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> 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> 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 <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Dan Levitas <
>> 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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