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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 < MHOFFMANN@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-con... [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile

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From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Dan Levitas < djlevitas208@gmail.com> Sent: Thursday, June 6, 2024 10:55 To: Freesurfer support list Subject: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

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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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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 djlevitas208@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

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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 <djlevitas208@gmail.commailto:djlevitas208@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 <MHOFFMANN@mgh.harvard.edumailto:MHOFFMANN@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-con... [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Dan Levitas <djlevitas208@gmail.commailto:djlevitas208@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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline https://www.massgeneralbrigham.org/complianceline .