(Questions for all, but maybe more directed towards Martin)
I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used in for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks.
-Derin
Bumping this back up to the list. Could someone please address?
To be more concise, during longitudinal processing, where are wm/gm edits made? On the cross-sectional runs, to the base, or on the .long. runs themselves? Thanks.
-Derin
Begin forwarded message:
From: Derin Cobia d-cobia@northwestern.edu Date: February 1, 2010 3:54:46 PM CST To: "freesurfer@nmr.mgh.harvard.edu Help" freesurfer@nmr.mgh.harvard.edu Subject: Longitudinal processing clarification
(Questions for all, but maybe more directed towards Martin)
I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks.
-Derin
edits should be made to the cross-sectional subjects and the base subjects. edits do not need to be made to the longitudinal runs, as they will be transferred from the cross-sectional subject run. the base subject does not get edits transferred from the composing set of cross-sectional subjects because each of those runs will be slightly different, and edits to one time-point may not apply to another time-point.
n.
On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
Bumping this back up to the list. Could someone please address?
To be more concise, during longitudinal processing, where are wm/gm edits made? On the cross-sectional runs, to the base, or on the .long. runs themselves? Thanks.
-Derin
Begin forwarded message:
From: Derin Cobia d-cobia@northwestern.edu
Date: February 1, 2010 3:54:46 PM CST
To: "freesurfer@nmr.mgh.harvard.edu Help" freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal processing clarification
(Questions for all, but maybe more directed towards Martin)
I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Derin,
this is how I see it:
The base might need edits and if it does, they should be made. As you say, the surfaces of the longitudinal runs are initialized with the surface of the base, so, if it is not correct, this will pollute all time points.
Another reason to edit the base is that wm edits (255) and deletes (1) are copied from the base to all time points, as you mentioned.
Usually this should be sufficient, but maybe you need further edits in a specific longitudinal run, never happened to me.
The old longitudinal processing stream really did not have any cross sectional runs. Instead of the base they processed TP1 (introducing a bias) and copied the edits from there to the longitudinals. We now copy it from the base.
Hope that helps.
Nick mentioned that edits are copied from the cross sectionals, but I think they only come from the base. At least that is what I think was done and therefore put it on the wiki. Maybe Nick can verify what really goes on in recon-all as he programmed that part?
It might make sense to edit the cross sectionals anyway because: - you then get more reliable cross sectional results (to compare to etc). - the cross sectional asegs are 'fused' (probabilistic voting), to initialize the labeling in the longitudinal runs, so more accuracy in the cross sectionals cannot hurt. However I never really found this to be necessary, but my data was usually high quality.
Best, Martin
On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
Bumping this back up to the list. Could someone please address?
To be more concise, during longitudinal processing, where are wm/gm edits made? On the cross-sectional runs, to the base, or on the .long. runs themselves? Thanks.
-Derin
Begin forwarded message:
From: Derin Cobia d-cobia@northwestern.edu
Date: February 1, 2010 3:54:46 PM CST
To: "freesurfer@nmr.mgh.harvard.edu Help" freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal processing clarification
(Questions for all, but maybe more directed towards Martin)
I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick (and Martin)
Could you please clarify if the edits come only from the base or if they are copied from the cross-sectionals ?
It would be great if I only had to make edit in the base . We have 5 timepoints for each subject (each a year apart) and i want to use the results from the longitudinal pipeline only. If I did not need to edit the cross-sectional timepoints and if editing only the base was okay this would be very helpful.
Martin, do you normally only make edits to base when using the longitudinal pipeline ? Thanks Mehul
On Fri, Feb 12, 2010 at 6:01 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Derin,
this is how I see it:
The base might need edits and if it does, they should be made. As you say, the surfaces of the longitudinal runs are initialized with the surface of the base, so, if it is not correct, this will pollute all time points.
Another reason to edit the base is that wm edits (255) and deletes (1) are copied from the base to all time points, as you mentioned.
Usually this should be sufficient, but maybe you need further edits in a specific longitudinal run, never happened to me.
The old longitudinal processing stream really did not have any cross sectional runs. Instead of the base they processed TP1 (introducing a bias) and copied the edits from there to the longitudinals. We now copy it from the base.
Hope that helps.
Nick mentioned that edits are copied from the cross sectionals, but I think they only come from the base. At least that is what I think was done and therefore put it on the wiki. Maybe Nick can verify what really goes on in recon-all as he programmed that part?
It might make sense to edit the cross sectionals anyway because:
- you then get more reliable cross sectional results (to compare to
etc).
- the cross sectional asegs are 'fused' (probabilistic voting), to
initialize the labeling in the longitudinal runs, so more accuracy in the cross sectionals cannot hurt. However I never really found this to be necessary, but my data was usually high quality.
Best, Martin
On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
Bumping this back up to the list. Could someone please address?
To be more concise, during longitudinal processing, where are wm/gm edits made? On the cross-sectional runs, to the base, or on the .long. runs themselves? Thanks.
-Derin
Begin forwarded message:
From: Derin Cobia d-cobia@northwestern.edu
Date: February 1, 2010 3:54:46 PM CST
To: "freesurfer@nmr.mgh.harvard.edu Help" freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal processing clarification
(Questions for all, but maybe more directed towards Martin)
I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks.
-Derin
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
You can edit just the base if you will only be working with the longitudinal stream. Currently, running the cross-sectional stream is necessary only to get the 'norm.mgz' file, for input to the base subject.
n.
On Sun, 2010-02-14 at 14:06 -0800, Mehul Sampat wrote:
Hi Nick (and Martin)
Could you please clarify if the edits come only from the base or if they are copied from the cross-sectionals ?
It would be great if I only had to make edit in the base . We have 5 timepoints for each subject (each a year apart) and i want to use the results from the longitudinal pipeline only. If I did not need to edit the cross-sectional timepoints and if editing only the base was okay this would be very helpful.
Martin, do you normally only make edits to base when using the longitudinal pipeline ? Thanks Mehul
On Fri, Feb 12, 2010 at 6:01 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Derin,
this is how I see it: The base might need edits and if it does, they should be made. As you say, the surfaces of the longitudinal runs are initialized with the surface of the base, so, if it is not correct, this will pollute all time points. Another reason to edit the base is that wm edits (255) and deletes (1) are copied from the base to all time points, as you mentioned. Usually this should be sufficient, but maybe you need further edits in a specific longitudinal run, never happened to me. The old longitudinal processing stream really did not have any cross sectional runs. Instead of the base they processed TP1 (introducing a bias) and copied the edits from there to the longitudinals. We now copy it from the base. Hope that helps. Nick mentioned that edits are copied from the cross sectionals, but I think they only come from the base. At least that is what I think was done and therefore put it on the wiki. Maybe Nick can verify what really goes on in recon-all as he programmed that part? It might make sense to edit the cross sectionals anyway because: - you then get more reliable cross sectional results (to compare to etc). - the cross sectional asegs are 'fused' (probabilistic voting), to initialize the labeling in the longitudinal runs, so more accuracy in the cross sectionals cannot hurt. However I never really found this to be necessary, but my data was usually high quality. Best, Martin On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote: > Bumping this back up to the list. Could someone please address? > > > To be more concise, during longitudinal processing, where are wm/gm > edits made? On the cross-sectional runs, to the base, or on > the .long. runs themselves? Thanks. > > > -Derin > > Begin forwarded message: > > > From: Derin Cobia <d-cobia@northwestern.edu> > > > > Date: February 1, 2010 3:54:46 PM CST > > > > To: "freesurfer@nmr.mgh.harvard.edu Help" > > <freesurfer@nmr.mgh.harvard.edu> > > > > Subject: Longitudinal processing clarification > > > > > > (Questions for all, but maybe more directed towards Martin) > > > > > > I have some questions about manual edits in regard to the > > longitudinal stream. Based on the current info on the wiki page, it > > appears that no edits are pushed forward from the cross-sectional > > (initial) runs of the subject data, as any information on > > the *.long.* runs come from the template. However, I've noticed > > that WM edits and surfs from the template are used for the *.long.* > > processing. In essence, my question is when/where should manual > > edits (i.e., control points, WM, pial edits) occur when conducting > > longitudinal processing in 4.5? It seems I remember that in 4.3 > > edits in the cross-sectional work would be pushed forward to the > > *.long.* images, but such is not the case anymore (?). Are edits to > > occur in the template (i.e., 'base') now, or in the *.long.* runs? > > Thanks. > > > > > > -Derin > > > > > > > > > > > _______________________________________________ > 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
freesurfer@nmr.mgh.harvard.edu
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Derin Cobia -
Derin Cobia
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Martin Reuter -
Mehul Sampat -
Nick Schmansky