not running... probably a beginner's mistake.

[jcrdubois]

Hi Erin

thanks for the suggestion to use your work to convert fmriprep outputs to HCP-like outputs.

I just installed ciftify on my ubuntu 16.04; I'm trying it out, but can't get it to run yet. Here is the command: $ ciftify_recon_all \ --ciftify-work-dir /data/MRI/YALE-trt/derivatives/hcp \ --fs-subjects-dir /data/MRI/YALE-trt/derivatives/freesurfer \ --resample-to-T1w32k \ --surf-reg MSMSulc \ --fs-license /usr/local/freesurfer/license.txt \ --n_cpus 20 \ --debug \ sub-032401

which outputs the following: Usage: ciftify_recon_all [options]

as if I made a mistake in the command line. I probably did, but I can't see where. Help? Thanks!

• Julien

[edickie]

Weird, your right that it is definitely a command-line usage error. But the command looks correct to me.. Maybe there's a hidden carriage return? What happens when you echo the line?

Also, is there a reason you are using the functions by themselves instead of the docker runner? The docker runner should detect the fmriprep and freesurfer outputs and only perform the extra HCP conversion if you set the "output" to the derivatives directory.. Although that only works for fmriprep < 2.0 at the moment.

Sorry I couldn't be more the help. Erin

On Mon, Jan 7, 2019 at 12:38 AM Julien Dubois notifications@github.com wrote:

Hi Erin

thanks for the suggestion to use your work to convert fmriprep outputs to HCP-like outputs.

I just installed ciftify on my ubuntu 16.04; I'm trying it out, but can't get it to run yet. Here is the command: $ ciftify_recon_all --ciftify-work-dir /data/MRI/YALE-trt/derivatives/hcp --fs-subjects-dir /data/MRI/YALE-trt/derivatives/freesurfer --resample-to-T1w32k --surf-reg MSMSulc --fs-license /usr/local/freesurfer/license.txt --n_cpus 20 --debug sub-032401

which outputs the following: Usage: ciftify_recon_all [options]

as if I made a mistake in the command line. I probably did, but I can't see where. Help? Thanks!

• Julien

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/edickie/ciftify/issues/97, or mute the thread https://github.com/notifications/unsubscribe-auth/AMl59goOZaMRFWSi8Hpceyjnhl3Oo79uks5vAt08gaJpZM4Zy5Et .

[jcrdubois]

Hi Erin

after some trial and error I got the command to run, by removing the following arguments:

--surf-reg MSMSulc 
--fs-license /usr/local/freesurfer/license.txt 

Re: the docker runner: I have already run fmriprep 1.2.5. How would I run ciftify?

Julien

[edickie]

Ooooh I that makes sense. The I may not have pushed the version with the --fs-license option to pypi yet. Either way, the '--surf-reg MSMSulc' is the default (so it should run the same) and the --fs-license flag should not be required if freesurfer already set up in the environment. So that makes sense.

The ciftify runner still only expects the old fmriprep output filenames (i.e. 1.1.8 and earlier) so I guess you will need to run the steps manually. i.e. once ciftify_recon_all has run you need to then call ciftify_subject_fmri on each preprocessed fMRI file. There's a little bit of info towards that here https://edickie.github.io/ciftify/#/tutorials/example-usage. Let me know if anything is unclear.

Thanks, Erin

On Mon, Jan 7, 2019 at 12:22 PM Julien Dubois notifications@github.com wrote:

Hi Erin

after some trial and error I got the command to run, by removing the following arguments:

--surf-reg MSMSulc --fs-license /usr/local/freesurfer/license.txt

Re: the docker runner: I have already run fmriprep 1.2.5. How would I run ciftify?

• Julien

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/edickie/ciftify/issues/97#issuecomment-452011824, or mute the thread https://github.com/notifications/unsubscribe-auth/AMl59t1FapYm55NiJ_khWFK61JBkOFDeks5vA4JYgaJpZM4Zy5Et .

[jcrdubois]

excellent. Thanks Erin! I'll be watching ciftify for future releases, in the meantime I'll run things in my own prepared environment. Great work!