Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

Wed, 08 Feb 2017 17:14:02 -0800 

Hi Qian

if you look at the recon-all help you will see:

USAGE: recon-all

 Required Arguments:
   -subjid <subjid>
   -<process directive>

 Fully-Automated Directive:
  -all           : performs all stages of cortical reconstruction
  -autorecon-all : same as -all

 Manual-Intervention Workflow Directives:
  -autorecon1    : process stages 1-5 (see below)
  -autorecon2    : process stages 6-23
                   after autorecon2, check white surfaces:
                     a. if wm edit was required, then run -autorecon2-wm
                     b. if control points added, then run -autorecon2-cp
                     c. proceed to run -autorecon3
-autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) 
  -autorecon2-wm : process stages 15-23
  -autorecon2-inflate1 : 6-18
-autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon 
  -autorecon3    : process stages 24-34
if edits made to correct pial, then run -autorecon-pial 
  -hemi ?h       : just do lh or rh (default is to do both)


the pial surface regeneration is now part of autorecon3

cheers
Bruce
On Thu, 9 Feb 2017, 冉倩 wrote: 



Hi Bruce,
I am a little confused about it. I found 'Manual-Intervention Workflow
Directives' on recon-all free surfer wiki web. 
[IMAGE]
It said if edits made to correct pial, run-autorecon2-pial. 
If I only edit pial, I run >recon-all -autrecon-pial -s <subject id> -sd
<subjects_dir> to fix this issue, I also should rerunning autorecon3? or
which command I should use to continue to next step? Thanks a lot.
Best Regards,
Qian Ran



At 2017-02-09 08:55:34, "Bruce Fischl" <[email protected]> wrote:
>Hi Qian
>
>if you just want to regenerate the pial, then yes, edit the >brain.finalsurfs.mgz and run: 
>
>recon-all -autrecon-pial -s <subject id> -sd <subjects_dir>
>
>note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the

>'2')
>
>cheeers
>Bruce
>
>
>On Thu, 9 Feb 2017, 冉倩 wrote:
>
>> Hi Bruce,
>> If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid
>> sub01 or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3
>> still need rerunning? Thanks!
>> Best Regards,
>> Qian Ran
>> >> >> >> >> At 2017-02-08 12:19:35, "Bruce Fischl" <[email protected]> wrote 
:
>> brain.finalsurfs is fine if you are just rerunning the pial. Edit
>> brainmask if you are starting earlier so all the downstream volumes
>> including brain.finalsurfs will have the dura removed
>> Cheers
>> Bruce
>> >> On Feb 7, 2017, at 10:45 PM, 冉倩 <[email protected]> wrote: >> >> >> >> 
>>       brain.finalsurfs.mgz? not brainmask.mgz? 
>> or brain.finalsurfs.mgz for pial surface edit and brainmask for
>> wm surface edit?
>> >> >> At 2017-02-08 11:41:40, "Douglas Greve" 
>> <[email protected]> wrote:
>>
>>       You should edit the brain.finalsurfs.mgz to remove
>>       the non-brain then run with -autorecon-pial
>> >> 
>>       On 2/7/17 10:37 PM, 冉倩 wrote:
>> >> 
>>       Hi Prof.Douglas Greve,
>> >> Yes, probematic surface normally existed near 
>> supeiror dura ( aroun superior frontal lobe or
>> parietal lobe or central gry area). Just now I am
>> confused about the next steps.  If I manually erase
>> ( whether I can modfiy control point just like
>> modify wm) the dura on the brainmask.mgz to correct
>> pial surface. Then I shoud re-run command: recon-all
>> -autorecon2 -autorecon-3 sub01? or just recon-all
>> -autorecon2-pial -autorecon3 sub01? Thanks!
>> >> Best Regards, 
>> Qian Ran
>> >> At 2017-02-08 11:21:57, "Douglas Greve" 
>> <[email protected]> wrote:
>>
>>       I think Bruce is referring only to the
>>       first image. For the second image, it
>>       looks like most of the problematic
>>       surface is going through the amygdala or
>>       hippocampus in which case it does not
>>       need to be fixed.
>> >> 
>>       On 2/7/17 9:57 PM, Bruce Fischl wrote:
>>       oh yes, it's grabbing a bit of
>>       dura. If you have a 1mm-ish T2 or
>>       FLAIR you can use it to
>>       automatically correct this type of
>>       problem. Or you can erase the dura
>>       in those regions on the
>>       brainmask.mgz and recreate the
>>       pial surface
>>
>>       cheers
>>       Bruce
>> >> >> 
>>       On Wed, 8 Feb 2017, 冉倩 wrote:
>>
>>             Hi Bruce,
>>             Thanks for your reply.
>>
>>             [IMAGE]
>>             For this, I think pial
>>             surface  (the location
>>             where I circle)
>>              already
>>             located outside of
>>             brain. 
>>             [IMAGE]
>>             For this, pail surface
>>             (near hippcamps I
>>             think) located inside
>>             of cortical I
>>             think. 
>>
>>             I mean if I manually
>>             modify surface, how do
>>             it? Thanks very much!
>>             Best Regards,
>>             Qian Ran
>>
>>             At 2017-02-08
>>             09:54:30, "Bruce
>>             Fischl"
>>             <[email protected]>
>>             wrote:
>>             >Hi Qian
>>             >
>>             >I'm not sure I
>>             understand what you
>>             think is wrong in the
>>             images you >included.
>>             The first two
>>             locations look quite
>>             accurate to me, and
>>             I'm not >positive but
>>             I think the third
>>             image the locations
>>             you circle are
>>             amygdala,
>>
>>             >so not neocortical at
>>             all
>>             >
>>             >cheers
>>             >Bruce
>>             >
>>             >
>>             >
>>             >
>>             >
>>             >On Wed, 8 Feb 2017,
>>             冉倩 wrote:
>>             >
>>             >> >> >> Dear
>>             Prof.Douglas Greve,
>>             >>  Thanks for your
>>             reply. I add parts of
>>             problem screenshot of
>>             white/pial
>>             >> surface. 
>>             >> >>   When I did
>>             freesurfer for
>>             structure analysis, I
>>             was confused by some
>>             st
>>             eps
>>             >> and results. The
>>             analysis stream was:
>>             >> >> 1st: check data
>>             orientation
>>             >> >> 2nd : convert
>>             nii.gz  to mgz
>>             >> >> 3rd: recon-all
>>             –all –subjid sub01
>>             >> >> After these
>>             steps finished , I
>>             checked skullstrip,
>>             segmentation quality.
>>             The
>>             >> problems as
>>             following:
>>             >> >> 1st: skullstrip
>>             result not very well,
>>             almost need manually
>>             operation.
>>             >> >>      After
>>             manually operation, I
>>             run:
>>             >> >>  recon-all
>>             –autorecon2
>>             –autorecon3 –subjid
>>             sub01
>>             >> >> 2nd: parts of
>>             white surface and pial
>>             surface not very
>>             exactly. I only did
>>             >> adding control
>>             points to modify white
>>             surface, then I run:
>>             >> >>        Recon-all
>>             –autorecon2-cp
>>             –autorecon3 –subjid
>>             sub01 brainmask.mgz
>>             >> >> Several parts of
>>             pial surface exit
>>             errors. I added these
>>             as screenshot:
>>             >> >> >> >> >> [IMAGE]
>>             >> >> [IMAGE]
>>             >> [IMAGE]
>>             >> [IMAGE]
>>             >> >> [IMAGE]
>>             >> >> So when I met
>>             such issues, I should
>>             add control points for
>>             pial surface  as
>>             >> white surface did
>>             (or how I correct or
>>             edit pial; still use
>>             tkmedit tool?
>>             ) ?
>>             >> Then I run: 
>>             >> >> recon-all
>>             –autorecon2-pial 
>>             –autorecon3 sub01 ?
>>             >> >> If white surface
>>             and pial surface all
>>             needed manually
>>             operated, whether I
>>             >> could do like this:
>>             I add control points
>>             (-cp), edit wm (-wm),
>>             correct pi
>>             al
>>             >> (-pial ) at the
>>             same time, then I run:
>>             >> >> recon-all
>>             –autorecon2-cp
>>             –autorecon2-wm
>>             –autorecon2-pail
>>             –autorecon3 sub0
>>             1
>>             >> or recon-all
>>             -autorecon2-cp brainmask.mgz
>>             -autorecon2-wm
>>             -autorecon2-pial
>>             >> -autorecon3 sub01?
>>             >> >> or any other
>>             suggestions?
>>             >> >> Thanks very
>>             much!
>>             >> Best Regards,
>>             >> Qian Ran
>>             >> >> At 2017-02-08
>>             07:18:51, "Douglas
>>             Greve"
>>             <[email protected]>
>>             wrote
>>             :
>>             >>
>>             >>       Hi Qian,
>>             things will be a lot
>>             easier if you imbed
>>             your comments
>>             >>       and images in
>>             the email. From the
>>             text, I can't tell
>>             what you
>>             >>       want exactly.
>>             The first question had
>>             to do with skull
>>             stripping.
>>             >>       It looks like
>>             you had to make a
>>             manual edit. This is
>>             expected
>>             >>       sometimes. 
>>             If it is more than
>>             that, what is the
>>             problem. In the
>>             >>       second
>>             question, you had some
>>             problem with the
>>             quality of the
>>             >>       white/pial
>>             surfaces, but there
>>             was not much detail or
>>             a picture.
>>             >> >> >>
>>             >>       On 2/7/17
>>             8:22 AM, 冉倩 wrote:
>>             >>       Hello
>>             Freesurfer Developers,
>>             >> I have had last
>>             September Freesurfer
>>             course. When I
>>             operated my
>>             >> data following that
>>             stream I met some
>>             problem in reon-all
>>             -all
>>             >> step. Because I
>>             need put some
>>             screenshout to
>>             exaplain that
>>             >> problems, I add
>>             word document in
>>             attachment. Thanks
>>             very much!
>>             >> Best Regards,
>>             >> Qian Ran
>>             >> >> >>  
>>             >> >> >> >>
>>             _______________________________________________
>>             >> Freesurfer mailing
>>             list
>>             >>
>>             [email protected]
>>             >>
>>             https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>             >> >> >> >> >>  
>>             >> >> >>
>> >> 
>>              
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