Return func(ax, *map(sanitize_sequence, args), **kwargs)įile “/data/home/s4333238/sct_4.2.0/python/envs/venv_sct/lib/python3.6/site-packages/matplotlib/cbook/deprecation.py”, line 369, in wrapperįile “/data/home/s4333238/sct_4.2.0/python/envs/venv_sct/lib/python3.6/site-packages/matplotlib/axes/_axes.py”, line 5679, in imshowįile “/data/home/s4333238/sct_4.2.0/python/envs/venv_sct/lib/python3.6/site-packages/matplotlib/image.
Self.sagittal_canvas = widgets.SagittalCanvas(self, plot_points=True, horizontal_nav=True)įile “/data/home/s4333238/sct_4.2.0/spinalcordtoolbox/gui/widgets.py”, line 289, in init Launch_centerline_dialog(im_data, im_mask_viewer, params)įile “/data/home/s4333238/sct_4.2.0/spinalcordtoolbox/gui/centerline.py”, line 260, in launch_centerline_dialogįile “/data/home/s4333238/sct_4.2.0/spinalcordtoolbox/gui/centerline.py”, line 138, in init Im_labels = _call_viewer_centerline(Image(fname_data), interslice_gap=interslice_gap)įile “/data/home/s4333238/sct_4.2.0/spinalcordtoolbox/centerline/core.py”, line 286, in call_viewer_centerline I then swapped dim using sct_image -i 3890_dwi_ -setorient RPI -o dwi_3890_ as the orientation of the dwi data was set in ASL.įile_type sct_get_centerline -i dwi_3890_ -method viewerįile “/data/home/s4333238/sct_4.2.0/scripts/sct_get_centerline.py”, line 147, inįile “/data/home/s4333238/sct_4.2.0/scripts/sct_get_centerline.py”, line 127, in run_main I tried to run sct_get_centerline to start but unfortunately ended with the following error (please have a look at the data details, command, output). I would like to use SCT toolbox to analyze them. I think the biggest hurdle will be figuring out an unambiguous specification.Thank you very much for your continues help and support. It looks like we don't support modifying the resolution of non-standard spaces. If you don't do some padding on your slices, motion correction is going to place some values outside the image bounds.Īnd whether it is possible to resample the BOLD so that the resolution matches in the T1 within fmriprep? The space-func outputs should be in your original space, although with limited FoV that seems like a bad idea.
If you're interested in the details, it's defined here:
#Fslinfo dim1 dim2 dim3 series#
The idea is not to upsample data needlessly, but we did still need a common target to resample each BOLD series to, to ensure alignment. To resample to T1w, the T1w is down-sampled to the BOLD resolution, and that is used as the resampling target. I just wondered why the dimensions where different between the preproc and the original BOLD, datatype INT16 dim1 256 dim2 256 dim3 128 dim4 1 datatype 4 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3. The pre-processed data matches neither of these data:įslinfo sub-0014_ses-1_task-rest_acq-TR2200_space-T1w_desc-preproc_
The original T1 has the following dimensions: The original bold has the following dimensions:įslinfo sub-0014_ses-1_task-rest_acq-TR2200_bold.nii I am running this command as I want my pre-processed data to be registered to my T1 before I put the data through Melodic:įmriprep-docker /media/HDD/BIDS/Nifti/ /media/HDD/BIDS/derivatives/ participant -participant-label 0062 -output-spaces fsnative T1w func I wonder if anyone can let me know why the dimensions of my pre-processed functional data do not match any of the input spaces.
0 kommentar(er)
