obtained as a cifti dtseries...
Hi, As you mentioned you use data which has been preprocessed with FMRIPREP. But in FMRIPREP no denoising is done. So is this step done somewhere in the ciftify commands?...
I am running the following command: docker run -ti --rm \ -v /Users/neurolab/Desktop/Test_sub_002_fcmriprep_ciftify:/data:ro \ -v /Users/neurolab/Desktop/Test_sub_002_fcmriprep_ciftify:/out \ tigrlab/fmriprep_ciftify:1.1.8-2.1.1 \ /data /out/out participant And receive the following message: /usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids...