Fmriprep --fs-no-reconall saves time?

Dear all,

I only need the …_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz output and already pre-run freesurfer. After fmriprep, I continue with ciftify.
Could I use --fs-no-reconall command to save some time?
Because fmriprep needs about 7 hrs for a single subject with the command below (Using a MBP 2019 with 2.3GHz i9, 64GB Ram):
fmriprep-docker /Users/neurolab/Desktop/Drmed/GSP_reoriented /Users/neurolab/Desktop/Drmed/GSP_reoriented/derivatives/participant --participant-label $i --fs-license-file /Users/neurolab/Desktop/Programmes/freesurfer/license.txt --fs-subjects-dir /Users/neurolab/Desktop/Drmed/GSP_reoriented/derivatives/freesurfer/sub-$i


If you’re going to use ciftify, you presumably need FreeSurfer outputs anyway.

--fs-subjects-dir /Users/neurolab/Desktop/Drmed/GSP_reoriented/derivatives/freesurfer/sub-$i

I would probably not create a new subjects directory for each subject. Using the same one will get you a more normal-looking subjects directory.

So you mean I do not need the

–fs-subjects-dir /Users/neurolab/Desktop/Drmed/GSP_reoriented/derivatives/freesurfer/sub-$i

And just put the pre-run freesurfer outputs in this folder

/Users/neurolab/Desktop/Drmed/GSP_reoriented/derivatives/participant with …/freesurfer/sub-$i

If I do so:
fmriprep creates a new sub-$i folder in the freesurfer folder and runs: (although recon-all finished successfully before)

201005-08:25:42,285 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 7 -subjid sub-4 -sd /out/freesurfer
201005-08:25:42,285 nipype.workflow INFO:
[Node] Running “autorecon2_vol” (“smriprep.interfaces.freesurfer.ReconAll”), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 7 -subjid sub-4 -sd /out/freesurfer
201005-08:25:42,288 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 7 -subjid sub-4 -sd /out/freesurfer

Maybe because for this subject I only have a ses-2 file and not ses-1 file:
name of rawdata: sub-4_ses-2_T1w.nii.gz

Sorry, I did not see this reply. No, I meant use

–fs-subjects-dir /Users/neurolab/Desktop/Drmed/GSP_reoriented/derivatives/freesurfer

If you include sub-$i, then you will end up with a difficult-to-work with subjects directory.

Thanks a lot!