This is great to hear! The brain mask of the base is created from the cross
runs, and the long runs use the base mask, so you don't need `-synthstrip` for
base or long. I believe it's similar for the aseg but you might have to specify
`-synthseg` when you run the base - not sure, sorry.
________________________________________
From: Dan Levitas <djlevitas...@gmail.com>
Sent: Friday, June 7, 2024 15:13
To: Freesurfer support list
Cc: Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all
External Email - Use Caution
To update my progress, I modified my expert.opts file to only contain a single
line (synthstrip --no-csf) and successfully ran recon-all using the following
command:
recon-all -subjid sub-${sub}_ses-${ses} -i /path/to/anat.nii.gz -synthstrip
-synthseg -expert /path/to/expert.opts -3T -qcache -all
The results are much improved from before (i.e. more accurate pial and white
matter boundaries).
My only remaining question is whether or not I need to include the -synthstrip
-synthseg -expert flags for the BASE and LONG recon-all commands.
Thanks again.
On Fri, Jun 7, 2024 at 9:10 AM Dan Levitas
<djlevitas...@gmail.com<mailto:djlevitas...@gmail.com>> wrote:
Hi Malte,
Thanks for this helpful information. Based on your response, I have a few
follow-up questions.
1). Can the expert file (expert.opts) contain a line for the SynthStrip
workflow and another line for the SynthSeg workflow, or do I need separate
expert files for each process? Assuming the former, is the following an
appropriate example example:
synthstrip --no-csf
synthseg --o $SUBJECTS_DIR/freesurfer/sub-${sub}_ses-${ses}/mri --threads 4
2). In addition to adding the -expert flag into my recon-all command, do I also
need to provide -noskullstrip at the end since SynthStrip is overriding the
watershed skullstripping, or is that implied by the inclusion of the
expert.opts file?
3). Although this is for the cross-sectional (CROSS) portion of my longitudinal
pipeline, do the BASE and LONG portions also need the -expert flag?
Dan
On Fri, Jun 7, 2024 at 8:43 AM Hoffmann, Malte,PhD
<mhoffm...@mgh.harvard.edu<mailto:mhoffm...@mgh.harvard.edu>> wrote:
Hi Dan,
I'm afraid these options aren't currently easy to find as they are being parsed
by scripts/rca-config. You can find a set of recon-all options along with a
description in distribution/etc/recon-config.yaml [1].
To pass additional options to SynthStrip, you'll need to specify an expert
options file by calling recon-all with the `-expert` flag [2]. That file could
then include the line `synthstrip --no-csf`, for example.
Malte
[1]
https://github.com/freesurfer/freesurfer/blob/dev/distribution/etc/recon-config.yaml
[2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
________________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Dan Levitas
<djlevitas...@gmail.com<mailto:djlevitas...@gmail.com>>
Sent: Thursday, June 6, 2024 10:55
To: Freesurfer support list
Subject: [Freesurfer] Incoporating synthstrip and synthseg into recon-all
External Email - Use Caution
Hello,
I am using freesurfer version 7.4.1, and would like to incorporate the recently
introduced synthstrip and synthseg functions into my recon-all command, if
that's possible. From this archive message
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75148.html) it
seems that adding the -synthstrip option enables synthstrip; however, I don't
see this as an option in the recon-all documentation
(https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) nor as a command line
option for recon-all.
Assuming that both synthstrip and synthseg can be used in recon-all, would the
command need to look something like this:
recon-all -subjid sub-${sub}_ses-${ses} -i $anat_file -3T -synthstrip --no-csf
-synthseg -qcache -all
I'm adding the --no-csf synthstrip option based on this comment
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75172.html).
I should also note that I'm performing a longitudinal analysis, so this
specific recon-all pertains to the cross-sectional portion of the workflow.
Thanks,
Dan
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