Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
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 Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
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! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
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
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote:
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi...
Thanks, Dan
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
That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”).
I think some of the subsequent back-and-forth with Bruce and Nick was off the list, so I’ve included the key email (where Bruce diagnosed the problem) below.
Has this been fixed in the forthcoming FS 6.0?
thanks, -MH
**** snip ****
ok, I see what's going on. Here is the sequence of calls:
1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs L408_base lh
Makes the white surface *without* using the aparc. Because there are a string of "hypointensity" labels in the aseg, the white surface is frozen in these locations.
2. mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base lh
internally recreates the white surface but doesn't save it. The frozen vertices are allowed to move since the aparc *is* used in this call, and the vertices are deemed to be in real cortical regions.
The pial surface then starts from the (inwards deformed but not written to disk) white surface, and then settles inside the white surface that is on disk.
I'm not sure how we settled on this logic. Why recreate the white surface? Why not run with -nowhite -orig_pial white? That way the algorithm uses the white surface that the user can see and things should be consistent
Bruce
**** end-snip ****
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 4/21/16, 9:41 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgw" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgwakeman@gmail.com> wrote:
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote:
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
none of the edits were incorporated.
Is the FLAIRpial flag incompatible with autorecon2-wm?
Is there some other misake?
I followed this guide
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits _freeview
Thanks, Dan
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 materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Hi Mike
yes, I think it is fixed. Daniel: can you try out dev and see if it fixes this for you? Bruce
On Thu, 21 Apr 2016, Harms, Michael wrote:
That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”).
I think some of the subsequent back-and-forth with Bruce and Nick was off the list, so I’ve included the key email (where Bruce diagnosed the problem) below.
Has this been fixed in the forthcoming FS 6.0?
thanks, -MH
**** snip ****
ok, I see what's going on. Here is the sequence of calls:
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh
Makes the white surface *without* using the aparc. Because there are a string of "hypointensity" labels in the aseg, the white surface is frozen in these locations.
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh
internally recreates the white surface but doesn't save it. The frozen vertices are allowed to move since the aparc *is* used in this call, and the vertices are deemed to be in real cortical regions.
The pial surface then starts from the (inwards deformed but not written to disk) white surface, and then settles inside the white surface that is on disk.
I'm not sure how we settled on this logic. Why recreate the white surface? Why not run with -nowhite -orig_pial white? That way the algorithm uses the white surface that the user can see and things should be consistent
Bruce
**** end-snip ****
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 4/21/16, 9:41 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgw" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgwakeman@gmail.com> wrote:
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote:
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote: > Hi, > > I recently edited a brain with a gyral cyst, carefully filling the > cyst with white matter in the wm.mgz. Unfortunately after running: > /usr/local/freesurfer/stable5_3_0/bin/recon-all > -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 > > none of the edits were incorporated. > > Is the FLAIRpial flag incompatible with autorecon2-wm? > > Is there some other misake? > > I followed this guide > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits > _freeview > > Thanks, > Dan
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 materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I solved it (with help from a colleague) by just calling the individual mri_make_surfaces command separately (adjusting the nowhite), and the subsequent ones through the flair pial command. I am now running -make all, to finish the rest (note it did miss one step in the re-start: it didn't re-run mris_calc, for bug hunting purposes), I will re-run after it finishes.
Thanks everyone! d
On Thu, Apr 21, 2016 at 4:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mike
yes, I think it is fixed. Daniel: can you try out dev and see if it fixes this for you? Bruce
On Thu, 21 Apr 2016, Harms, Michael wrote:
That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”).
I think some of the subsequent back-and-forth with Bruce and Nick was off the list, so I’ve included the key email (where Bruce diagnosed the problem) below.
Has this been fixed in the forthcoming FS 6.0?
thanks, -MH
**** snip ****
ok, I see what's going on. Here is the sequence of calls:
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh
Makes the white surface *without* using the aparc. Because there are a string of "hypointensity" labels in the aseg, the white surface is frozen in these locations.
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh
internally recreates the white surface but doesn't save it. The frozen vertices are allowed to move since the aparc *is* used in this call, and the vertices are deemed to be in real cortical regions.
The pial surface then starts from the (inwards deformed but not written to disk) white surface, and then settles inside the white surface that is on disk.
I'm not sure how we settled on this logic. Why recreate the white surface? Why not run with -nowhite -orig_pial white? That way the algorithm uses the white surface that the user can see and things should be consistent
Bruce
**** end-snip ****
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 4/21/16, 9:41 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgw" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgwakeman@gmail.com> wrote:
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote:
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked On Tue, 19 Apr 2016, dgw wrote:
> Just to follow up, I have tried several different options with > recon-all to get the white matter edits to stick on this participant, > and it doesn't seem to be working: > > re-editing wm.mgz and running recon-all -autorecon2-wm > re-editing wm.mgz and running recon-all -make all > > I can't seem to get any appreciable change in the white matter > surface. I have attached a screenshot, for an example. > > hth > d > > > On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote: >> >> Hi, >> >> I recently edited a brain with a gyral cyst, carefully filling the >> cyst with white matter in the wm.mgz. Unfortunately after running: >> /usr/local/freesurfer/stable5_3_0/bin/recon-all >> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 >> >> none of the edits were incorporated. >> >> Is the FLAIRpial flag incompatible with autorecon2-wm? >> >> Is there some other misake? >> >> I followed this guide >> >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >> _freeview >> >> Thanks, >> Dan > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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yes, I think that's what V6 does I think On Thu, 21 Apr 2016, dgw wrote:
Hi,
I solved it (with help from a colleague) by just calling the individual mri_make_surfaces command separately (adjusting the nowhite), and the subsequent ones through the flair pial command. I am now running -make all, to finish the rest (note it did miss one step in the re-start: it didn't re-run mris_calc, for bug hunting purposes), I will re-run after it finishes.
Thanks everyone! d
On Thu, Apr 21, 2016 at 4:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Mike
yes, I think it is fixed. Daniel: can you try out dev and see if it fixes this for you? Bruce
On Thu, 21 Apr 2016, Harms, Michael wrote:
That looks very similar in principle to something I posted back in Oct. 2014 (“pial surface crossing white”).
I think some of the subsequent back-and-forth with Bruce and Nick was off the list, so I’ve included the key email (where Bruce diagnosed the problem) below.
Has this been fixed in the forthcoming FS 6.0?
thanks, -MH
**** snip ****
ok, I see what's going on. Here is the sequence of calls:
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh
Makes the white surface *without* using the aparc. Because there are a string of "hypointensity" labels in the aseg, the white surface is frozen in these locations.
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh
internally recreates the white surface but doesn't save it. The frozen vertices are allowed to move since the aparc *is* used in this call, and the vertices are deemed to be in real cortical regions.
The pial surface then starts from the (inwards deformed but not written to disk) white surface, and then settles inside the white surface that is on disk.
I'm not sure how we settled on this logic. Why recreate the white surface? Why not run with -nowhite -orig_pial white? That way the algorithm uses the white surface that the user can see and things should be consistent
Bruce
**** end-snip ****
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 4/21/16, 9:41 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgw" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgwakeman@gmail.com> wrote:
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote:
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > > can you send us the recon-all.log? I don't see an obvious reason why > it > wouldn't have worked > On Tue, 19 Apr 2016, dgw wrote: > >> Just to follow up, I have tried several different options with >> recon-all to get the white matter edits to stick on this participant, >> and it doesn't seem to be working: >> >> re-editing wm.mgz and running recon-all -autorecon2-wm >> re-editing wm.mgz and running recon-all -make all >> >> I can't seem to get any appreciable change in the white matter >> surface. I have attached a screenshot, for an example. >> >> hth >> d >> >> >> On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote: >>> >>> Hi, >>> >>> I recently edited a brain with a gyral cyst, carefully filling the >>> cyst with white matter in the wm.mgz. Unfortunately after running: >>> /usr/local/freesurfer/stable5_3_0/bin/recon-all >>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 >>> >>> none of the edits were incorporated. >>> >>> Is the FLAIRpial flag incompatible with autorecon2-wm? >>> >>> Is there some other misake? >>> >>> I followed this guide >>> >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits >>> _freeview >>> >>> Thanks, >>> Dan >> >> > _______________________________________________ > 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 Daniel
I'm out if town , can you remind me next week? This is fixed in v6 I think if you want to just run the pial stuff in it Bruce
On Apr 21, 2016, at 10:41 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote: Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked
On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
> On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote: > Hi, > > I recently edited a brain with a gyral cyst, carefully filling the > cyst with white matter in the wm.mgz. Unfortunately after running: > /usr/local/freesurfer/stable5_3_0/bin/recon-all > -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 > > none of the edits were incorporated. > > Is the FLAIRpial flag incompatible with autorecon2-wm? > > Is there some other misake? > > I followed this guide > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi... > > Thanks, > Dan
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<pial_surface.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Harms, Michael