Does the beta permit volumes bigger than 256^3 voxels? just asking....and just asking about raw dimensions in unit-voxels at the start of pipeline
cheers
Colin
On 18 January 2013 17:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- v5.2.0 beta, round two (Nick Schmansky)
- Re: pial not computing (Borzello, Mia)
- Re: pial not computing (Bruce Fischl)
- Re: FW: longitudinal analysis (Alex Hanganu)
---------- Forwarded message ---------- From: Nick Schmansky nicks@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:20:43 -0500 Subject: [Freesurfer] v5.2.0 beta, round two For those willing and brave enough, another beta of v5.2.0 has been posted here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard is 32b).
The final release still awaits some critical improvements to the Tracula stream, but the main recon-all stream with this beta is final. The final release is expected the first week of February.
Freesurfer team
---------- Forwarded message ---------- From: "Borzello, Mia" MBORZELLO@partners.org To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 16:25:40 +0000 Subject: Re: [Freesurfer] pial not computing great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but
not the rh.pial. What would be the cause of this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Borzello, Mia" MBORZELLO@partners.org Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Fri, 18 Jan 2013 11:28:00 -0500 Subject: Re: [Freesurfer] pial not computing it's run as part of recon-all. If you grab a new one and run
recon-all -make all ...
you should be all set Bruce
On Fri, 18 Jan 2013, Borzello, Mia wrote:
great. is there a freesurfer page on mris_topo_fixer? I'm not sure
how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ______________________________**__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ______________________________**__________ From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu[ freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Alex Hanganu al.hanganu@yahoo.ca To: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:39:31 -0500 Subject: Re: [Freesurfer] FW: longitudinal analysis Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
Date: Fri, 18 Jan 2013 08:54:48 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] longitudinal analysis
Hi Paul
can you cc the list so that others can answer?
thanks Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi Brian,
Thanks for your reply.
I am running freesurfer 4.5.0. We are using the older version so that
the
analyses performed are the same across subjects.
Best wishes
Paul
Date: Fri, 18 Jan 2013 08:21:05 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analysis
Hi Paul
what is the actual binary being run?
Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi guys,
I am currently running a longitudinal analysis on a set of scan. It
is
currently running and so far it has taken 5 days. It seems to be
taking a
large amount of time on a process called labelling slice. I have run
the
same analysis on other subjects which took about 6 hours to
complete. So
I
was wondering if you know of any reason why a set of scans would
take long
er
to process than others. I have checked the inital scans and nothing
seems
obviously wrong with them.
Best Wishes
Paul
_______________________________________________ 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.
Colin,
It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible.
Nick
Does the beta permit volumes bigger than 256^3 voxels? just asking....and just asking about raw dimensions in unit-voxels at the start of pipeline
cheers
Colin
On 18 January 2013 17:00, freesurfer-request@nmr.mgh.harvard.edu wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- v5.2.0 beta, round two (Nick Schmansky)
- Re: pial not computing (Borzello, Mia)
- Re: pial not computing (Bruce Fischl)
- Re: FW: longitudinal analysis (Alex Hanganu)
---------- Forwarded message ---------- From: Nick Schmansky nicks@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:20:43 -0500 Subject: [Freesurfer] v5.2.0 beta, round two For those willing and brave enough, another beta of v5.2.0 has been posted here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard is 32b).
The final release still awaits some critical improvements to the Tracula stream, but the main recon-all stream with this beta is final. The final release is expected the first week of February.
Freesurfer team
---------- Forwarded message ---------- From: "Borzello, Mia" MBORZELLO@partners.org To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 16:25:40 +0000 Subject: Re: [Freesurfer] pial not computing great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but
not the rh.pial. What would be the cause of this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Borzello, Mia" MBORZELLO@partners.org Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Fri, 18 Jan 2013 11:28:00 -0500 Subject: Re: [Freesurfer] pial not computing it's run as part of recon-all. If you grab a new one and run
recon-all -make all ...
you should be all set Bruce
On Fri, 18 Jan 2013, Borzello, Mia wrote:
great. is there a freesurfer page on mris_topo_fixer? I'm not sure
how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ______________________________**__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ______________________________**__________ From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu[ freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Alex Hanganu al.hanganu@yahoo.ca To: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:39:31 -0500 Subject: Re: [Freesurfer] FW: longitudinal analysis Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
Date: Fri, 18 Jan 2013 08:54:48 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] longitudinal analysis
Hi Paul
can you cc the list so that others can answer?
thanks Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi Brian,
Thanks for your reply.
I am running freesurfer 4.5.0. We are using the older version so
that the
analyses performed are the same across subjects.
Best wishes
Paul
Date: Fri, 18 Jan 2013 08:21:05 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analysis
Hi Paul
what is the actual binary being run?
Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi guys,
I am currently running a longitudinal analysis on a set of scan.
It is
currently running and so far it has taken 5 days. It seems to be
taking a
large amount of time on a process called labelling slice. I have
run the
same analysis on other subjects which took about 6 hours to
complete. So
I
was wondering if you know of any reason why a set of scans would
take long
er
to process than others. I have checked the inital scans and
nothing seems
obviously wrong with them.
Best Wishes
Paul
_______________________________________________ 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh
On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Colin,
It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible.
Nick
Does the beta permit volumes bigger than 256^3 voxels? just asking....and just asking about raw dimensions in unit-voxels at the start of pipeline
cheers
Colin
On 18 January 2013 17:00, freesurfer-request@nmr.mgh.harvard.edu
wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- v5.2.0 beta, round two (Nick Schmansky)
- Re: pial not computing (Borzello, Mia)
- Re: pial not computing (Bruce Fischl)
- Re: FW: longitudinal analysis (Alex Hanganu)
---------- Forwarded message ---------- From: Nick Schmansky nicks@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:20:43 -0500 Subject: [Freesurfer] v5.2.0 beta, round two For those willing and brave enough, another beta of v5.2.0 has been posted here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard is 32b).
The final release still awaits some critical improvements to the Tracula stream, but the main recon-all stream with this beta is final. The final release is expected the first week of February.
Freesurfer team
---------- Forwarded message ---------- From: "Borzello, Mia" MBORZELLO@partners.org To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 16:25:40 +0000 Subject: Re: [Freesurfer] pial not computing great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but
not the rh.pial. What would be the cause of this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Borzello, Mia" MBORZELLO@partners.org Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Fri, 18 Jan 2013 11:28:00 -0500 Subject: Re: [Freesurfer] pial not computing it's run as part of recon-all. If you grab a new one and run
recon-all -make all ...
you should be all set Bruce
On Fri, 18 Jan 2013, Borzello, Mia wrote:
great. is there a freesurfer page on mris_topo_fixer? I'm not sure
how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ______________________________**__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ______________________________**__________ From: freesurfer-bounces@nmr.mgh.**harvard.edu<
freesurfer-bounces@nmr.mgh.harvard.edu>[
freesurfer-bounces@nmr.mgh.**harvard.edu<
freesurfer-bounces@nmr.mgh.harvard.edu>]
on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
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______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
---------- Forwarded message ---------- From: Alex Hanganu al.hanganu@yahoo.ca To: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:39:31 -0500 Subject: Re: [Freesurfer] FW: longitudinal analysis Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
Date: Fri, 18 Jan 2013 08:54:48 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] longitudinal analysis
Hi Paul
can you cc the list so that others can answer?
thanks Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi Brian,
Thanks for your reply.
I am running freesurfer 4.5.0. We are using the older version so
that the
analyses performed are the same across subjects.
Best wishes
Paul
Date: Fri, 18 Jan 2013 08:21:05 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analysis
Hi Paul
what is the actual binary being run?
Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi guys,
I am currently running a longitudinal analysis on a set of scan.
It is
currently running and so far it has taken 5 days. It seems to be
taking a
large amount of time on a process called labelling slice. I have
run the
same analysis on other subjects which took about 6 hours to
complete. So
I
was wondering if you know of any reason why a set of scans would
take long
er
to process than others. I have checked the inital scans and
nothing seems
obviously wrong with them.
Best Wishes
Paul
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contains
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just to be clear:
my question is indeed about very high resoliution data. but it is at present possible to use freesurfer with any resolution you like; you simply fake nifti-headers or do whatever you need to do such that the data appears 1mm, and then you can rescale meshes if you need to afterwards. and so on.
You can't do with with just "recon-all" you need to look things up and write your own "recon-all" with FS components for your data.
however there is still a hard limit on 256 voxels. it doesn't matter what size you call them, that's the limit.
if you have more there is no trick way around it (if you want a dense, well fitted mesh commensurate with the MRI data, obviously you can downsample the MRI data).
Whether recon-all and FS in general will deal excplicitly with sub 1mm, or with >256^3 data I do not know.
I'd suspect that it will and will be called freesufer V6.0.
I was jusk asking if this beta 5.2 happens to do >256 in a raw sense for e.g. mri-tesselate
On 21 January 2013 19:59, Joshua Lee jkilee@ucdavis.edu wrote:
Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh
On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky <nicks@nmr.mgh.harvard.edu
wrote:
Colin,
It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible.
Nick
Does the beta permit volumes bigger than 256^3 voxels? just
asking....and
just asking about raw dimensions in unit-voxels at the start of pipeline
cheers
Colin
On 18 January 2013 17:00, freesurfer-request@nmr.mgh.harvard.edu
wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- v5.2.0 beta, round two (Nick Schmansky)
- Re: pial not computing (Borzello, Mia)
- Re: pial not computing (Bruce Fischl)
- Re: FW: longitudinal analysis (Alex Hanganu)
---------- Forwarded message ---------- From: Nick Schmansky nicks@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:20:43 -0500 Subject: [Freesurfer] v5.2.0 beta, round two For those willing and brave enough, another beta of v5.2.0 has been posted here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard
is
32b).
The final release still awaits some critical improvements to the
Tracula
stream, but the main recon-all stream with this beta is final. The final release is expected the first week of February.
Freesurfer team
---------- Forwarded message ---------- From: "Borzello, Mia" MBORZELLO@partners.org To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 16:25:40 +0000 Subject: Re: [Freesurfer] pial not computing great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no
cerebellum
or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fischl@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed,
but
not the rh.pial. What would be the cause of this?
Thanks, m
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Borzello, Mia" MBORZELLO@partners.org Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Fri, 18 Jan 2013 11:28:00 -0500 Subject: Re: [Freesurfer] pial not computing it's run as part of recon-all. If you grab a new one and run
recon-all -make all ...
you should be all set Bruce
On Fri, 18 Jan 2013, Borzello, Mia wrote:
great. is there a freesurfer page on mris_topo_fixer? I'm not sure
how/where to run this and I don't see a page on the freesurfer site.
Thanks so much, m ______________________________**__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new
mris_topo_fixer
and you rerun and it should be all set. You probably should take a
look
at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ______________________________**__________ From: freesurfer-bounces@nmr.mgh.**harvard.edu<
freesurfer-bounces@nmr.mgh.harvard.edu>[
freesurfer-bounces@nmr.mgh.**harvard.edu<
freesurfer-bounces@nmr.mgh.harvard.edu>]
on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers, > > I just ran a recon, and it seems that only the lh.pial computed,
but
> not the rh.pial. What would be the cause of this? > Thanks, > m > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
> > > > ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
---------- Forwarded message ---------- From: Alex Hanganu al.hanganu@yahoo.ca To: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:39:31 -0500 Subject: Re: [Freesurfer] FW: longitudinal analysis Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
Date: Fri, 18 Jan 2013 08:54:48 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] longitudinal analysis
Hi Paul
can you cc the list so that others can answer?
thanks Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi Brian,
Thanks for your reply.
I am running freesurfer 4.5.0. We are using the older version so
that the
analyses performed are the same across subjects.
Best wishes
Paul
Date: Fri, 18 Jan 2013 08:21:05 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analysis
Hi Paul
what is the actual binary being run?
Bruce On Fri, 18 Jan 2013, paul horton wrote:
> Hi guys, > > I am currently running a longitudinal analysis on a set of scan.
It is
> currently running and so far it has taken 5 days. It seems to be
taking a
> large amount of time on a process called labelling slice. I have
run the
> same analysis on other subjects which took about 6 hours to
complete. So
I > was wondering if you know of any reason why a set of scans would
take long
er > to process than others. I have checked the inital scans and
nothing seems
> obviously wrong with them. > > Best Wishes > > Paul > >
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addressed. If
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contains
patient information, please contact the Partners Compliance
HelpLine
at
http://www.partners.org/complianceline . If the e-mail was sent to
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error but does not contain patient information, please contact the
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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 athttp://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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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 Josh
the way we are handling sub-mm data is to run it through the standard recon-all, then run a postprocessing surface deformation on the higher res data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs.
cheers Bruce
On Mon, 21 Jan 2013, Joshua Lee wrote:
Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh
On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Colin,
It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible. Nick > Does the beta permit volumes bigger than 256^3 voxels? just asking....and > just asking about raw dimensions in unit-voxels at the start of pipeline > > cheers > > Colin > > On 18 January 2013 17:00, <freesurfer-request@nmr.mgh.harvard.edu> wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-request@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-owner@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> Today's Topics: >> >> 1. v5.2.0 beta, round two (Nick Schmansky) >> 2. Re: pial not computing (Borzello, Mia) >> 3. Re: pial not computing (Bruce Fischl) >> 4. Re: FW: longitudinal analysis (Alex Hanganu) >> >> >> ---------- Forwarded message ---------- >> From: Nick Schmansky <nicks@nmr.mgh.harvard.edu> >> To: <freesurfer@nmr.mgh.harvard.edu> >> Cc: >> Date: Fri, 18 Jan 2013 11:20:43 -0500 >> Subject: [Freesurfer] v5.2.0 beta, round two >> For those willing and brave enough, another beta of v5.2.0 has been >> posted >> here for you to download and test: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ >> >> The Mac builds should work (note: the lion build is 64b, snow-leopard is >> 32b). >> >> The final release still awaits some critical improvements to the Tracula >> stream, but the main recon-all stream with this beta is final. The >> final >> release is expected the first week of February. >> >> Freesurfer team >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: "Borzello, Mia" <MBORZELLO@partners.org> >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Cc: >> Date: Fri, 18 Jan 2013 16:25:40 +0000 >> Subject: Re: [Freesurfer] pial not computing >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure >> how/where to run this and I don't see a page on the freesurfer site. >> >> Thanks so much, >> m >> ________________________________________ >> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Thursday, January 17, 2013 1:30 PM >> To: Borzello, Mia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] pial not computing >> >> Hi Mia >> >> this is fixed in the newest version. You can grab a new mris_topo_fixer >> and you rerun and it should be all set. You probably should take a look >> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum >> or skull attached, and the hemispherees successfully separated) >> >> cheers >> Bruce >> On Thu, 17 >> Jan 2013, Borzello, Mia wrote: >> >> > Okay, so it didn't complete without error. I've attached the >> recon-all.log. Also, I was using another post op patient's MRI scans. >> > >> > thanks so much, >> > m >> > ________________________________________ >> > From: freesurfer-bounces@nmr.mgh.harvard.edu [ >> freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ >> fischl@nmr.mgh.harvard.edu] >> > Sent: Thursday, January 17, 2013 11:22 AM >> > To: Borzello, Mia >> > Cc: freesurfer@nmr.mgh.harvard.edu >> > Subject: Re: [Freesurfer] pial not computing >> > >> > Hi Mia >> > >> > we need to see the recon-all.log. Did it end with an error? >> > Bruce >> > On Thu, 17 Jan >> > 2013, Borzello, Mia wrote: >> > >> >> Hi Freesurfers, >> >> >> >> I just ran a recon, and it seems that only the lh.pial computed, but >> not the rh.pial. What would be the cause of this? >> >> Thanks, >> >> m >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> ---------- Forwarded message ---------- >> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >> To: "Borzello, Mia" <MBORZELLO@partners.org> >> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Date: Fri, 18 Jan 2013 11:28:00 -0500 >> Subject: Re: [Freesurfer] pial not computing >> it's run as part of recon-all. If you grab a new one and run >> >> recon-all -make all ... >> >> you should be all set >> Bruce >> >> >> On Fri, 18 Jan 2013, Borzello, Mia wrote: >> >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure >>> how/where to run this and I don't see a page on the freesurfer site. >>> >>> Thanks so much, >>> m______________________________**__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ______________________________**__________ From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu[ freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers,
I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Alex Hanganu al.hanganu@yahoo.ca To: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Cc: Date: Fri, 18 Jan 2013 11:39:31 -0500 Subject: Re: [Freesurfer] FW: longitudinal analysis Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
Date: Fri, 18 Jan 2013 08:54:48 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] longitudinal analysis
Hi Paul
can you cc the list so that others can answer?
thanks Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi Brian,
Thanks for your reply.
I am running freesurfer 4.5.0. We are using the older version so
that the
analyses performed are the same across subjects.
Best wishes
Paul
Date: Fri, 18 Jan 2013 08:21:05 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analysis
Hi Paul
what is the actual binary being run?
Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi guys,
I am currently running a longitudinal analysis on a set of scan.
It is
currently running and so far it has taken 5 days. It seems to be
taking a
large amount of time on a process called labelling slice. I have
run the
same analysis on other subjects which took about 6 hours to
complete. So
I
was wondering if you know of any reason why a set of scans would
take long
er
to process than others. I have checked the inital scans and
nothing seems
obviously wrong with them.
Best Wishes
Paul
_______________________________________________ Freesurfer mailing
list
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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
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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.
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Thanks Bruce. That sounds great. Will subcortical segmentations also benefit yet. I remember that you once told me that there were some problems with it. - Josh
On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Josh
the way we are handling sub-mm data is to run it through the standard recon-all, then run a postprocessing surface deformation on the higher res data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs.
cheers Bruce
On Mon, 21 Jan 2013, Joshua Lee wrote:
Does this mean that using Freesurfer at sub-1mm isotropic resolutions
will not be possible next version? Josh
On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky < nicks@nmr.mgh.harvard.edu> wrote: Colin,
It will still error if any dimension is greater than 256, whichthen means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible.
Nick > Does the beta permit volumes bigger than 256^3 voxels? justasking....and > just asking about raw dimensions in unit-voxels at the start of pipeline > > cheers > > Colin > > On 18 January 2013 17:00, <freesurfer-request@nmr.mgh.** harvard.edu freesurfer-request@nmr.mgh.harvard.edu> wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-request@nmr.mgh.**harvard.edufreesurfer-request@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-owner@nmr.mgh.**harvard.edufreesurfer-owner@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> Today's Topics: >> >> 1. v5.2.0 beta, round two (Nick Schmansky) >> 2. Re: pial not computing (Borzello, Mia) >> 3. Re: pial not computing (Bruce Fischl) >> 4. Re: FW: longitudinal analysis (Alex Hanganu) >> >> >> ---------- Forwarded message ---------- >> From: Nick Schmansky nicks@nmr.mgh.harvard.edu >> To: <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu
>> Cc: >> Date: Fri, 18 Jan 2013 11:20:43 -0500 >> Subject: [Freesurfer] v5.2.0 beta, round two >> For those willing and brave enough, another beta of v5.2.0 hasbeen >> posted >> here for you to download and test: >> >> ftp://surfer.nmr.mgh.harvard.**edu/pub/dist/freesurfer/5.2.0-** BETA/ ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ >> >> The Mac builds should work (note: the lion build is 64b, snow-leopard is >> 32b). >> >> The final release still awaits some critical improvements to the Tracula >> stream, but the main recon-all stream with this beta is final. The >> final >> release is expected the first week of February. >> >> Freesurfer team >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: "Borzello, Mia" MBORZELLO@partners.org >> To: "freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.**edu freesurfer@nmr.mgh.harvard.edu> >> Cc: >> Date: Fri, 18 Jan 2013 16:25:40 +0000 >> Subject: Re: [Freesurfer] pial not computing >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure >> how/where to run this and I don't see a page on the freesurfer site. >> >> Thanks so much, >> m >> ______________________________**__________ >> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Thursday, January 17, 2013 1:30 PM >> To: Borzello, Mia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] pial not computing >> >> Hi Mia >> >> this is fixed in the newest version. You can grab a new mris_topo_fixer >> and you rerun and it should be all set. You probably should take a look >> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum >> or skull attached, and the hemispherees successfully separated) >> >> cheers >> Bruce >> On Thu, 17 >> Jan 2013, Borzello, Mia wrote: >> >> > Okay, so it didn't complete without error. I've attached the >> recon-all.log. Also, I was using another post op patient's MRI scans. >> > >> > thanks so much, >> > m >> > ______________________________**__________ >> > From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu[ >> freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ >> fischl@nmr.mgh.harvard.edu] >> > Sent: Thursday, January 17, 2013 11:22 AM >> > To: Borzello, Mia >> > Cc: freesurfer@nmr.mgh.harvard.edu >> > Subject: Re: [Freesurfer] pial not computing >> > >> > Hi Mia >> > >> > we need to see the recon-all.log. Did it end with an error? >> > Bruce >> > On Thu, 17 Jan >> > 2013, Borzello, Mia wrote: >> > >> >> Hi Freesurfers, >> >> >> >> I just ran a recon, and it seems that only the lh.pial computed, but >> not the rh.pial. What would be the cause of this? >> >> Thanks, >> >> m >> >> >> >> ______________________________**_________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> ---------- Forwarded message ---------- >> From: Bruce Fischl fischl@nmr.mgh.harvard.edu >> To: "Borzello, Mia" MBORZELLO@partners.org >> Cc: "freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.**edu freesurfer@nmr.mgh.harvard.edu> >> Date: Fri, 18 Jan 2013 11:28:00 -0500 >> Subject: Re: [Freesurfer] pial not computing >> it's run as part of recon-all. If you grab a new one and run >> >> recon-all -make all ... >> >> you should be all set >> Bruce >> >> >> On Fri, 18 Jan 2013, Borzello, Mia wrote: >> >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure >>> how/where to run this and I don't see a page on the freesurfer site. >>> >>> Thanks so much, >>> m
______________________________****__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
this is fixed in the newest version. You can grab a new
mris_topo_fixer
and you rerun and it should be all set. You probably should take a
look
at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)
cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Okay, so it didn't complete without error. I've attached the
recon-all.log. Also, I was using another post op patient's MRI scans.
thanks so much, m ______________________________****__________ From: freesurfer-bounces@nmr.mgh.**h**arvard.edu http://harvard.edu<
freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu
[
freesurfer-bounces@nmr.mgh.**h**arvard.edu http://harvard.edu<
freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu
]
on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing
Hi Mia
we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:
Hi Freesurfers, > > I just ran a recon, and it seems that only the lh.pial computed,
but
> not the rh.pial. What would be the cause of this? > Thanks, > m > > ______________________________****_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/****freesurfer< https://mail.nmr.**mgh.harvard.edu/mailman/**listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > _____________________________**_**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/****freesurfer< https://mail.nmr.**mgh.harvard.edu/mailman/**listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________****_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/****freesurfer< https://mail.nmr.**mgh.harvard.edu/mailman/**listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Alex Hanganu al.hanganu@yahoo.ca To: FS Mailing List <Freesurfer@nmr.mgh.harvard.**eduFreesurfer@nmr.mgh.harvard.edu
Cc: Date: Fri, 18 Jan 2013 11:39:31 -0500 Subject: Re: [Freesurfer] FW: longitudinal analysis Hi Paul,
I also had such problems previously. My initial analyses were performed on mac. Though it might seem strange, some analyses resolved after I just restarted the computer. Other ones I analysed on centos. Now I am doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
Date: Fri, 18 Jan 2013 08:54:48 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com Subject: RE: [Freesurfer] longitudinal analysis
Hi Paul
can you cc the list so that others can answer?
thanks Bruce On Fri, 18 Jan 2013, paul horton wrote:
Hi Brian,
Thanks for your reply.
I am running freesurfer 4.5.0. We are using the older version so
that the
analyses performed are the same across subjects.
Best wishes
Paul
Date: Fri, 18 Jan 2013 08:21:05 -0500 From: fischl@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analysis
Hi Paul
what is the actual binary being run?
Bruce On Fri, 18 Jan 2013, paul horton wrote:
> Hi guys, > > I am currently running a longitudinal analysis on a set of scan.
It is
> currently running and so far it has taken 5 days. It seems to be
taking a
> large amount of time on a process called labelling slice. I have
run the
> same analysis on other subjects which took about 6 hours to
complete. So
I > was wondering if you know of any reason why a set of scans would
take long
er > to process than others. I have checked the inital scans and
nothing seems
> obviously wrong with them. > > Best Wishes > > Paul > >
______________________________**_________________ Freesurfer
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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
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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 athttp://www.partners.org/**compliancelinehttp://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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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/**compliancelinehttp://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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no, it won't change anything on the subcortical side yet On Mon, 21 Jan 2013, Joshua Lee wrote:
Thanks Bruce. That sounds great. Will subcortical segmentations also benefit yet. I remember that you once told me that there were some problems with it.
Josh
On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Josh
the way we are handling sub-mm data is to run it through the standard recon-all, then run a postprocessing surface deformation on the higher res data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs. cheers Bruce On Mon, 21 Jan 2013, Joshua Lee wrote: Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not be possible next version? Josh On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote: Colin, It will still error if any dimension is greater than 256, which then means the flag -cw256 must be added to recon-all. This flag chops dimensions greater than 256 down to 256. The reason it doesnt do it automatically is that with this chopping, its not certain that it isnt removing into the head, so the user needs to be aware of this, so that they can inspect orig.mgz with freeview to make sure the head is fully visible. Nick > Does the beta permit volumes bigger than 256^3 voxels? just asking....and > just asking about raw dimensions in unit-voxels at the start of pipeline > > cheers > > Colin > > On 18 January 2013 17:00, <freesurfer-request@nmr.mgh.harvard.edu> wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-request@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-owner@nmr.mgh.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> Today's Topics: >> >> 1. v5.2.0 beta, round two (Nick Schmansky) >> 2. Re: pial not computing (Borzello, Mia) >> 3. Re: pial not computing (Bruce Fischl) >> 4. Re: FW: longitudinal analysis (Alex Hanganu) >> >> >> ---------- Forwarded message ---------- >> From: Nick Schmansky <nicks@nmr.mgh.harvard.edu> >> To: <freesurfer@nmr.mgh.harvard.edu> >> Cc: >> Date: Fri, 18 Jan 2013 11:20:43 -0500 >> Subject: [Freesurfer] v5.2.0 beta, round two >> For those willing and brave enough, another beta of v5.2.0 has been >> posted >> here for you to download and test: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ >> >> The Mac builds should work (note: the lion build is 64b, snow-leopard is >> 32b). >> >> The final release still awaits some critical improvements to the Tracula >> stream, but the main recon-all stream with this beta is final. The >> final >> release is expected the first week of February. >> >> Freesurfer team >> >> >> >> >> >> ---------- Forwarded message ---------- >> From: "Borzello, Mia" <MBORZELLO@partners.org> >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Cc: >> Date: Fri, 18 Jan 2013 16:25:40 +0000 >> Subject: Re: [Freesurfer] pial not computing >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure >> how/where to run this and I don't see a page on the freesurfer site. >> >> Thanks so much, >> m >> ________________________________________ >> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] >> Sent: Thursday, January 17, 2013 1:30 PM >> To: Borzello, Mia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] pial not computing >> >> Hi Mia >> >> this is fixed in the newest version. You can grab a new mris_topo_fixer >> and you rerun and it should be all set. You probably should take a look >> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum >> or skull attached, and the hemispherees successfully separated) >> >> cheers >> Bruce >> On Thu, 17 >> Jan 2013, Borzello, Mia wrote: >> >> > Okay, so it didn't complete without error. I've attached the >> recon-all.log. Also, I was using another post op patient's MRI scans. >> > >> > thanks so much, >> > m >> > ________________________________________ >> > From: freesurfer-bounces@nmr.mgh.harvard.edu [ >> freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ >> fischl@nmr.mgh.harvard.edu] >> > Sent: Thursday, January 17, 2013 11:22 AM >> > To: Borzello, Mia >> > Cc: freesurfer@nmr.mgh.harvard.edu >> > Subject: Re: [Freesurfer] pial not computing >> > >> > Hi Mia >> > >> > we need to see the recon-all.log. Did it end with an error? >> > Bruce >> > On Thu, 17 Jan >> > 2013, Borzello, Mia wrote: >> > >> >> Hi Freesurfers, >> >> >> >> I just ran a recon, and it seems that only the lh.pial computed, but >> not the rh.pial. What would be the cause of this? >> >> Thanks, >> >> m >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> ---------- Forwarded message ---------- >> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >> To: "Borzello, Mia" <MBORZELLO@partners.org> >> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Date: Fri, 18 Jan 2013 11:28:00 -0500 >> Subject: Re: [Freesurfer] pial not computing >> it's run as part of recon-all. If you grab a new one and run >> >> recon-all -make all ... >> >> you should be all set >> Bruce >> >> >> On Fri, 18 Jan 2013, Borzello, Mia wrote: >> >> great. is there a freesurfer page on mris_topo_fixer? I'm not sure >>> how/where to run this and I don't see a page on the freesurfer site. >>> >>> Thanks so much, >>> m >>> ______________________________**__________ >>> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Thursday, January 17, 2013 1:30 PM >>> To: Borzello, Mia >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] pial not computing >>> >>> Hi Mia >>> >>> this is fixed in the newest version. You can grab a new mris_topo_fixer >>> and you rerun and it should be all set. You probably should take a look >>> at the ?h.orig.nofix to make sure it's reasonable (meaning no >>> cerebellum >>> or skull attached, and the hemispherees successfully separated) >>> >>> cheers >>> Bruce >>> On Thu, 17 >>> Jan 2013, Borzello, Mia wrote: >>> >>> Okay, so it didn't complete without error. I've attached the >>>> recon-all.log. Also, I was using another post op patient's MRI scans. >>>> >>>> thanks so much, >>>> m >>>> ______________________________**__________ >>>> From: >>>> freesurfer-bounces@nmr.mgh.**harvard.edu<freesurfer-bounces@nmr.mgh.harvard.edu>[ >>>> freesurfer-bounces@nmr.mgh.**harvard.edu<freesurfer-bounces@nmr.mgh.harvard.edu>] >>>> on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>>> Sent: Thursday, January 17, 2013 11:22 AM >>>> To: Borzello, Mia >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] pial not computing >>>> >>>> Hi Mia >>>> >>>> we need to see the recon-all.log. Did it end with an error? >>>> Bruce >>>> On Thu, 17 Jan >>>> 2013, Borzello, Mia wrote: >>>> >>>> Hi Freesurfers, >>>>> >>>>> I just ran a recon, and it seems that only the lh.pial computed, but >>>>> not the rh.pial. What would be the cause of this? >>>>> Thanks, >>>>> m >>>>> >>>>> ______________________________**_________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>> >>>>> >>>>> >>>>> ______________________________**_________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> >>> >> >> >> ---------- Forwarded message ---------- >> From: Alex Hanganu <al.hanganu@yahoo.ca> >> To: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu> >> Cc: >> Date: Fri, 18 Jan 2013 11:39:31 -0500 >> Subject: Re: [Freesurfer] FW: longitudinal analysis >> Hi Paul, >> >> I also had such problems previously. My initial analyses were performed >> on >> mac. Though it might seem strange, some analyses resolved after I just >> restarted the computer. Other ones I analysed on centos. Now I am doing >> all >> the recons on linux. >> >> best wishes, >> >> Alex. >> >> >> >> Le 1/18 9:22, paul horton a écrit : >> >> >> >> > Date: Fri, 18 Jan 2013 08:54:48 -0500 >> > From: fischl@nmr.mgh.harvard.edu >> > To: horton_paul@hotmail.com >> > Subject: RE: [Freesurfer] longitudinal analysis >> > >> > Hi Paul >> > >> > can you cc the list so that others can answer? >> > >> > thanks >> > Bruce >> > On Fri, 18 Jan 2013, paul >> > horton wrote: >> > >> > > Hi Brian, >> > > >> > > Thanks for your reply. >> > > >> > > I am running freesurfer 4.5.0. We are using the older version so >> that >> the >> > > analyses performed are the same across subjects. >> > > >> > > Best wishes >> > > >> > > Paul >> > > >> > > Date: Fri, 18 Jan 2013 08:21:05 -0500 >> > > From: fischl@nmr.mgh.harvard.edu >> > > To: horton_paul@hotmail.com >> > > CC: freesurfer@nmr.mgh.harvard.edu >> > > Subject: Re: [Freesurfer] longitudinal analysis >> > > >> > > Hi Paul >> > > >> > > what is the actual binary being run? >> > > >> > > Bruce >> > > On Fri, 18 Jan 2013, paul horton wrote: >> > > >> > > > Hi guys, >> > > > >> > > > I am currently running a longitudinal analysis on a set of scan. >> It >> is >> > > > currently running and so far it has taken 5 days. It seems to be >> taking a >> > > > large amount of time on a process called labelling slice. I have >> run >> the >> > > > same analysis on other subjects which took about 6 hours to >> complete. So >> > > I >> > > > was wondering if you know of any reason why a set of scans would >> take long >> > > er >> > > > to process than others. I have checked the inital scans and >> nothing >> seems >> > > > obviously wrong with them. >> > > > >> > > > Best Wishes >> > > > >> > > > Paul >> > > > >> > > > >> > > >> > > _______________________________________________ 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 >> listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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