I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough?
Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint.
stephen
Hi Stephen
Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce
On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" stephen.v.sheph...@gmail.com wrote:
Greetings,
I've been reconstructing a surface in an NHP using a Kolster T1 scan and FS5.3. It went very well, at first, but I've hit a wall. I have trouble
in
occipital (due to poor signal strength/constrast) and some
typical-with-NHP
problems in ACC and OFC. I think there are three related questions.
- I lose parts of the ACC near the genu of the corpus callosum. I have
attached a screen shot -- the white matter and gray matter both look
decent.
I wondered if the corpus callosum might be handled specially, and if differences between human and nhp callosi might prevent the ACC from
growing
normally?
- In trying to deal with this, I greyed out the ACA, which was bright
and
potentially confounding. I wasn't sure how to do this in brain.finalsurfs.manedit, since my understanding is that only 1s
(nonbrain)
and 255s (wm) were preserved. I tried brain, which got overwritten, but ultimately succeeded by editing brainmask and rerunning -autorecon2-wm.
Is
there a way to repain gray matter in brain.finalsurfs.manedit?
Alternately,
if I continue editing brainmask (or equivalent) directly, should I be darkening or lightening the gray matter in the excluded section of the
ACC?
I would assume lighten -- but in the OFC, some gray matter (not shown) appears to be excluded for being too bright.
- In some places I've specified wm (e.g. in the ACC, here) but it hasn't
stuck. I assume this is because autorecon isn't convinced by the wm specification after looking at brain.finalsurfs -- how might I (gently!) override this?
Thanks very much for your time and patience.
stephen
<Capture1.PNG><Capture2.PNG>
Hi Stephen
can you upload the whole subject dir? Also, why is there no aseg for this subject? Bruce On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote:
I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough?
Ares of concern are
- ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC?
- OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright.
- Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint.
stephen
Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>
Hi Bruce,
As requested, I'm transferring over the entire folder. It's saved as 140107OTIS_from_Shepherd_attn_Fischl.tar.gz
Our pipeline appears to sidestep aseg (I'm not precisely sure why or how). I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear to be the two key files to target for manual edits. But when I proceed to the next step: recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 -pons-crs 128 255 128 -noaseg there are divots in the grey matter in the ACC just anterior and dorsal to the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in occipital do not appear to be helping. This is easiest to see if I run tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs select a point just to the side of midline (e.g. 125 103 128) and switch to a sagittal view.
Thanks for your help.
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Stephen
can you upload the whole subject dir? Also, why is there no aseg for this subject?
Bruce On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote:
I believe ventricles and callosum are correctly labeled. I've been
viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough?
Ares of concern are
- ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow
grey from CC?
- OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too
bright.
- Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual
overpaint.
stephen
Hi Stephen Are the ventricles and callosum correctly labeled? If you upload asubject I'll try to take a look Cheers Bruce
> On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>
Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd still value your input even though I know you work only with humans.
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:48 PM, S.V.Shepherd [work] < stephen.v.shepherd@gmail.com> wrote:
Hi Bruce,
As requested, I'm transferring over the entire folder. It's saved as 140107OTIS_from_Shepherd_attn_Fischl.tar.gz
Our pipeline appears to sidestep aseg (I'm not precisely sure why or how). I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear to be the two key files to target for manual edits. But when I proceed to the next step: recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 -pons-crs 128 255 128 -noaseg there are divots in the grey matter in the ACC just anterior and dorsal to the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in occipital do not appear to be helping. This is easiest to see if I run
tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs select a point just to the side of midline (e.g. 125 103 128) and switch to a sagittal view.
Thanks for your help.
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Hi Stephen
can you upload the whole subject dir? Also, why is there no aseg for this subject?
Bruce On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote:
I believe ventricles and callosum are correctly labeled. I've been
viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough?
Ares of concern are
- ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow
grey from CC?
- OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too
bright.
- Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual
overpaint.
stephen
Hi Stephen Are the ventricles and callosum correctly labeled? If you upload asubject I'll try to take a look Cheers Bruce
> On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>
Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Stephen
no, sorry. There are others on the list that have extensive experience in using FS for NHP. Hopefully one of them can answer?
Bruce On Mon, 21 Apr 2014, S.V.Shepherd [work] wrote:
Hi,
Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd still value your input even though I know you work only with humans.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:48 PM, S.V.Shepherd [work] stephen.v.shepherd@gmail.com wrote: Hi Bruce,
As requested, I'm transferring over the entire folder. It's saved as 140107OTIS_from_Shepherd_attn_Fischl.tar.gzOur pipeline appears to sidestep aseg (I'm not precisely sure why or how). I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear to be the two key files to target for manual edits. But when I proceed to the next step: recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 -pons-crs 128 255 128 -noaseg there are divots in the grey matter in the ACC just anterior and dorsal to the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in occipital do not appear to be helping. This is easiest to see if I run tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs select a point just to the side of midline (e.g. 125 103 128) and switch to a sagittal view.
Thanks for your help.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
can you upload the whole subject dir? Also, why is there no aseg for this subject? Bruce On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote: I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough? Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint. stephen Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>
Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bruce,
Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well?
Thanks!
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Mon, Apr 21, 2014 at 11:28 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Stephen
no, sorry. There are others on the list that have extensive experience in using FS for NHP. Hopefully one of them can answer?
Bruce
On Mon, 21 Apr 2014, S.V.Shepherd [work] wrote:
Hi,
Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd still value your input even though I know you work only with humans.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:48 PM, S.V.Shepherd [work] stephen.v.shepherd@gmail.com wrote: Hi Bruce,
As requested, I'm transferring over the entire folder. It's saved as 140107OTIS_from_Shepherd_attn_Fischl.tar.gzOur pipeline appears to sidestep aseg (I'm not precisely sure why or how). I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear to be the two key files to target for manual edits. But when I proceed to the next step: recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 -pons-crs 128 255 128 -noaseg there are divots in the grey matter in the ACC just anterior and dorsal to the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in occipital do not appear to be helping. This is easiest to see if I run tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs select a point just to the side of midline (e.g. 125 103 128) and switch to a sagittal view.
Thanks for your help.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
can you upload the whole subject dir? Also, why is there no aseg for this subject? Bruce On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote: I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough? Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint. stephen Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>
Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Stephen
why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean)
cheers Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well?
Thanks!
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Mon, Apr 21, 2014 at 11:28 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
no, sorry. There are others on the list that have extensive experience in using FS for NHP. Hopefully one of them can answer? Bruce On Mon, 21 Apr 2014, S.V.Shepherd [work] wrote: Hi, Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd still value your input even though I know you work only with humans. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Wed, Apr 16, 2014 at 10:48 PM, S.V.Shepherd [work] <stephen.v.shepherd@gmail.com> wrote: Hi Bruce, As requested, I'm transferring over the entire folder. It's saved as 140107OTIS_from_Shepherd_attn_Fischl.tar.gz Our pipeline appears to sidestep aseg (I'm not precisely sure why or how). I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear to be the two key files to target for manual edits. But when I proceed to the next step: recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 -pons-crs 128 255 128 -noaseg there are divots in the grey matter in the ACC just anterior and dorsal to the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in occipital do not appear to be helping. This is easiest to see if I run tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs select a point just to the side of midline (e.g. 125 103 128) and switch to a sagittal view. Thanks for your help. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen can you upload the whole subject dir? Also, why is there no aseg for this subject? Bruce On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote: I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough? Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint. stephen Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...@gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG> _______________________________________________ Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi Bruce,
This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial).
My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses.
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Stephen
why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean)
cheers Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well?
Thanks!
stephen
Hi Stephen
only the thickness estimates should matter, unless you've lost an entire gyrus or something Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial).
My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean) cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well? Thanks! stephen
Hi Bruce,
How would I go about updating the thickness estimates (?h.thickness, I presume) after manually adjusting the pial surface in FreeView? Are the other surfaces (inflated, sphere, etc.) unaffected by this change, or should they be recalculated as well?
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Stephen
only the thickness estimates should matter, unless you've lost an entire gyrus or something
Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial).
My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
why do you say it invalidates the morphometry? And we need to knowwhat pial surface editing you did in order to answer your questions (and what recon-all steps you rerean)
cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I'vecorrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well?
Thanks! stephen
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Looking over our scripts, it appears we normally generates the surfaces etc. through recon-all -autorecon2-wm <...> -noaseg despite that ?h.pial isn't explicitly listed as an output in the dev table ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).
It looks like a step from autorecon3 might be useful: mris_make_surfaces <subjID> ?h -orig_white ?h.orig orig_pial ?h.pial to update the curvature and thickness files without changing the wm and pial -- but I'm not sure this is how it works.
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work] < stephen.v.shepherd@gmail.com> wrote:
Hi Bruce,
How would I go about updating the thickness estimates (?h.thickness, I presume) after manually adjusting the pial surface in FreeView? Are the other surfaces (inflated, sphere, etc.) unaffected by this change, or should they be recalculated as well?
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Stephen
only the thickness estimates should matter, unless you've lost an entire gyrus or something
Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial).
My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen
why do you say it invalidates the morphometry? And we need to knowwhat pial surface editing you did in order to answer your questions (and what recon-all steps you rerean)
cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I'vecorrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well?
Thanks! stephen
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
don't rerun that as it will rerun the surface deformation. Use mris_thickness and mris_curvature
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Looking over our scripts, it appears we normally generates the surfaces etc. through recon-all -autorecon2-wm <...> -noaseg despite that ?h.pial isn't explicitly listed as an output in the dev table (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).
It looks like a step from autorecon3 might be useful: mris_make_surfaces <subjID> ?h -orig_white ?h.orig orig_pial ?h.pial to update the curvature and thickness files without changing the wm and pial -- but I'm not sure this is how it works.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work] stephen.v.shepherd@gmail.com wrote: Hi Bruce,
How would I go about updating the thickness estimates (?h.thickness, I presume) after manually adjusting the pial surface in FreeView? Are the other surfaces (inflated, sphere, etc.) unaffected by this change, or should they be recalculated as well? stephenstephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
only the thickness estimates should matter, unless you've lost an entire gyrus or something Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial). My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean) cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well? Thanks! stephen
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Just to follow up, it looks like mris_thickness needs to be run, but mris_curvature is unchanged by changes to the pial surface. Thanks again for the help!
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
don't rerun that as it will rerun the surface deformation. Use mris_thickness and mris_curvature
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Looking over our scripts, it appears we normally generates the surfaces
etc. through recon-all -autorecon2-wm <...> -noaseg despite that ?h.pial isn't explicitly listed as an output in the dev table (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).
It looks like a step from autorecon3 might be useful: mris_make_surfaces <subjID> ?h -orig_white ?h.orig orig_pial ?h.pial to update the curvature and thickness files without changing the wm and pial -- but I'm not sure this is how it works.
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work] < stephen.v.shepherd@gmail.com> wrote: Hi Bruce,
How would I go about updating the thickness estimates(?h.thickness, I presume) after manually adjusting the pial surface in FreeView? Are the other surfaces (inflated, sphere, etc.) unaffected by this change, or should they be recalculated as well?
stephenstephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
only the thickness estimates should matter, unless you've lost anentire gyrus or something Bruce
On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial). My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean) cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well? Thanks! stephen
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
the pial curvatures will change, but you probably don't use them anyway
cheers Bruce
On Tue, 13 May 2014, S.V.Shepherd [work] wrote:
Just to follow up, it looks like mris_thickness needs to be run, but mris_curvature is unchanged by changes to the pial surface. Thanks again for the help!
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 9:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: don't rerun that as it will rerun the surface deformation. Use mris_thickness and mris_curvature
On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Looking over our scripts, it appears we normally generates the surfaces etc. through recon-all -autorecon2-wm <...> -noaseg despite that ?h.pial isn't explicitly listed as an output in the dev table (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable). It looks like a step from autorecon3 might be useful: mris_make_surfaces <subjID> ?h -orig_white ?h.orig orig_pial ?h.pial to update the curvature and thickness files without changing the wm and pial -- but I'm not sure this is how it works. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work] <stephen.v.shepherd@gmail.com> wrote: Hi Bruce, How would I go about updating the thickness estimates (?h.thickness, I presume) after manually adjusting the pial surface in FreeView? Are the other surfaces (inflated, sphere, etc.) unaffected by this change, or should they be recalculated as well? stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen only the thickness estimates should matter, unless you've lost an entire gyrus or something Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial). My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean) cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well? Thanks! stephen _______________________________________________ Freesurfer mailing list 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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just use mris_thickness. The others should be fine On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
Hi Bruce,
How would I go about updating the thickness estimates (?h.thickness, I presume) after manually adjusting the pial surface in FreeView? Are the other surfaces (inflated, sphere, etc.) unaffected by this change, or should they be recalculated as well?
stephen
stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620
On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Stephen
only the thickness estimates should matter, unless you've lost an entire gyrus or something Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, This is the manual edit of the pial surface in FreeView, correcting locations where the grey matter failed to grow out of the white matter. It took place after the pipeline had completed, but I'm not sure if I need to rerun/regenerate steps which are dependent on the pial surface. For example, are mris_sphere, mris_curvature, and mris_flatten dependent upon the pial surface or cortical thickness, or do they work directly off the wm/orig surface? If the former, I should rerun them; if the latter I don't need to do anything but just repaint the functional statistics of interest using mri_vol2surf and the updated cortical bounds (which I presume happens automatically, having corrected ?h.pial). My comment about morphometry was meant to note that, since I'm manually changing the distance between the wm and pial surface in places where there were medial surface artifacts, it would be unwise to try to draw any conclusions from comparing manually-adjusted and automatically-calculated cortical thicknesses. stephen stephen v. shepherd phd The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Stephen why do you say it invalidates the morphometry? And we need to know what pial surface editing you did in order to answer your questions (and what recon-all steps you rerean) cheers Bruce On Sun, 11 May 2014, S.V.Shepherd [work] wrote: Hi Bruce, Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well? Thanks! stephen
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