StephDcTUM

Example of rDCM question

2

Dear all, I have applied the rDCM method to dysconnective areas (dysconnective areas are defined in glioma patients, where the correlation values of the bold signals deviate over a certain...

Hi, I want to use keras-vis for a 3D mri image with the following model: `def standart_model(tiefe, breite, länge,color_depth = 1): model = Sequential() model.add(Conv3D(8,(3, 3, 3), activation='relu', padding='same', name='conv1',...

Error running ICA-AROMA

22

Dear all, I ran ICA-AROMA for several subjects and everything worked well. For some subjects I encounter the following error, although they are very similar to the ones where ICA-AROMA...

RecursionError: maximum recursion depth exceeded while calling a Python object

3

I am using a correlation matrix based on the Schaefer Atlas with 400x400 fc values. When running `gm.fit(correlation_matrix)`, I encounter the above mentioned error. When I set the sys.setrecursionlimit(10000), my...

Different dimensions of timeseries and atlas

1

Dear all, I am using the fmriprep output which has the dimension of [325325, 238]. E.g. as in the example given using the atlas = datasets.fetch_atlas_surf_destrieux() only has 20484 regions....

Trouble with MSM

32

Hi, I am having troubles with using MSM for ciftify (FS-Reg works) Do I have to install fsl from source code with that here FslInstallation/SourceCode - FslWiki It wont work...

ciftify_recon_all error

7

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...

freesurfer license not found

5

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...

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...

Ciftify output and correlation

4

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?...