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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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Returned error with mismatch between version of MSM and the config file #126

Closed helloTC closed 4 years ago

helloTC commented 4 years ago

Hi Erin, I got an error when calling ciftify function of _ciftify_reconall as

Running version of MSM does not match config [ciftify_path]/data/hcp_config/MSMSulcStrainFinalconf.

I installed ciftify using pip in my account with pip install ciftify --user, the version of ciftify-2.2.2.post1 were successfully installed in my Ubuntu 16.04 system. I then set PATH, PYTHONPATH, CIFTIFY_TEMPLATES and CIFTIFY_WORDDIR in my .bashrc. Outside python I have installed connectome-workbench, FSL and Freesurfer, but I'm not quite sure whether I need to install Multimodal Surface Matching (MSM) from here for FSL originally contained it. And more importantly, I'm not sure how to set MSM from the above link so that ciftify could identify and work properly.

My _ciftify_reconall command is

ciftify_recon_all --fs-subjects-dir /nfs/s2/userhome/huangtaicheng/hworkingshop/try_htc/mri_image/subjects --hcp-data-dir /nfs/s2/userhome/huangtaicheng/hworkingshop/try_htc/mri_image/output S0001

Could you please give me some advices to solve the error? Thanks for your help.

helloTC commented 4 years ago

I solved this issue by downloading the MSM from here. It's different from the one in FSL and the one in this github page (https://github.com/ecr05/MSM_HOCR).

mharms commented 4 years ago

Hopefully this can get resolved within ciftify, so that you can use the latest version. The https://github.com/ecr05/MSM_HOCR version is that one that we are using for HCP-Lifespan processing within the HCPpipelines.

jelee2498 commented 3 years ago

I downloaded MSM from your link . But still, i'm not sure how to make ciftify identify new msm.

As you put it this problem as:

And more importantly, I'm not sure how to set MSM from the above link so that ciftify could identify and work properly.

edickie commented 3 years ago

The easiest way is to make sure the newer version of MSM is "upstream" in your environment "PATH" variable.

export PATH=/path/to/good/msm:$PATH

does that make sense?

To test what version try typing msm --help and make sure help message for the correct version appears. You can also try which msm and it should show the path to the correct version.

Thanks, Erin

On Sat, Dec 12, 2020 at 3:24 AM jelee2498 notifications@github.com wrote:

I downloaded MSM from your link https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/. But still, i'm not sure how to make ciftify identify new msm.

As you put it this problem as: And more importantly, I'm not sure how to set MSM from the above link so that ciftify could identify and work properly.

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jelee2498 commented 3 years ago

Finally, it works!!

The problem was the name of new version of MSM.
I wondered why 'which msm' gave me same path even after I add a new MSM path. So, I changed the

'msm_centos_v3' -> 'msm'

then, _ciftify_reconall identifies my new MSM.

Thank u so much Erin and thank u for making such a useful tool.

yetianmed commented 2 years ago

Hi Erin,

I added the new version of MSM to the PATH as below: export PATH=/path/to/MSM_HOCR_v2/MacOSX/msm:$PATH

However, when I type which msm, it still shows /usr/local/fsl/bin/msm

And when I run ciftify_recon_all subjectID, it still shows: Running version of MSM does not match config /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/ciftify/data/hcp_config/MSMSulcStrainFinalconf

Any ideas?

Thanks, Ye

sophieraible commented 1 year ago

Hi Ye,

did you manage to solve this problem? If yes, would you mind sharing your solution? I also renamed msm_centos_v3 to msm and added the path, but ciftify still seems to use /fsl/bin/msm.

Thank you! Sophie

yetianmed commented 1 year ago

Hi Sophie,

Yes, it worked. I adjusted the path slightly and it worked. See below:

export PATH=/mydirectory/MSM_HOCR_v2/MacOSX/:$PATH

Ye

Hi Ye,

did you manage to solve this problem? If yes, would you mind sharing your solution? I also renamed msm_centos_v3 to msm and added the path, but ciftify still seems to use /fsl/bin/msm.

Thank you! Sophie