Hi everyone,
Just a quick word of warning (plus two follow-up questions): there are more instances where your brain can get flipped. For example, I just regenerated my surface, using the correct orientation, certain about that. If I then do bbregister afterwards using the structural I convert back from the struct freesurfer used to contruct the surface (001.mgz, so mri_convert 001.mgz freesurferstruct.nii) like this
bbregister --mov freesurferstruct.nii --init-spm --reg someRegFile.dat --t1
Note: this should be perfect to start with. But, in contrast, it's flipped again. Why? Because of the init-spm. If I use init-header (or use tksurfer to generate the reg file) everything is fine, which makes kinda sense (I use a converted freesurfer file) not quite (it is a nifti file which has the right orientation in SPM viewer).
So why is this happening? Because of an incorrect/incomplete dicom conversion by the SPM-tools, which causes it to lose crucial orientation information?
Moreover: is there an easy sanity check to see whether the orientation is right now? I thought about superimposing the original structural, to see how it ends up on the surface (should nicely follow the sulci/gyrii), but apparently there is a strong gradient in there and it is quite dotted, so it ends up not showing me all gyrii, just a subset, and a bit scattered. Is there a better way?
Thanks again, hope also this is useful for others,
best, Frank ----- "Dan Wakeman" dgwakeman@gmail.com schreef:
Van: "Dan Wakeman" dgwakeman@gmail.com Aan: "F.T.M. Léoné (Frank)" f.leone@donders.ru.nl Verzonden: Donderdag 19 januari 2012 18:14:07 Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
Hi Frank,
If your problem is solved then it's fine. I didn't understand what you said, and I am not sure I still understand your hemisphere problems. Especially, because you cannot check the left right alignment (or even view any volume) in tksurfer.
In general I would say it makes more sense to align your functional data to your structural (as your higher resolution more accurate scan is then the "gold standard" that others get matched to: though I don't know if there is any scientific validity to that claim). It also fits better with the general FreeSurfer approach (correct me if I'm wrong list). I would also recommend converting your dicoms to nii using mri_convert, because mri_convert has much broader support for the nifti format than the SPM tools for converting dicoms i.e. more coordinate frame information is included in a nifti generated by mri_convert than by the default SPM tools.
D
On Thu, Jan 19, 2012 at 11:59 AM, Léoné, F.T.M. (Frank) f.leone@fcdonders.ru.nl wrote:
Hi Dan,
Sure. It was in my earlier e-mail of today: I use tksurfer, see
below. For this last test, I used the SPM display function though, that now shows them to both have the same orientation, so appears to be okay. Or am I still missing something?
best,
Frank
Hi Douglas,
Ah, makes sense, sorry for that.
I do most of the work in SPM, so:
- I have a highres structural scan, nii file format
- I convert it to a surface using recon-all
- Coregister the highres structural to the functional scan, so it
is
in the voxel size and orientation as the functional scans (SPM)
- I try to bbregister the coregistered and resliced T1 with the
surface using something like: bbregister --s S7_FS --mov
~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --init-spm --reg ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --t1
and view it with vglrun tkregister2 --mov
/home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --reg /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --surf
Here you see that I already use a flipped structural scan. If I do
it like this, bbregister converges to a nice and correct solution (everything aligns). If I don't, tkregister2 showms unregistered struc and func, while it is obvious it would be roughly aligned if you would flip either of them.
In addition/in general: What would be the recommended way to do the
coregistration etc. if you do all you analyses in SPM? Would it for example be better to coregistrate and reslice all functionals with the structural, so they are automatically aligned with the surface? Now I have a structural which is coregistered with the funcional and I realign that one, but that makes for one extra step where it can go wrong. Don't think this is related to the flip, but I also have a few alignment problems for other subjects.
Thanks a lot in advance,
best,
Frank ----- "Dan Wakeman" dgwakeman@gmail.com schreef:
Van: "Dan Wakeman" dgwakeman@gmail.com Aan: "F.T.M. Léoné (Frank)" f.leone@donders.ru.nl Cc: freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 19 januari 2012 17:09:28 Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
Hi Frank,
I think we still need to know. What software are you using to view
the
volumes?
D
On Thu, Jan 19, 2012 at 10:59 AM, Léoné, F.T.M. (Frank) f.leone@fcdonders.ru.nl wrote:
Hi Doug,
Ah, I found the cause myself, which might be useful for others.
It
happens already in the first step, before the ones I listed: in mri_convert. I do:
mri_convert struct.nii 001.mgz
And it flips. This I can see because I converted the mgz back
(mri_convert 001.mgz orig.nii) and then it's indeed reversed (and shifted, rotated, all rigid body transformations one can think
of).
Why does this happen? Is it normal for nii-files? I see that I can specify the orientation in mri_convert by doing mri_convert -in_orientation and then a three letter specification. I chose PSR
and
now the changes are far less severe (only a small shift still) and most importantly: no flip anymore. Do I now need to reconvert my
all
my surfaces? I don't hope, but I'm at least glad I have this one fixed.
best,
Frank
----- "Douglas N Greve" greve@nmr.mgh.harvard.edu schreef:
Van: "Douglas N Greve" greve@nmr.mgh.harvard.edu Aan: "Frank Leoné" f.leone@donders.ru.nl Cc: freesurfer@nmr.mgh.harvard.edu Verzonden: Woensdag 18 januari 2012 18:34:31 Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
Hi Frank, we'll need a lot more detail. Are you doing all of
this
in
FreeSurfer? What are your command lines? How are you evaluating whether volumes are flipped? doug
Léoné wrote:
Dear all,
I must be missing something really obvious, but it seems my
brains
are flipped. What I do:
- I have a highres structural scan, nii file format
- I convert it to a surface using recon-all
- Coregister the highres structural to the functional scan, so
it
is
in the voxel size and orientation as the functional scans
- I try to bbregister the coregistered and resliced T1 with
the
surface
But then: hey, it doesn't fit, my low-res T1 is flipped
compared
to
my y surface, hence to my original T1. So is it indeed true that
my
T1
might have been flipped? If so, does it make a wrong assumption
on
neurological vs radiological convention, or what is going on?
Thanks in advance,
best,
Frank _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Hi Frank, I think this problem is only spm related when using bbregister with the --init-spm option. This will in no way affect the anatomical analysis. According to my notes, this happens with spm8 when it uses analyze format. analyze is the default format used intermediate files by spmregister (called by bbregister). The lrrev should be apparent when you look at the registration with tkregister2. It should also be apparent in the mincost file created by bbregister. The mincost will probably be around .9 if lrrev. For proper registrations it will probably be less than .7.
doug
Léoné wrote:
Hi everyone,
Just a quick word of warning (plus two follow-up questions): there are more instances where your brain can get flipped. For example, I just regenerated my surface, using the correct orientation, certain about that. If I then do bbregister afterwards using the structural I convert back from the struct freesurfer used to contruct the surface (001.mgz, so mri_convert 001.mgz freesurferstruct.nii) like this
bbregister --mov freesurferstruct.nii --init-spm --reg someRegFile.dat --t1
Note: this should be perfect to start with. But, in contrast, it's flipped again. Why? Because of the init-spm. If I use init-header (or use tksurfer to generate the reg file) everything is fine, which makes kinda sense (I use a converted freesurfer file) not quite (it is a nifti file which has the right orientation in SPM viewer).
So why is this happening? Because of an incorrect/incomplete dicom conversion by the SPM-tools, which causes it to lose crucial orientation information?
Moreover: is there an easy sanity check to see whether the orientation is right now? I thought about superimposing the original structural, to see how it ends up on the surface (should nicely follow the sulci/gyrii), but apparently there is a strong gradient in there and it is quite dotted, so it ends up not showing me all gyrii, just a subset, and a bit scattered. Is there a better way?
Thanks again, hope also this is useful for others, best, Frank----- "Dan Wakeman" dgwakeman@gmail.com schreef:
Van: "Dan Wakeman" dgwakeman@gmail.com Aan: "F.T.M. Léoné (Frank)" f.leone@donders.ru.nl Verzonden: Donderdag 19 januari 2012 18:14:07 Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
Hi Frank,
If your problem is solved then it's fine. I didn't understand what you said, and I am not sure I still understand your hemisphere problems. Especially, because you cannot check the left right alignment (or even view any volume) in tksurfer.
In general I would say it makes more sense to align your functional data to your structural (as your higher resolution more accurate scan is then the "gold standard" that others get matched to: though I don't know if there is any scientific validity to that claim). It also fits better with the general FreeSurfer approach (correct me if I'm wrong list). I would also recommend converting your dicoms to nii using mri_convert, because mri_convert has much broader support for the nifti format than the SPM tools for converting dicoms i.e. more coordinate frame information is included in a nifti generated by mri_convert than by the default SPM tools.
D
On Thu, Jan 19, 2012 at 11:59 AM, Léoné, F.T.M. (Frank) f.leone@fcdonders.ru.nl wrote:
Hi Dan,
Sure. It was in my earlier e-mail of today: I use tksurfer, see
below. For this last test, I used the SPM display function though, that now shows them to both have the same orientation, so appears to be okay. Or am I still missing something?
best, FrankHi Douglas,
Ah, makes sense, sorry for that.
I do most of the work in SPM, so:
- I have a highres structural scan, nii file format
- I convert it to a surface using recon-all
- Coregister the highres structural to the functional scan, so it
is
in the voxel size and orientation as the functional scans (SPM)
- I try to bbregister the coregistered and resliced T1 with the
surface using something like: bbregister --s S7_FS --mov
~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --init-spm --reg ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --t1
and view it with vglrun tkregister2 --mov
/home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --reg /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --surf
Here you see that I already use a flipped structural scan. If I do
it like this, bbregister converges to a nice and correct solution (everything aligns). If I don't, tkregister2 showms unregistered struc and func, while it is obvious it would be roughly aligned if you would flip either of them.
In addition/in general: What would be the recommended way to do the
coregistration etc. if you do all you analyses in SPM? Would it for example be better to coregistrate and reslice all functionals with the structural, so they are automatically aligned with the surface? Now I have a structural which is coregistered with the funcional and I realign that one, but that makes for one extra step where it can go wrong. Don't think this is related to the flip, but I also have a few alignment problems for other subjects.
Thanks a lot in advance,
best, Frank----- "Dan Wakeman" dgwakeman@gmail.com schreef:
Van: "Dan Wakeman" dgwakeman@gmail.com Aan: "F.T.M. Léoné (Frank)" f.leone@donders.ru.nl Cc: freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 19 januari 2012 17:09:28 Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
Hi Frank,
I think we still need to know. What software are you using to view
the
volumes?
D
On Thu, Jan 19, 2012 at 10:59 AM, Léoné, F.T.M. (Frank) f.leone@fcdonders.ru.nl wrote:
Hi Doug,
Ah, I found the cause myself, which might be useful for others.
It
happens already in the first step, before the ones I listed: in mri_convert. I do:
mri_convert struct.nii 001.mgz
And it flips. This I can see because I converted the mgz back
(mri_convert 001.mgz orig.nii) and then it's indeed reversed (and shifted, rotated, all rigid body transformations one can think
of).
Why does this happen? Is it normal for nii-files? I see that I can specify the orientation in mri_convert by doing mri_convert -in_orientation and then a three letter specification. I chose PSR
and
now the changes are far less severe (only a small shift still) and most importantly: no flip anymore. Do I now need to reconvert my
all
my surfaces? I don't hope, but I'm at least glad I have this one fixed.
best, Frank----- "Douglas N Greve" greve@nmr.mgh.harvard.edu schreef:
Van: "Douglas N Greve" greve@nmr.mgh.harvard.edu Aan: "Frank Leoné" f.leone@donders.ru.nl Cc: freesurfer@nmr.mgh.harvard.edu Verzonden: Woensdag 18 januari 2012 18:34:31 Onderwerp: Re: [Freesurfer] Freesurfer flips brains?
Hi Frank, we'll need a lot more detail. Are you doing all of
this
in
FreeSurfer? What are your command lines? How are you evaluating whether volumes are flipped? doug
Léoné wrote:
> Dear all, > > I must be missing something really obvious, but it seems my >
brains
are flipped. What I do:
> - I have a highres structural scan, nii file format > - I convert it to a surface using recon-all > - Coregister the highres structural to the functional scan, so >
it
is
in the voxel size and orientation as the functional scans
> - I try to bbregister the coregistered and resliced T1 with >
the
surface
> But then: hey, it doesn't fit, my low-res T1 is flipped >
compared
to
my y surface, hence to my original T1. So is it indeed true that
my
T1
might have been flipped? If so, does it make a wrong assumption
on
neurological vs radiological convention, or what is going on?
> Thanks in advance, > > best, > > Frank > _______________________________________________ > 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Léoné, F.T.M. (Frank)