ciftify
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edickie
The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
If confounds are not given then an error occurs. The PR is a minimal patch for this ```console Traceback (most recent call last): File "/home/mrphys/marzwi/.conda/envs/ciftify/bin/ciftify_clean_img", line 8, in sys.exit(main()) File...
I have multiple runs and tasks per subject, but `ciftify_subject_fmri` handles only one func volume at a time. Do I have to run it multiple times and remove the logfile...
https://github.com/edickie/ciftify/blob/ce1876b22747ef76b797de5056ec38cab8fc5e66/ciftify/bin/ciftify_statclust_report.py#L287 I was trying to use the statclust_report to get peak tables from a CIFTI file. I built my singularity image using the docker2singularity command from the installation instructions. Unfortunately,...
The problem Currently: https://github.com/edickie/ciftify/blob/master/ciftify/bin/ciftify_meants.py [line 100] ``` ciftify.utils.run(['wb_command', '-cifti-parcellate', settings.func.path, settings.seed.path, 'COLUMN', tmp_parcelated, '-include-empty']) ``` BUT as of wb_command 1.4 (I believe) "'-include-empty' is deprecated but is now the default...
Hi! Lately, I've been experiencing problems when running ciftify_subject_fmri. It seems like the subcortical structures are no longer recognized; I'm getting the following warnings/erros: > WARNING: volume label file has...
Hi, On a HPC I run: ``` singularity run --cleanenv \ -B $DATA:/data \ -B $FS_LICENSE:/fs-license \ $LAB_PATH/Singularity/tigrlab_fmriprep_ciftify_latest-2019-08-16-6ea864911724.simg \ /data/BIDS /data participant \ --participant_label=${SBJ} \ --session_label=01 \ --fs-license="/fs-license/license.txt" \ --read-from-derivatives...
I am trying to run the anatomical pipeline in ciftify using docker. I already have freesurfer output, but I am unable to get the code to run. My folder structure...
Good afternoon Dr.Dickie, I'm an M2 student of neuroscience. I performed a vertex-wise comparison of cortical thickness maps (fs_32k) with FSL_PALM, thus obtaining statistical results for each hemisphere. Thereafter, I...
Happy holidays!! I am hoping to use ciftify as a prerequisite for our upcoming [BIDS app](https://github.com/hptaylor/connectome_harmonic_core) but am experiencing an issue. Starting from raw HCP data, I ran fMRIprep and...
runngin ciftify_recon_all in a docker container leads to: Traceback (most recent call last): File "/home/code/ciftify/ciftify/bin/ciftify_recon_all", line 1570, in main() File "/home/code/ciftify/ciftify/bin/ciftify_recon_all", line 1567, in main run_ciftify_recon_all(tmpdir, settings) File "/home/code/ciftify/ciftify/bin/ciftify_recon_all", line...
