Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/
Hi Guang,
Depending on what you do you can choose different routes. Note, for both of these you first need to run the new timepoint cross sectionally (step 1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
1. you have only very few timepoints in the base/template so far (2 or 3). In those cases I would recommend to rerun the base and rerun all the longitudinals with the new and more accurate base. The commands are on the Wiki and are the same as usual.
2. you have many time points in your base, the additional time point is not likely to change the base much. In that case you can simply 'patch' the base without reprocessing and only run a single longitudinal run.
Let me know if you want to go route 2 because I am writing a script to patch the base (there are a few files that need to be added so that the longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, Martin,
Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description.
What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them.
Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct?
Thanks! Guang
Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points.
Subject: Re: [Freesurfer] modification made to longitudinal results From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Thu, 25 Feb 2010 10:33:36 -0500
Hi Guang,
Depending on what you do you can choose different routes. Note, for both of these you first need to run the new timepoint cross sectionally (step 1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
- you have only very few timepoints in the base/template so far (2 or
3). In those cases I would recommend to rerun the base and rerun all the longitudinals with the new and more accurate base. The commands are on the Wiki and are the same as usual.
- you have many time points in your base, the additional time point is
not likely to change the base much. In that case you can simply 'patch' the base without reprocessing and only run a single longitudinal run.
Let me know if you want to go route 2 because I am writing a script to patch the base (there are a few files that need to be added so that the longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/
OK I get it. There was a confusion about adding control points and adding new time points. My answer concerns adding new time points, so you can ignore it. Do not add any edited results as new time points.
Concerning your question see the discussion on this list from Feb 12 that treats exactly this topic.
In short: - edit the cross sectionals (you have done that) - run the base and edit the base - then the longitudinals should be fine
Martin
On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote:
Hello, Martin,
Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description.
What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them.
Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct?
Thanks! Guang
Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points.
Subject: Re: [Freesurfer] modification made to longitudinal results From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Thu, 25 Feb 2010 10:33:36 -0500
Hi Guang,
Depending on what you do you can choose different routes. Note, for
both
of these you first need to run the new timepoint cross sectionally
(step
1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
- you have only very few timepoints in the base/template so far (2
or
3). In those cases I would recommend to rerun the base and rerun all
the
longitudinals with the new and more accurate base. The commands are
on
the Wiki and are the same as usual.
- you have many time points in your base, the additional time point
is
not likely to change the base much. In that case you can simply
'patch'
the base without reprocessing and only run a single longitudinal
run.
Let me know if you want to go route 2 because I am writing a script
to
patch the base (there are a few files that need to be added so that
the
longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should
I
use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
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Sign up
now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Martin,
Not to add more to the confusion, but what if the final longitudinal scans are "not fine" and need some editing. Can they be rerun in the standard way to incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something different be done? Will rerunning these edited long scans in the standard fashion disrupt them in some way? My hunch is that it won't, but I want to make sure. Thanks.
-Derin
On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote:
OK I get it. There was a confusion about adding control points and adding new time points. My answer concerns adding new time points, so you can ignore it. Do not add any edited results as new time points.
Concerning your question see the discussion on this list from Feb 12 that treats exactly this topic.
In short:
- edit the cross sectionals (you have done that)
- run the base and edit the base
- then the longitudinals should be fine
Martin
On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote:
Hello, Martin,
Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description.
What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them.
Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct?
Thanks! Guang
Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points.
Subject: Re: [Freesurfer] modification made to longitudinal results From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Thu, 25 Feb 2010 10:33:36 -0500
Hi Guang,
Depending on what you do you can choose different routes. Note, for
both
of these you first need to run the new timepoint cross sectionally
(step
1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
- you have only very few timepoints in the base/template so far (2
or
3). In those cases I would recommend to rerun the base and rerun all
the
longitudinals with the new and more accurate base. The commands are
on
the Wiki and are the same as usual.
- you have many time points in your base, the additional time point
is
not likely to change the base much. In that case you can simply
'patch'
the base without reprocessing and only run a single longitudinal
run.
Let me know if you want to go route 2 because I am writing a script
to
patch the base (there are a few files that need to be added so that
the
longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should
I
use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
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Sign up
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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.
Derin,
You probably mean the final longitudinal runs (not 'scans'). The longitudinal (-long) runs really should be fine without extra editing. We have never tried editing them as it was never necessary. They should be OK, if not there is likely a problem before that needs to be fixed (e.g. inaccurate registration with the template etc). If that happens, please let us know.
So I went back and checked a few things:
-brainmask is taken from the base, so if it is wrong, check the base -talairach.lta also comes from the base and needs to be checked there -talairach.xfm (only for etiv) is currently taken from the cross sectionals and needs to be checked there. It might be easier to just take the ICV from the base-template instead for all time points, ICV should not change (in adults). - WM edits are merged in from the base (so editing the longitudinal in addition should work, but probably not necessary). - The normalization control points are the only thing I am not really sure about. We played around with several options (copying it from the base, or from the cross sectional). I am not sure what the current mechanism is, maybe the CP go into the long stream indirectly? We'll check and update the WIKI.
Best, Martin
On Wed, 2010-03-10 at 15:16 -0600, Derin Cobia wrote:
Martin,
Not to add more to the confusion, but what if the final longitudinal scans are "not fine" and need some editing. Can they be rerun in the standard way to incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something different be done? Will rerunning these edited long scans in the standard fashion disrupt them in some way? My hunch is that it won't, but I want to make sure. Thanks.
-Derin
On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote:
OK I get it. There was a confusion about adding control points and adding new time points. My answer concerns adding new time points, so you can ignore it. Do not add any edited results as new time points.
Concerning your question see the discussion on this list from Feb 12 that treats exactly this topic.
In short:
- edit the cross sectionals (you have done that)
- run the base and edit the base
- then the longitudinals should be fine
Martin
On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote:
Hello, Martin,
Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description.
What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them.
Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct?
Thanks! Guang
Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points.
Subject: Re: [Freesurfer] modification made to longitudinal results From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Thu, 25 Feb 2010 10:33:36 -0500
Hi Guang,
Depending on what you do you can choose different routes. Note, for
both
of these you first need to run the new timepoint cross sectionally
(step
1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
- you have only very few timepoints in the base/template so far (2
or
3). In those cases I would recommend to rerun the base and rerun all
the
longitudinals with the new and more accurate base. The commands are
on
the Wiki and are the same as usual.
- you have many time points in your base, the additional time point
is
not likely to change the base much. In that case you can simply
'patch'
the base without reprocessing and only run a single longitudinal
run.
Let me know if you want to go route 2 because I am writing a script
to
patch the base (there are a few files that need to be added so that
the
longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should
I
use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
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Sign up
now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
Derin
OK, Allison discovered it in the depth of recon-all :-)
The control points are copied from the cross sectional by default (and should be edited there). There is an optional flag to get them from the base, but that has never been really tested. It only makes sense if there is very little structural change across time. But might save people some editing time, if they have 10 images with almost no WM change. We'll probably do a similar setup for the WM edits in the next release.
Cheers, Martin
On Wed, 2010-03-10 at 15:16 -0600, Derin Cobia wrote:
Martin,
Not to add more to the confusion, but what if the final longitudinal scans are "not fine" and need some editing. Can they be rerun in the standard way to incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something different be done? Will rerunning these edited long scans in the standard fashion disrupt them in some way? My hunch is that it won't, but I want to make sure. Thanks.
-Derin
On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote:
OK I get it. There was a confusion about adding control points and adding new time points. My answer concerns adding new time points, so you can ignore it. Do not add any edited results as new time points.
Concerning your question see the discussion on this list from Feb 12 that treats exactly this topic.
In short:
- edit the cross sectionals (you have done that)
- run the base and edit the base
- then the longitudinals should be fine
Martin
On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote:
Hello, Martin,
Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description.
What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them.
Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct?
Thanks! Guang
Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points.
Subject: Re: [Freesurfer] modification made to longitudinal results From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Thu, 25 Feb 2010 10:33:36 -0500
Hi Guang,
Depending on what you do you can choose different routes. Note, for
both
of these you first need to run the new timepoint cross sectionally
(step
1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
- you have only very few timepoints in the base/template so far (2
or
3). In those cases I would recommend to rerun the base and rerun all
the
longitudinals with the new and more accurate base. The commands are
on
the Wiki and are the same as usual.
- you have many time points in your base, the additional time point
is
not likely to change the base much. In that case you can simply
'patch'
the base without reprocessing and only run a single longitudinal
run.
Let me know if you want to go route 2 because I am writing a script
to
patch the base (there are a few files that need to be added so that
the
longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should
I
use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
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Sign up
now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
Hi Martin,
Just wanted to clarify one question about edits to the longitudinal pipeline.
Lets say there is a data-set with 200 subjects with 5 time-points each (1000 scans total).
I create the base image and i would only like to make corrections in the 200 base images (if required) and not in the cross-sectional time-points. My understanding from an earlier thread was that this should be fine.
But in this thread you said control points are copied from the 'cross-sectional by default' So is the following correct? I should only make edits to the wm.mgz (from the base) and avoid adding any control points to the base ?
I apologize for the repeated questions on the issue, but just wanted to make sure that I was making the corrections correctly.
Thanks Mehul
On Thu, Mar 11, 2010 at 7:20 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Derin
OK, Allison discovered it in the depth of recon-all :-)
The control points are copied from the cross sectional by default (and should be edited there). There is an optional flag to get them from the base, but that has never been really tested. It only makes sense if there is very little structural change across time. But might save people some editing time, if they have 10 images with almost no WM change. We'll probably do a similar setup for the WM edits in the next release.
Cheers, Martin
On Wed, 2010-03-10 at 15:16 -0600, Derin Cobia wrote:
Martin,
Not to add more to the confusion, but what if the final longitudinal
scans are "not fine" and need some editing. Can they be rerun in the standard way to incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something different be done? Will rerunning these edited long scans in the standard fashion disrupt them in some way? My hunch is that it won't, but I want to make sure. Thanks.
-Derin
On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote:
OK I get it. There was a confusion about adding control points and adding new time points. My answer concerns adding new time points, so you can ignore it. Do not add any edited results as new time points.
Concerning your question see the discussion on this list from Feb 12 that treats exactly this topic.
In short:
- edit the cross sectionals (you have done that)
- run the base and edit the base
- then the longitudinals should be fine
Martin
On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote:
Hello, Martin,
Thanks a lot for your reply, but I am still not very clear about few issues. I think that is because of my unclear description.
What happen is: I have two scans which I want to do longitudinal analysis, however, when I finish the cross-sectional analysis, I found the results are not so good because of the low contrast between white matter and gray matter. I added control points to these two scans, rerun them. The results looks much better now, then I go to the longitudinal stream. However, when I load the longitudinal results, I found the kind of problem happens again (lots of no-label region in superior frontal). So I added control points to the longitudinal results directly, and I want rerun them.
Based on your reply, I need consider those longitudinal results which I added control points to as new timepoints, rerun them cross-sectionally again, is it correct?
Thanks! Guang
Here, I just want to add some control points to the FreeSurfer longitudinal results, not new time points.
Subject: Re: [Freesurfer] modification made to longitudinal results From: mreuter@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Thu, 25 Feb 2010 10:33:36 -0500
Hi Guang,
Depending on what you do you can choose different routes. Note, for
both
of these you first need to run the new timepoint cross sectionally
(step
1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom
Here are the two options once the cross sectional results are there:
- you have only very few timepoints in the base/template so far (2
or
3). In those cases I would recommend to rerun the base and rerun all
the
longitudinals with the new and more accurate base. The commands are
on
the Wiki and are the same as usual.
- you have many time points in your base, the additional time point
is
not likely to change the base much. In that case you can simply
'patch'
the base without reprocessing and only run a single longitudinal
run.
Let me know if you want to go route 2 because I am writing a script
to
patch the base (there are a few files that need to be added so that
the
longitudinal run will go through). If there is demand, I will put priority on this and make it available.
Best, Martin
On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote:
Hi, there,
I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should
I
use?
recon-all -s subj.long.baseid .... or recon-all -long subj baseid ....
Thanks! Guang
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Sign up
now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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 Mehul,
in FS4.5:
- if there are manual CP edits in the cross sectionals, the longitudinal will automatically copy them. - there is a flag (-uselongbasectrlvol) to optionally use the CP from the base (mapped to the current time point)
The WM edits are transferred from the base by default, probably we'll do it similar as above in the next release.
So yes: WM edits in the base currently. CP in the Cross sectionals, or edit the base and try the flag. The problem with the flag is, that because of atrophy/change, the points might be added into regions that are not WM in a specific longitudinal run.
Best, Martin
On Mon, 2010-03-15 at 23:44 -0700, Mehul Sampat wrote:
Hi Martin,
Just wanted to clarify one question about edits to the longitudinal pipeline.
Lets say there is a data-set with 200 subjects with 5 time-points each (1000 scans total).
I create the base image and i would only like to make corrections in the 200 base images (if required) and not in the cross-sectional time-points. My understanding from an earlier thread was that this should be fine.
But in this thread you said control points are copied from the 'cross-sectional by default' So is the following correct? I should only make edits to the wm.mgz (from the base) and avoid adding any control points to the base ?
I apologize for the repeated questions on the issue, but just wanted to make sure that I was making the corrections correctly.
Thanks Mehul
On Thu, Mar 11, 2010 at 7:20 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Derin
OK, Allison discovered it in the depth of recon-all :-) The control points are copied from the cross sectional by default (and should be edited there). There is an optional flag to get them from the base, but that has never been really tested. It only makes sense if there is very little structural change across time. But might save people some editing time, if they have 10 images with almost no WM change. We'll probably do a similar setup for the WM edits in the next release. Cheers, Martin On Wed, 2010-03-10 at 15:16 -0600, Derin Cobia wrote: > Martin, > > Not to add more to the confusion, but what if the final longitudinal scans are "not fine" and need some editing. Can they be rerun in the standard way to incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should something different be done? Will rerunning these edited long scans in the standard fashion disrupt them in some way? My hunch is that it won't, but I want to make sure. Thanks. > > -Derin > > On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote: > > > OK I get it. There was a confusion about adding control points and > > adding new time points. My answer concerns adding new time points, so > > you can ignore it. Do not add any edited results as new time points. > > > > Concerning your question see the discussion on this list from Feb 12 > > that treats exactly this topic. > > > > In short: > > - edit the cross sectionals (you have done that) > > - run the base and edit the base > > - then the longitudinals should be fine > > > > > > Martin > > > > On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote: > >> Hello, Martin, > >> > >> Thanks a lot for your reply, but I am still not very clear about few > >> issues. > >> I think that is because of my unclear description. > >> > >> What happen is: > >> I have two scans which I want to do longitudinal analysis, however, > >> when I finish the > >> cross-sectional analysis, I found the results are not so good because > >> of the low contrast > >> between white matter and gray matter. I added control points to these > >> two scans, rerun them. > >> The results looks much better now, then I go to the longitudinal > >> stream. However, when I load the > >> longitudinal results, I found the kind of problem happens again (lots > >> of no-label region in superior frontal). > >> So I added control points to the longitudinal results directly, and I > >> want rerun them. > >> > >> Based on your reply, I need consider those longitudinal results which > >> I added control points to as new timepoints, > >> rerun them cross-sectionally again, is it correct? > >> > >> Thanks! > >> Guang > >> > >> > >> Here, I just want to add some control points to the FreeSurfer > >> longitudinal results, > >> not new time points. > >> > >>> Subject: Re: [Freesurfer] modification made to longitudinal results > >>> From: mreuter@nmr.mgh.harvard.edu > >>> To: freesurfer_zg@hotmail.com > >>> CC: freesurfer@nmr.mgh.harvard.edu > >>> Date: Thu, 25 Feb 2010 10:33:36 -0500 > >>> > >>> Hi Guang, > >>> > >>> Depending on what you do you can choose different routes. Note, for > >> both > >>> of these you first need to run the new timepoint cross sectionally > >> (step > >>> 1 in the description > >>> http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): > >>> recon-all -all -s newtpid -i path/to/dicom > >>> > >>> Here are the two options once the cross sectional results are there: > >>> > >>> 1. you have only very few timepoints in the base/template so far (2 > >> or > >>> 3). In those cases I would recommend to rerun the base and rerun all > >> the > >>> longitudinals with the new and more accurate base. The commands are > >> on > >>> the Wiki and are the same as usual. > >>> > >>> 2. you have many time points in your base, the additional time point > >> is > >>> not likely to change the base much. In that case you can simply > >> 'patch' > >>> the base without reprocessing and only run a single longitudinal > >> run. > >>> > >>> Let me know if you want to go route 2 because I am writing a script > >> to > >>> patch the base (there are a few files that need to be added so that > >> the > >>> longitudinal run will go through). If there is demand, I will put > >>> priority on this and make it available. > >>> > >>> Best, Martin > >>> > >>> On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote: > >>>> Hi, there, > >>>> > >>>> I need add some control points to the longitudinal results. > >>>> After adding control points, I need rerun it. which command should > >> I > >>>> use? > >>>> > >>>> recon-all -s subj.long.baseid .... > >>>> or > >>>> recon-all -long subj baseid .... > >>>> > >>>> > >>>> Thanks! > >>>> Guang > >>>> > >>>> > >>>> > >> ______________________________________________________________________ > >>>> Your E-mail and More On-the-Go. 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Mehul Sampat