cmtk-users

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Feb 6

Hi, Could you tell me how to process a stroke patient using the GUI? I wish there were no connections

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Hi, Could you tell me how to process a stroke patient using the GUI? I wish there were no connections

Feb 6

Dominika Slušná

11/23/22

Multi-Scale Brain Parcellator - how long does it run?

Hi all, Does anybody have an estimate about how long does the Multi-Scale Brain Parcellator take to

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Multi-Scale Brain Parcellator - how long does it run?

Hi all, Does anybody have an estimate about how long does the Multi-Scale Brain Parcellator take to

11/23/22

Alexandre Cionca, Sebastien Tourbier3

10/26/22

DWI processing only - existing anat derivatives

Dear Seb, Many thanks for your answer - As you suggest, it would be easier to run the anatomical and

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DWI processing only - existing anat derivatives

Dear Seb, Many thanks for your answer - As you suggest, it would be easier to run the anatomical and

10/26/22

milad najafzadeh, Sebastien Tourbier3

7/9/22

Probelm in using anatomically constraint tractography

Dear Sebastian Thanks to your fast response. Surly. I create a new topic in that link and provide all

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Probelm in using anatomically constraint tractography

Dear Sebastian Thanks to your fast response. Surly. I create a new topic in that link and provide all

7/9/22

milad najafzadeh, Sebastien Tourbier6

7/9/22

loading data using GUI

Dear Sebastien Many thanks for your detailed answers With kind regards, -Milad On Friday, July 8,

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loading data using GUI

Dear Sebastien Many thanks for your detailed answers With kind regards, -Milad On Friday, July 8,

7/9/22

Rory Piper, Sebastien Tourbier2

6/27/22

Thalamus parcellation not combined

Hi Rory, It is hard say what is happening. It would be great if you could provide me with the

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Thalamus parcellation not combined

Hi Rory, It is hard say what is happening. It would be great if you could provide me with the

6/27/22

milad najafzadeh, Sebastien Tourbier3

6/11/22

Adding laussane2018 atlas to the mrtrix

Dear Sebastien Many thanks to your helps. I have changed my pipeline to use cmp3. -Best regards -

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Adding laussane2018 atlas to the mrtrix

Dear Sebastien Many thanks to your helps. I have changed my pipeline to use cmp3. -Best regards -

6/11/22

Fatemeh Sadeghi

3/15/22

Hi, just noticed two small typos in this page: https://connectome-mapper-3.readthedocs.io/en/latest/

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Hi, just noticed two small typos in this page: https://connectome-mapper-3.readthedocs.io/en/latest/

3/15/22

FarNaf, … Sebastien Tourbier5

8/17/21

error "RuntimeError: No pyface.toolkits plugin could be loaded for qt" when calling GUI

Dear FarNaf and Pascal, I have good news! I managed to get access to a windows machine today and to

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error "RuntimeError: No pyface.toolkits plugin could be loaded for qt" when calling GUI

Dear FarNaf and Pascal, I have good news! I managed to get access to a windows machine today and to

8/17/21

Isotta Rigoni, Sebastien Tourbier6

6/7/21

problems running SHORE on DSI data

Hi Isotta, I had to leave for family reasons and I am now back to work. So it seems it is really

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problems running SHORE on DSI data

Hi Isotta, I had to leave for family reasons and I am now back to work. So it seems it is really

6/7/21

小明, Sebastien Tourbier7

6/7/21

outputs question of volume

Hi, This corresponds to the number of voxels of each ROI after applying the transformation from T1w

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outputs question of volume

Hi, This corresponds to the number of voxels of each ROI after applying the transformation from T1w

6/7/21

Isotta Rigoni, Sebastien Tourbier2

4/30/21

failed visualisation of diffusion outputs

Hi Isotta! The quality inspector is indeed generating the command to open the outputs with

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failed visualisation of diffusion outputs

Hi Isotta! The quality inspector is indeed generating the command to open the outputs with

4/30/21

4/30/21

cmp stuck at MAP-MRI but no error message given

Good morning, the issue above has been solved by disabling the option 'map-mri'. The .dwi

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cmp stuck at MAP-MRI but no error message given

Good morning, the issue above has been solved by disabling the option 'map-mri'. The .dwi

4/30/21

Isotta Rigoni, Sebastien Tourbier3

4/16/21

failed visualisation of segmentation stage

Hi Sebastien, the problem was the Freesurfer version: I had the 7 installed. Now that I have

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failed visualisation of segmentation stage

Hi Sebastien, the problem was the Freesurfer version: I had the 7 installed. Now that I have

4/16/21

Isotta Rigoni, Sebastien Tourbier3

4/10/21

invalid BIDS dataset

Hi Sebastien, I am using the Connectome Mapper v3.0.0-RC4. I tried to import the BIDSLayout with the

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invalid BIDS dataset

Hi Sebastien, I am using the Connectome Mapper v3.0.0-RC4. I tried to import the BIDSLayout with the

4/10/21

Ellen van Maren, Sebastien Tourbier3

3/26/21

multiscalebrainparcellator Error in freesurfer

Hi Sebastien Thank you very much. This solved the problem! Best, Ellen Von: "cmtk-users@

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multiscalebrainparcellator Error in freesurfer

Hi Sebastien Thank you very much. This solved the problem! Best, Ellen Von: "cmtk-users@

3/26/21

Yuta Katsumi, Sebastien Tourbier4

3/3/21

Unable to specify existing FreeSurfer directories for multiple subjects in ref_anatomical_config.ini

Hi Yuta! It seems to have indeed worked! You can see that these 2 attributes are well set at the

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Unable to specify existing FreeSurfer directories for multiple subjects in ref_anatomical_config.ini

Hi Yuta! It seems to have indeed worked! You can see that these 2 attributes are well set at the

3/3/21

pavanc...@gmail.com, Sebastien Tourbier2

3/1/21

multi scale brain parcellator install without docker

Hi Pavan! Could you use singularity? If yes, you could run connectomemapper3 which provides a

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multi scale brain parcellator install without docker

Hi Pavan! Could you use singularity? If yes, you could run connectomemapper3 which provides a

3/1/21

2/5/21

Lausanne 2008 nifti

Dear cmtk-experts, I used the Lausanne 2008 atlas in my DTI preprocessing. Now, I would like to

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Lausanne 2008 nifti

Dear cmtk-experts, I used the Lausanne 2008 atlas in my DTI preprocessing. Now, I would like to

2/5/21

pavanc...@gmail.com

1/25/21

bids directory not working

Hey there, I'm using the connectome mapper 3 gui. I am getting an error that my dataset is not a

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bids directory not working

Hey there, I'm using the connectome mapper 3 gui. I am getting an error that my dataset is not a

1/25/21

小明, Sebastien Tourbier15

1/14/21

Please， Why my GUI lose something

Also please could you open new topics in the future, this would help others to access support

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Please， Why my GUI lose something

Also please could you open new topics in the future, this would help others to access support

1/14/21

Octavian Lie, Sebastien Tourbier10

1/13/21

Connectome viewer question

You're welcome! Sebastien On Wed, Jan 13, 2021 at 4:30 AM Octavian Lie <octavi...@gmail.com

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Connectome viewer question

You're welcome! Sebastien On Wed, Jan 13, 2021 at 4:30 AM Octavian Lie <octavi...@gmail.com

1/13/21

Pavan Chaggar, Sebastien Tourbier4

5/12/20

Multiscale parcellation MNI reference

I forgot to mention, for scaled 3:5 there are also a different number of nodes. I've summarised

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Multiscale parcellation MNI reference

I forgot to mention, for scaled 3:5 there are also a different number of nodes. I've summarised

5/12/20

David Nothdurfter

5/8/20

Problems while setting up the conda environment/ cannot find libffi

Hello, sorry for the many questions, but I also have an issue when installing the Connectome Mapper -

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Problems while setting up the conda environment/ cannot find libffi

Hello, sorry for the many questions, but I also have an issue when installing the Connectome Mapper -

5/8/20

David Nothdurfter, … Sebastien Tourbier9

5/8/20

Multi-Scale Brain Parcellator

Hi Sebastien, hi Pavan, thank you for your help. Unfortunately, changing the location of the licencse

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Multi-Scale Brain Parcellator

Hi Sebastien, hi Pavan, thank you for your help. Unfortunately, changing the location of the licencse

5/8/20

maryam tayebi, Sebastien Tourbier2

3/24/20

Install cmtk on Mac, version of libraries

Hi Mary, I do not know which version of CMP you are trying to install but it seems you are not trying

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Install cmtk on Mac, version of libraries

Hi Mary, I do not know which version of CMP you are trying to install but it seems you are not trying

3/24/20

3/18/20

Question about subcortical areas in Laussann atlas

Hi, I have found the Laussann 2008 atlas '.annot' file and visualize the ROIs in freeview.

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Question about subcortical areas in Laussann atlas

Hi, I have found the Laussann 2008 atlas '.annot' file and visualize the ROIs in freeview.

3/18/20

3/11/20

How to visualize brian activity in Lausanne 2008

Hi, I want to ask a question about the extraction of Lausanne 2008 ROIs for Freesurfer. So is it

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How to visualize brian activity in Lausanne 2008

Hi, I want to ask a question about the extraction of Lausanne 2008 ROIs for Freesurfer. So is it

3/11/20

Feng Fang, Sebastien Tourbier6

3/11/20

Which version of Python should we use to install the CMTK toolbox?

Hi Sebastien, Thanks for your instructions and now I can run the app. But when I set everything up,

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Which version of Python should we use to install the CMTK toolbox?

Hi Sebastien, Thanks for your instructions and now I can run the app. But when I set everything up,

3/11/20

Ariana Familiar, Sebastien Tourbier8

1/20/20

multiscalebrainparcellator Error during parcellation

Great!! Thanks also for your feedback :) Best, Sebastien On Fri, Jan 17, 2020 at 9:59 PM Ariana

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multiscalebrainparcellator Error during parcellation

Great!! Thanks also for your feedback :) Best, Sebastien On Fri, Jan 17, 2020 at 9:59 PM Ariana

1/20/20

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