Qsiprep "freesurfer data is required to make HSVS 5tt image"... does anyone know what these "files" that are needed are?

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1

I am trying the run the pre-configured reconstruction pipeline : mrtrix_multishell_msmt_ACT-hsvs (Reconstruction — qsiprep version documentation)

Because I am using data that was already preprocessed, I only need to do reconstruction. However, I realized that when I ran it, the error code, FreeSurfer data is required to make HSVS 5tt image. popped up.

Because I did not use FreeSurfer for preprocessing, I do not know what files freesurfer gives and hence do not know which files have to be inside of the freesurfer directory in order to make the reconstruction work… Does anyone know what kind of data I need and how I can get it?

Thank you!!!

2

Hi,

You would need to run recon-all from FreeSurfer on the subject’s T1 image.

Best,
Steven

1 Like
3

Thank you! I’ll try that:)

5

I had same problem.

  1. Is there specific file format about recon-all data files?

  2. Can I make recon-all file by using qsiprep Preprocessing pipeline?

If someone helps me, it will be really helpful for me.

Thank you.
Joseph

6

Yes, there is very specific folder and file naming conventions. It would not be worth the effort trying to make it manually based on files you may or may not have.

Yes, you can add --do-reconall to your qsiprep command.

1 Like
7

Thanks, Steven!

I’ll try it. Have a nice day! :grinning:

8

Update some information for people who may need it:

“–do-reconall” have been removed from qsiprep 0.15.0 because it took up a ton of space in the docker image .

More information can found in:

9

Our group usually runs freesurfer as part of fmriprep and then uses its output for the 5tt hsvs workflow in qsiprep. Almost any normal run of recon-all will produce everything you need for 5tt hsvs