Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Douglas Greve]

There is no way to set a hard and fast threshold. I would recommend  
running a set of them (20ish), checking them manually to assure that 
they are correct, then compute the mean and stddev of the mincost. For a 
new data set, you can compute a z-score of the mincost and then pick a 
threshold that you are comforatable with (you only have to worrry about 
it when the mincost is larger than the mean)



On 3/14/17 1:29 PM, Christopher Markiewicz wrote:

Hi Doug,

As an update, --init-coreg produced essentially the same result as 
--init-fsl; however, that was on EPIs we've discovered were LR flipped 
during reconstruction, so I've switched to a different test subject 
for now.


Now, for --init-fsl and --init-coreg, respectively, we get:
MinCost: 0.552768 531.638763 549.553173 0.397916
MinCost: 0.552773 531.586204 549.501644 0.394639
Again, very little difference between the two cases, so that's good. 
I'm not really sure how to judge what a reasonable min cost is. What 
criteria do you use, and is there more detailed documentation somewhere?

Thanks,
Chris
On Fri, Mar 10, 2017 at 10:41 AM, Douglas Greve 
> wrote:


That min cost (.86) is too high for sure. My guess is that it is
the fsl init. In general, bbregister is pretty insensitive to the
initialization method (as long as the init does not fail), so I
would not worry about some being done with coreg and some with flirt


On 3/9/17 3:40 PM, Christopher Markiewicz wrote:

Hi Doug,

This is the final line with "cost" in it:

MinCost: 0.862331 7440.183178 7411.264107 -1.819400

We're switching from FLIRT BBR (two-pass) to bbregister when
there's a reconstructed subject available, so I'm using
`--init-fsl` to try to minimize the differences in the pipeline
in the two cases, but I can try `--init-coreg` if there's
something wrong with the initialization.

Thanks,
Chris


On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve
> wrote:

that should have worked. what was the bbregister final cost
function? It
could have been that fsl did not provide a good initial
registration. If
you have v6, you can leave off --init-fsl and it will use
mri_coreg
(which is more robust).


On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> Hi all,
>
> Suppose you have a sub-pipeline:
>
> $ recon-all -s $SUBJ -i $T1 -all
> $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg
bbreg.dat
> --fslmat fsl.mat
>
> Now `bbreg.dat`/`fsl.mat` is registered to
> `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to
register to $T1?
>
> I've tried:
>
> $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
> --fslregout adjusted.mat
>
> And that's clearly wrong, but I'm kind of stuck on where to
go from
> here. Anybody see where I'm going wrong?
>
> Thanks,
> Chris
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


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Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi Doug,

As an update, --init-coreg produced essentially the same result as
--init-fsl; however, that was on EPIs we've discovered were LR flipped
during reconstruction, so I've switched to a different test subject for now.

Now, for --init-fsl and --init-coreg, respectively, we get:

MinCost: 0.552768 531.638763 549.553173 0.397916
MinCost: 0.552773 531.586204 549.501644 0.394639

Again, very little difference between the two cases, so that's good. I'm
not really sure how to judge what a reasonable min cost is. What criteria
do you use, and is there more detailed documentation somewhere?

Thanks,
Chris


On Fri, Mar 10, 2017 at 10:41 AM, Douglas Greve 
wrote:

> That min cost (.86) is too high for sure. My guess is that it is the fsl
> init. In general, bbregister is pretty insensitive to the initialization
> method (as long as the init does not fail), so I would not worry about some
> being done with coreg and some with flirt
>
> On 3/9/17 3:40 PM, Christopher Markiewicz wrote:
>
> Hi Doug,
>
> This is the final line with "cost" in it:
>
> MinCost: 0.862331 7440.183178 7411.264107 -1.819400
>
> We're switching from FLIRT BBR (two-pass) to bbregister when there's a
> reconstructed subject available, so I'm using `--init-fsl` to try to
> minimize the differences in the pipeline in the two cases, but I can try
> `--init-coreg` if there's something wrong with the initialization.
>
> Thanks,
> Chris
>
>
> On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve  > wrote:
>
>> that should have worked. what was the bbregister final cost function? It
>> could have been that fsl did not provide a good initial registration. If
>> you have v6, you can leave off --init-fsl and it will use mri_coreg
>> (which is more robust).
>>
>>
>> On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
>> > Hi all,
>> >
>> > Suppose you have a sub-pipeline:
>> >
>> > $ recon-all -s $SUBJ -i $T1 -all
>> > $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
>> > --fslmat fsl.mat
>> >
>> > Now `bbreg.dat`/`fsl.mat` is registered to
>> > `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to
>> $T1?
>> >
>> > I've tried:
>> >
>> > $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
>> > --fslregout adjusted.mat
>> >
>> > And that's clearly wrong, but I'm kind of stuck on where to go from
>> > here. Anybody see where I'm going wrong?
>> >
>> > Thanks,
>> > Chris
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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> 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
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Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Douglas Greve]

That min cost (.86) is too high for sure. My guess is that it is the fsl 
init. In general, bbregister is pretty insensitive to the initialization 
method (as long as the init does not fail), so I would not worry about 
some being done with coreg and some with flirt



On 3/9/17 3:40 PM, Christopher Markiewicz wrote:

Hi Doug,

This is the final line with "cost" in it:

MinCost: 0.862331 7440.183178 7411.264107 -1.819400

We're switching from FLIRT BBR (two-pass) to bbregister when there's a 
reconstructed subject available, so I'm using `--init-fsl` to try to 
minimize the differences in the pipeline in the two cases, but I can 
try `--init-coreg` if there's something wrong with the initialization.


Thanks,
Chris


On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve 
> wrote:


that should have worked. what was the bbregister final cost
function? It
could have been that fsl did not provide a good initial
registration. If
you have v6, you can leave off --init-fsl and it will use mri_coreg
(which is more robust).


On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> Hi all,
>
> Suppose you have a sub-pipeline:
>
> $ recon-all -s $SUBJ -i $T1 -all
> $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
> --fslmat fsl.mat
>
> Now `bbreg.dat`/`fsl.mat` is registered to
> `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to
register to $T1?
>
> I've tried:
>
> $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
> --fslregout adjusted.mat
>
> And that's clearly wrong, but I'm kind of stuck on where to go from
> here. Anybody see where I'm going wrong?
>
> Thanks,
> Chris
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/


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The information in this e-mail is intended only for the person to
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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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 . If the e-mail was sent
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi Doug,

This is the final line with "cost" in it:

MinCost: 0.862331 7440.183178 7411.264107 -1.819400

We're switching from FLIRT BBR (two-pass) to bbregister when there's a
reconstructed subject available, so I'm using `--init-fsl` to try to
minimize the differences in the pipeline in the two cases, but I can try
`--init-coreg` if there's something wrong with the initialization.

Thanks,
Chris


On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve 
wrote:

> that should have worked. what was the bbregister final cost function? It
> could have been that fsl did not provide a good initial registration. If
> you have v6, you can leave off --init-fsl and it will use mri_coreg
> (which is more robust).
>
>
> On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> > Hi all,
> >
> > Suppose you have a sub-pipeline:
> >
> > $ recon-all -s $SUBJ -i $T1 -all
> > $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
> > --fslmat fsl.mat
> >
> > Now `bbreg.dat`/`fsl.mat` is registered to
> > `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to
> $T1?
> >
> > I've tried:
> >
> > $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
> > --fslregout adjusted.mat
> >
> > And that's clearly wrong, but I'm kind of stuck on where to go from
> > here. Anybody see where I'm going wrong?
> >
> > Thanks,
> > Chris
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Douglas N Greve]

that should have worked. what was the bbregister final cost function? It 
could have been that fsl did not provide a good initial registration. If 
you have v6, you can leave off --init-fsl and it will use mri_coreg 
(which is more robust).


On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> Hi all,
>
> Suppose you have a sub-pipeline:
>
> $ recon-all -s $SUBJ -i $T1 -all
> $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat 
> --fslmat fsl.mat
>
> Now `bbreg.dat`/`fsl.mat` is registered to 
> `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?
>
> I've tried:
>
> $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1 
> --fslregout adjusted.mat
>
> And that's clearly wrong, but I'm kind of stuck on where to go from 
> here. Anybody see where I'm going wrong?
>
> Thanks,
> Chris
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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contains patient information, please contact the Partners Compliance HelpLine at
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