BUG: Problem to make diffusion pipeline config with ACT about connectomemapper3

[sebastientourbier]

Dear Milad,

Thanks for reporting this here 👍

By looking at the configuration file, the parameters for both preprocessing_stage and registration_stage seem to not have been updated, being:

"tracking_tool": "Dipy",
"act_tracking": false,

I am going to make my investigate, and make a fix, that would be integrated in the next release.

In the meantime, you could edit your config file and correct the values for both preprocessing_stage and registration_stage to:

"tracking_tool": "MRtrix",
"act_tracking": true,

Let me know if this works.

[milad7093]

Dear Sebastian

I changed the config file, ran my code and it worked ( see the attached log file). But when I try to visualize the cmp3's outputs, the bids-inspector create a folder called nipype-1.7.0 while the outputs are in another folder ( nipype-1.8.0) and I can't see them using the bids-inspector. Do you have any suggestion on how to solve this issue?

The program's outputs in the terminal after choosing the bids-inspector in the GUI:

Selection of subject (and session) for which to inspect outputs
.. INFO: Selected subject: sub-3102
.. INFO: Input dataset has sessions
['2', '1']

Initialize anatomical pipeline
Freesurfer subjects directory: /media/mn/355A4F4972A44ABF/PD_total/derivatives/freesurfer-7.1.1
Load anatomical project
.. LOAD: Load anatomical config file : /media/mn/355A4F4972A44ABF/PD_total/derivatives/cmp-v3.0.4/sub-3102/ses-1/sub-3102_ses-1_anatomical_config.json
.. INFO: Generated with the same CMP3 version
.. INFO: Created directory /media/mn/355A4F4972A44ABF/PD_total/derivatives/nipype-1.7.0/sub-3102/ses-1
Initialize diffusion pipeline
**** Check Inputs ****
Valid BIDS dataset with 169 subjects
/media/mn/355A4F4972A44ABF/PD_total/sub-3102/ses-1/dwi/sub-3102_ses-1_dwi.nii.gz
/media/mn/355A4F4972A44ABF/PD_total/sub-3102/ses-1/dwi/sub-3102_ses-1_dwi.bval
/media/mn/355A4F4972A44ABF/PD_total/sub-3102/ses-1/dwi/sub-3102_ses-1_dwi.bvec
Looking for....
dwi_file : /media/mn/355A4F4972A44ABF/PD_total/sub-3102/ses-1/dwi/sub-3102_ses-1_dwi.nii.gz
bvecs_file : /media/mn/355A4F4972A44ABF/PD_total/sub-3102/ses-1/dwi/sub-3102_ses-1_dwi.bvec
bvals_file : /media/mn/355A4F4972A44ABF/PD_total/sub-3102/ses-1/dwi/sub-3102_ses-1_dwi.bval
DWI available
Inputs check finished successfully.
Diffusion and morphological data available.
Load dMRI project
.. LOAD: Load diffusion config file : /media/mn/355A4F4972A44ABF/PD_total/derivatives/cmp-v3.0.4/sub-3102/ses-1/sub-3102_ses-1_diffusion_config.json
.. INFO: Generated with the same CMP3 version
.. INFO: Selected session ses-1
Anatomical pipeline output inspection
... Inspect stage <cmp.bidsappmanager.stages.segmentation.segmentation.SegmentationStageUI object at 0x7fb6caad4350>
... Inspect stage <cmp.bidsappmanager.stages.parcellation.parcellation.ParcellationStageUI object at 0x7fb6caad49b0>
Diffusion pipeline output inspection
... Inspect stage <cmp.bidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI object at 0x7fb6cab13d10>
... Inspect stage <cmp.bidsappmanager.stages.registration.registration.RegistrationStageUI object at 0x7fb6cab139b0>
... Inspect stage <cmp.bidsappmanager.stages.diffusion.diffusion.DiffusionStageUI object at 0x7fb6cab13b30>
... Inspect stage <cmp.bidsappmanager.stages.connectome.connectome.ConnectomeStageUI object at 0x7fb6cab13cb0>
.. Anatomical output(s) available : True
.. Diffusion output(s) available : False
.. fMRI output(s) available : False

sub-3102_ses-1_log.txt

[sebastientourbier]

Dear Milad,

Great to see that the execution worked!

Regarding, the last issue with the quality inspector window, the version of nipype in the BIDS App and the conda environment py37cmp-gui should be the same.

Your error makes me think that you might not use the latest version of the py37cmp-gui environment and nipype 1.7.0 installed in it. However, nipype has been updated to 1.8.0 in the v3.0.4 release. I see 2 options:

1. Re-creating the py37cmp-gui with the conda/environment[_macos].yml of the v3.0.4 release (the preferred):

   # If your have `py37cmp-gui` activated, you need to deactivate it
   $ conda deactivate
   # Remove your exisiting `py37cmp-gui` env 
   $ conda env remove -n py37cmp-gui
   # Create the environment corresponding to v3.0.4
   # You might use environment_macosx.yml instead of environment.yml
   # if you are on Mac
   $ conda env create -f https://github.com/connectomicslab/connectomemapper3/raw/v3.0.4/conda/environment.yml

   This would allow to have a consistent environment with the version of the BIDS App you used. This however might take some time.

2. Updating nipype 1.8.0 in your existing py37cmp-gui environment:

   (py37cmp-gui)$ pip install nipype==1.8.0
   

   This option would be faster, but this would not make your environment consistent to the one used in the BIDS App and the version of other dependencies might differ.

[milad7093]

Dear Sebastian

Many thanks for detailed response. I followed the first option (Re-creating the py37cmp-gui) installed the latest version of py37cmp-gui and installed the connectomemapper using the "pip install connectomemapper". All steps work well and the program installed successfully But there is an error when running cmp3 GUI as follow:

py37cmp-gui) mn@mn-HP-Z840-Workstation:~$ cmpbidsappmanager
Traceback (most recent call last):
File "/home/mn/miniconda3/envs/py37cmp-gui/bin/cmpbidsappmanager", line 5, in
from cmp.cli.cmpbidsappmanager import main
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/cli/cmpbidsappmanager.py", line 30, in
import cmp.bidsappmanager.gui.principal
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/gui/principal.py", line 21, in
import cmp.project
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/project.py", line 23, in
from cmp.pipelines.diffusion import diffusion as Diffusion_pipeline
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/pipelines/diffusion/diffusion.py", line 22, in
from cmp.stages.diffusion.diffusion import DiffusionStage
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/diffusion.py", line 18, in
from .reconstruction import *
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/reconstruction.py", line 33, in
from cmtklib.diffusion import FlipTable, FlipBvec
File "/home/mn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmtklib/diffusion.py", line 14, in
import nibabel.trackvis as tv
ModuleNotFoundError: No module named 'nibabel.trackvis'

I checked all packages in the y37cmp-gui ( please see below) and nibabel has been installed

(py37cmp-gui) mn@mn-HP-Z840-Workstation:~$ conda list -n py37cmp-gui

packages in environment at /home/mn/miniconda3/envs/py37cmp-gui:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
alsa-lib 1.2.6.1 h7f98852_0 conda-forge
annexremote 1.6.0 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
apscheduler 3.9.1 pypi_0 pypi
argcomplete 2.0.0 pypi_0 pypi
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py37h540881e_2 conda-forge
astor 0.8.1 pypi_0 pypi
atk-1.0 2.36.0 h3371d22_4 conda-forge
attr 2.5.1 h166bdaf_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports-zoneinfo 0.2.1 pypi_0 pypi
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bids-validator 1.9.5 pypi_0 pypi
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
boto 2.49.0 pypi_0 pypi
brotli 1.0.9 pypi_0 pypi
brotli-bin 1.0.9 h166bdaf_7 conda-forge
brotlipy 0.7.0 py37h540881e_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 ha61ee94_1011 conda-forge
certifi 2022.6.15 py37h89c1867_0 conda-forge
cffi 1.15.1 py37h43b0acd_0 conda-forge
chardet 5.0.0 pypi_0 pypi
charset-normalizer 2.1.0 pyhd8ed1ab_0 conda-forge
ci-info 0.2.0 pypi_0 pypi
citeproc-py 0.6.0 pypi_0 pypi
click 8.1.3 py37h89c1867_0 conda-forge
codecarbon 1.2.0 pypi_0 pypi
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
commonmark 0.9.1 py_0 conda-forge
configparser 5.2.0 pypi_0 pypi
connectomemapper 3.0.4 pypi_0 pypi
cryptography 37.0.4 py37h38fbfac_0 conda-forge
cvxopt 1.3.0 py37h9b79bc5_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dash 2.5.1 pypi_0 pypi
dash-bootstrap-components 0.13.1 pypi_0 pypi
dash-core-components 2.0.0 pypi_0 pypi
dash-html-components 2.0.0 pypi_0 pypi
dash-table 5.0.0 pypi_0 pypi
dataclasses 0.8 pyhc8e2a94_3 conda-forge
datalad 0.15.4 pypi_0 pypi
datalad-container 1.1.5 pypi_0 pypi
datalad-neuroimaging 0.3.1 pypi_0 pypi
dbus 1.13.6 h5008d03_3 conda-forge
dcm2niix 1.0.20211006 h924138e_0 conda-forge
debugpy 1.6.0 py37hd23a5d3_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.13 pypi_0 pypi
dill 0.3.5.1 pyhd8ed1ab_0 conda-forge
dipy 1.3.0 py37ha21ca33_0 conda-forge
docopt 0.6.2 pypi_0 pypi
docutils 0.18.1 py37h89c1867_1 conda-forge
dsdp 5.8 hd9d9efa_1203 conda-forge
duecredit 0.9.1 pypi_0 pypi
elfutils 0.186 he364ef2_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
etelemetry 0.3.0 pypi_0 pypi
exifread 3.0.0 pypi_0 pypi
expat 2.4.8 h27087fc_0 conda-forge
fasteners 0.17.3 pypi_0 pypi
fftw 3.3.10 nompi_h77c792f_102 conda-forge
file-tree 1.0.0 pyhd8ed1ab_0 conda-forge
file-tree-fsl 0.2.1 pyhd8ed1ab_0 conda-forge
filelock 3.7.1 pypi_0 pypi
fire 0.4.0 pypi_0 pypi
flask 2.1.3 pypi_0 pypi
flask-compress 1.12 pypi_0 pypi
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.34.4 py37h540881e_0 conda-forge
formulaic 0.2.4 pypi_0 pypi
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
fsleyes 1.3.3 py37h89c1867_1 conda-forge
fsleyes-props 1.7.3 pyhd8ed1ab_0 conda-forge
fsleyes-widgets 0.12.3 pyhd8ed1ab_0 conda-forge
fslpy 3.10.0 pyhd8ed1ab_0 conda-forge
future 0.18.2 py37h89c1867_5 conda-forge
gdk-pixbuf 2.42.8 hff1cb4f_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git-annex 8.20211123 nodep_h1234567_1 conda-forge
glib 2.72.1 h6239696_0 conda-forge
glib-tools 2.72.1 h6239696_0 conda-forge
glpk 4.65 h9202a9a_1004 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.7.6 hf3e180e_5 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.50.0 h5abf519_3 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.20.3 hf6a322e_0 conda-forge
gstreamer 1.20.3 hd4edc92_0 conda-forge
gtk2 2.24.33 h90689f9_2 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
h5py 3.7.0 nompi_py37hc97082c_100 conda-forge
harfbuzz 4.4.1 hf9f4e7c_0 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
httpretty 1.1.4 pypi_0 pypi
humanize 4.2.3 pypi_0 pypi
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py37h89c1867_0 conda-forge
importlib_metadata 4.11.4 hd8ed1ab_0 conda-forge
importlib_resources 5.8.0 pyhd8ed1ab_0 conda-forge
indexed_gzip 1.6.4 py37he2e3b7d_1 conda-forge
interface-meta 1.3.0 pypi_0 pypi
ipykernel 6.15.1 pyh210e3f2_0 conda-forge
ipython 7.33.0 py37h89c1867_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
iso8601 1.0.2 pypi_0 pypi
isodate 0.6.1 pyhd8ed1ab_0 conda-forge
itsdangerous 2.1.2 pypi_0 pypi
jack 1.9.18 h8c3723f_1002 conda-forge
jedi 0.18.1 py37h89c1867_1 conda-forge
jeepney 0.8.0 pypi_0 pypi
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
jsonschema 4.7.2 pyhd8ed1ab_0 conda-forge
jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.10.0 py37h89c1867_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
keyring 23.7.0 pypi_0 pypi
keyrings-alt 4.1.1 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.3 py37h7cecad7_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libarchive 3.5.2 hb890918_3 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcap 2.64 ha37c62d_0 conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libclang 14.0.6 default_h2e3cab8_0 conda-forge
libclang13 14.0.6 default_h3a83d3e_0 conda-forge
libcups 2.3.3 hf5a7f15_1 conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.12 h166bdaf_0 conda-forge
libdrm 2.4.112 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.3.4 h27087fc_0 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgd 2.3.3 h18fbbfe_3 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.72.1 h2d90d5f_0 conda-forge
libglu 9.0.0 he1b5a44_1001 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn2 2.3.3 h166bdaf_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
libllvm14 14.0.6 he0ac6c6_0 conda-forge
libmicrohttpd 0.9.75 h2603550_1 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.16 h516909a_0 conda-forge
libpng 1.6.37 h753d276_3 conda-forge
libpq 14.4 hd77ab85_0 conda-forge
librsvg 2.54.4 h7abd40a_0 conda-forge
libsndfile 1.0.31 h9c3ff4c_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libspatialindex 1.9.3 h9c3ff4c_4 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtasn1 4.18.0 h166bdaf_1 conda-forge
libtiff 4.4.0 hc85c160_1 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libudev1 249 h166bdaf_4 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.14 h22db469_3 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
lxml 4.9.1 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.1 py37h540881e_1 conda-forge
matplotlib-base 3.5.2 py37hc347a89_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mesalib 21.2.5 h0e4506f_3 conda-forge
metis 5.1.0 h58526e2_1006 conda-forge
mistune 0.8.4 py37h5e8e339_1005 conda-forge
mne 0.24.1 pypi_0 pypi
mpfr 4.1.0 h9202a9a_1 conda-forge
mrtrix3 3.0.3 h2bc3f7f_0 mrtrix3
msgpack 1.0.4 pypi_0 pypi
multidict 6.0.2 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mutagen 1.45.1 pypi_0 pypi
mysql-common 8.0.29 haf5c9bc_1 conda-forge
mysql-libs 8.0.29 h28c427c_1 conda-forge
nbclient 0.6.6 pyhd8ed1ab_0 conda-forge
nbconvert 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 6.5.0 pyhd8ed1ab_0 conda-forge
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge
nettle 3.8 hc379101_0 conda-forge
networkx 2.6.3 pypi_0 pypi
nibabel 4.0.1 pyhd8ed1ab_0 conda-forge
nipype 1.8.0 pypi_0 pypi
nomkl 1.0 h5ca1d4c_0 conda-forge
nose 1.3.7 pypi_0 pypi
notebook 6.4.12 pyha770c72_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.78 h2350873_0 conda-forge
num2words 0.5.10 pypi_0 pypi
numexpr 2.8.0 py37h85a3170_102 conda-forge
numpy 1.21.6 py37h976b520_0 conda-forge
obspy 1.2.2 pypi_0 pypi
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py37he8f5f7f_0 conda-forge
pandoc 2.18 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.50.8 hbd2fdc8_0 conda-forge
parse 1.19.0 pyh44b312d_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pathlib2 2.3.7.post1 py37h89c1867_1 conda-forge
patool 1.12 pypi_0 pypi
patsy 0.5.2 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.2.0 py37h44f0d7a_0 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
plotly 5.9.0 pypi_0 pypi
portaudio 19.6.0 h57a0ea0_5 conda-forge
progressbar2 4.0.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.14.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.30 pyha770c72_0 conda-forge
prov 2.0.0 pypi_0 pypi
psutil 5.9.1 py37h540881e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio 14.0 h7f54b18_8 conda-forge
py-cpuinfo 8.0.0 pypi_0 pypi
pybids 0.14.0 pypi_0 pypi
pycartool 0.1.1 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydicom 2.2.2 pypi_0 pypi
pydot 1.4.2 pypi_0 pypi
pyface 7.4.1 pypi_0 pypi
pygithub 1.55 pypi_0 pypi
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pyjwt 2.4.0 pypi_0 pypi
pynacl 1.5.0 pypi_0 pypi
pynvml 11.4.1 pypi_0 pypi
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyhd8ed1ab_1 conda-forge
pyperclip 1.8.2 pypi_0 pypi
pypubsub 4.0.3 py_0 conda-forge
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
pyrsistent 0.18.1 py37h540881e_1 conda-forge
pysocks 1.7.1 py37h89c1867_5 conda-forge
pytables 3.7.0 py37h5dea08b_0 conda-forge
python 3.7.12 hb7a2778_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.15.3 pyhd8ed1ab_0 conda-forge
python-gitlab 3.6.0 pypi_0 pypi
python-utils 3.3.3 pyhd8ed1ab_0 conda-forge
python-xmp-toolkit 2.0.1 pypi_0 pypi
python_abi 3.7 2_cp37m conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 23.2.0 py37h0c0c2a8_0 conda-forge
qt 5.15.4 hf11cfaa_0 conda-forge
qt-main 5.15.4 ha5833f6_2 conda-forge
qt-webengine 5.15.4 hcbadb6c_3 conda-forge
rdflib 6.1.1 pypi_0 pypi
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.1 pyhd8ed1ab_0 conda-forge
requests-ftp 0.3.1 pypi_0 pypi
requests-toolbelt 0.9.1 pypi_0 pypi
rich 12.5.1 pyhd8ed1ab_0 conda-forge
rtree 1.0.0 py37h0b55af0_1 conda-forge
scikit-learn 1.0.2 py37hf9e9bfc_0 conda-forge
scipy 1.7.3 py37hf2a6cf1_0 conda-forge
secretstorage 3.3.2 pypi_0 pypi
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 59.8.0 py37h89c1867_1 conda-forge
simplejson 3.17.6 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.1 pyhd8ed1ab_0 conda-forge
sphinx 5.0.2 pyh6c4a22f_0 conda-forge
sphinx_rtd_theme 0.5.2 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlalchemy 1.3.24 pypi_0 pypi
sqlite 3.39.1 h4ff8645_0 conda-forge
statsmodels 0.13.1 pypi_0 pypi
suitesparse 5.10.1 h9e50725_1 conda-forge
tbb 2021.5.0 h924138e_1 conda-forge
tenacity 8.0.1 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
terminado 0.15.0 py37h89c1867_0 conda-forge
textual 0.1.18 pyhd8ed1ab_1 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tornado 6.2 py37h540881e_0 conda-forge
tqdm 4.64.0 pypi_0 pypi
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
traits 6.3.2 pypi_0 pypi
traitsui 7.2.0 pypi_0 pypi
trimesh 3.12.0 pyh6c4a22f_0 conda-forge
typing-extensions 4.3.0 hd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
tzdata 2022.1 pypi_0 pypi
tzlocal 4.2 pypi_0 pypi
unicodedata2 14.0.0 py37h540881e_1 conda-forge
urllib3 1.26.10 pyhd8ed1ab_0 conda-forge
vcrpy 4.2.0 pypi_0 pypi
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 2.1.2 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
whoosh 2.7.4 pypi_0 pypi
wrapt 1.14.1 pypi_0 pypi
wxnatpy 0.4.0 pyhd8ed1ab_0 conda-forge
wxpython 4.1.1 py37hecb6014_7 conda-forge
xarray 0.20.2 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xnat 0.4.2 pyhd8ed1ab_0 conda-forge
xorg-damageproto 1.2.1 h7f98852_1002 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-glproto 1.4.17 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-randrproto 1.5.0 h7f98852_1001 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-util-macros 1.19.3 h7f98852_0 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yarl 1.7.2 pypi_0 pypi
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 h8a70e8d_2 conda-forge

Do you have any suggestion?

Best Regards,

-Milad

[sebastientourbier]

Dear Milad,

Thanks to report this with all the details. It seems you found a new bug!

For the moment, a version for nibabel is not imposed, but it seems nibabel had some major API changes in the latest 4.0.0 version, released on June 18th, and installed in your environment.
I just opened a new issue to integrate those changes in CMP3, such that it can support it in the future.
In the meantime, reinstalling nibabel to the prior 3.2.2 version should fix the problem. e.g.:

(py37cmp-gui)$ pip install nibabel==3.2.2

[milad7093]

Dear Sebastian

Many thanks for your detailed response. The suggested version of nibabel was installed and now I can visualize the outputs.Now I have a question regarding the SIFT algorithm, How many streamlines are filtered using this algorithm in the CMP3?

With kind regards,

-Milad

[sebastientourbier]

Dear Milad,

CMP3 uses tcksift with the default parameters for the number of filtered streamlines. It corresponds to the following code:

connectomemapper3/cmtklib/interfaces/mrtrix3.py

Lines 1491 to 1499 in 9126faa

	class FilterTractogramInputSpec(CommandLineInputSpec):
	in_tracks = File(exists=True, mandatory=True, argstr='%s',
	position=-3, desc='Input track file in TCK format')
	in_fod = File(exists=True, mandatory=True, argstr='%s', position=-2,
	desc='Input image containing the spherical harmonics of the fibre orientation distributions')
	act_file = File(exists=True, argstr='-act %s',
	position=-4, desc='ACT 5TT image file')
	out_file = File(argstr='%s', position=-1,
	desc='Output filtered tractogram')

Unfortunately, I have not managed to retrieve this information in the doc page: https://mrtrix.readthedocs.io/en/latest/reference/commands/tcksift.html.
That could be a question for the mrtrix3 community.

But if I remember well, it will keep about 10% of the streamlines of the input tractogram.