Hi all,
I used
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --manual
to register and edit the registration of a functional to its anatomical volume. The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using tkregister2, but I can't figure out how to make a flip. Does anyone know the best way to do that? If the registration looks so bad do I need to change something in the command for my initial registration process? Thanks!
Best,
Stacy
---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
Hi all,
I used
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --manual
to register and edit the registration of a functional to its anatomical volume. The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using tkregister2, but I can't figure out how to make a flip. Does anyone know the best way to do that? If the registration looks so bad do I need to change something in the command for my initial registration process? Thanks!
Best,
Stacy
This message was sent using IMP, the Internet Messaging Program.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, I actually ended up finding that SagMir button and after playing around with it I got it to fit the surface. By lowering the intensity and comparing the fit between the two hemi's in the sagittal view it became obvious which one fit better. The orientation was initialy completely upside down and flipped the wrong way. Is it very uncommon to need to adjust so much? What could be the reason? I am using nifti.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
Hi all,
I used
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --manual
to register and edit the registration of a functional to its anatomical
volume.
The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using
tkregister2,
but I can't figure out how to make a flip. Does anyone know the best way to
do
that? If the registration looks so bad do I need to change something in the command for my initial registration process? Thanks!
Best,
Stacy
This message was sent using IMP, the Internet Messaging Program.
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
No, you should not need to do that much adjustment. Is this a full or partial volume?
It could be that your nifti volume is oriented incorrectly. To check this,
tkmedit -f example_func.nii
Make sure that the different cardinal views are oriented correctly.
doug
Stacy Chu wrote:
Thanks, I actually ended up finding that SagMir button and after playing around with it I got it to fit the surface. By lowering the intensity and comparing the fit between the two hemi's in the sagittal view it became obvious which one fit better. The orientation was initialy completely upside down and flipped the wrong way. Is it very uncommon to need to adjust so much? What could be the reason? I am using nifti.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
Hi all,
I used
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --manual
to register and edit the registration of a functional to its anatomical
volume.
The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using
tkregister2,
but I can't figure out how to make a flip. Does anyone know the best way to
do
that? If the registration looks so bad do I need to change something in the command for my initial registration process? Thanks!
Best,
Stacy
This message was sent using IMP, the Internet Messaging Program.
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
Funny, I checked example_func in tkmedit like you said, and it looks fine. Attached are screenshots of that and the initial registration. Sorry the tkmedit window is a little distorted, it got squished when I pasted it into paint. After fixing it in tkregister2 the overlay looks correct (compared to how it looks in fslview) but let me know if you think there might have been a glitch somewhere in the whole process that I don't know about..I'm just suspicious because, like you said, I shouldn't have had to adjust so much. I'll have to do this later with other subjects, I'll email again if it happens again. Thanks for your help Doug.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
No, you should not need to do that much adjustment. Is this a full or partial volume?
It could be that your nifti volume is oriented incorrectly. To check this,
tkmedit -f example_func.nii
Make sure that the different cardinal views are oriented correctly.
doug
Stacy Chu wrote:
Thanks, I actually ended up finding that SagMir button and after playing
around
with it I got it to fit the surface. By lowering the intensity and
comparing
the fit between the two hemi's in the sagittal view it became obvious which
one
fit better. The orientation was initialy completely upside down and flipped
the
wrong way. Is it very uncommon to need to adjust so much? What could be
the
reason? I am using nifti.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
Hi all,
I used
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
--manual
to register and edit the registration of a functional to its anatomical
volume.
The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using
tkregister2,
but I can't figure out how to make a flip. Does anyone know the best way
to
do
that? If the registration looks so bad do I need to change something in
the
command for my initial registration process? Thanks!
Best,
Stacy
This message was sent using IMP, the Internet Messaging Program.
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
Out of curiosity, how does the registration to standard space look? Check it with:
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
You can also look at the initial func-struct registration with:
tkregister2 --mov example_func.nii --s FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --regheader --reg /tmp/junk
This will likely be way off, but it should get things more or less lined up (to within 45degrees rotation), if not, then that's a problem.
doug
Stacy Chu wrote:
Funny, I checked example_func in tkmedit like you said, and it looks fine. Attached are screenshots of that and the initial registration. Sorry the tkmedit window is a little distorted, it got squished when I pasted it into paint. After fixing it in tkregister2 the overlay looks correct (compared to how it looks in fslview) but let me know if you think there might have been a glitch somewhere in the whole process that I don't know about..I'm just suspicious because, like you said, I shouldn't have had to adjust so much. I'll have to do this later with other subjects, I'll email again if it happens again. Thanks for your help Doug.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
No, you should not need to do that much adjustment. Is this a full or partial volume?
It could be that your nifti volume is oriented incorrectly. To check this,
tkmedit -f example_func.nii
Make sure that the different cardinal views are oriented correctly.
doug
Stacy Chu wrote:
Thanks, I actually ended up finding that SagMir button and after playing
around
with it I got it to fit the surface. By lowering the intensity and
comparing
the fit between the two hemi's in the sagittal view it became obvious which
one
fit better. The orientation was initialy completely upside down and flipped
the
wrong way. Is it very uncommon to need to adjust so much? What could be
the
reason? I am using nifti.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
Hi all,
I used
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
--manual
to register and edit the registration of a functional to its anatomical
volume.
The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using
tkregister2,
but I can't figure out how to make a flip. Does anyone know the best way
to
do
that? If the registration looks so bad do I need to change something in
the
command for my initial registration process? Thanks!
Best,
Stacy
This message was sent using IMP, the Internet Messaging Program.
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
When I type
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
I get an error message saying ERROR: Option --feat unknown
I also did the second check you recommended and it looks good. But I just realized - and this could be why it came out fine when I checked example_func in tkmedit - I already fixed the registration using tkregister2. I dont know why I didn't realize this before. example_func.nii would get corrected when I save changes, no? So maybe it was just that the nifti volume was oriented incorrectly?
By the way, could I ask you to check the .gfeat problem I ran into when you get a chance? I sent it to the mailing list. Thanks very much for all your help!
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
Out of curiosity, how does the registration to standard space look? Check it with:
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
You can also look at the initial func-struct registration with:
tkregister2 --mov example_func.nii --s FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --regheader --reg /tmp/junk
This will likely be way off, but it should get things more or less lined up (to within 45degrees rotation), if not, then that's a problem.
doug
Stacy Chu wrote:
Funny, I checked example_func in tkmedit like you said, and it looks fine. Attached are screenshots of that and the initial registration. Sorry the tkmedit window is a little distorted, it got squished when I pasted it into paint. After fixing it in tkregister2 the overlay looks correct (compared
to
how it looks in fslview) but let me know if you think there might have been
a
glitch somewhere in the whole process that I don't know about..I'm just suspicious because, like you said, I shouldn't have had to adjust so much. I'll have to do this later with other subjects, I'll email again if it
happens
again. Thanks for your help Doug.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
No, you should not need to do that much adjustment. Is this a full or partial volume?
It could be that your nifti volume is oriented incorrectly. To check this,
tkmedit -f example_func.nii
Make sure that the different cardinal views are oriented correctly.
doug
Stacy Chu wrote:
Thanks, I actually ended up finding that SagMir button and after playing
around
with it I got it to fit the surface. By lowering the intensity and
comparing
the fit between the two hemi's in the sagittal view it became obvious
which
one
fit better. The orientation was initialy completely upside down and
flipped
the
wrong way. Is it very uncommon to need to adjust so much? What could be
the
reason? I am using nifti.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
Hi all,
I used
reg-feat2anat --feat
istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
--subject
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
and then
reg-feat2anat --feat
istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
--subject
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
--manual
to register and edit the registration of a functional to its anatomical
volume.
The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using
tkregister2,
but I can't figure out how to make a flip. Does anyone know the best
way
to
do
that? If the registration looks so bad do I need to change something in
the
command for my initial registration process? Thanks!
Best,
Stacy
This message was sent using IMP, the Internet Messaging Program.
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
You may have an older version, I've put an update (for Linux) here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2
Stacy Chu wrote:
When I type
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
I get an error message saying ERROR: Option --feat unknown
I also did the second check you recommended and it looks good. But I just realized - and this could be why it came out fine when I checked example_func in tkmedit - I already fixed the registration using tkregister2. I dont know why I didn't realize this before. example_func.nii would get corrected when I save changes, no? So maybe it was just that the nifti volume was oriented incorrectly?
By the way, could I ask you to check the .gfeat problem I ran into when you get a chance? I sent it to the mailing list. Thanks very much for all your help!
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
Out of curiosity, how does the registration to standard space look? Check it with:
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
You can also look at the initial func-struct registration with:
tkregister2 --mov example_func.nii --s FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --regheader --reg /tmp/junk
This will likely be way off, but it should get things more or less lined up (to within 45degrees rotation), if not, then that's a problem.
doug
Stacy Chu wrote:
Funny, I checked example_func in tkmedit like you said, and it looks fine. Attached are screenshots of that and the initial registration. Sorry the tkmedit window is a little distorted, it got squished when I pasted it into paint. After fixing it in tkregister2 the overlay looks correct (compared
to
how it looks in fslview) but let me know if you think there might have been
a
glitch somewhere in the whole process that I don't know about..I'm just suspicious because, like you said, I shouldn't have had to adjust so much. I'll have to do this later with other subjects, I'll email again if it
happens
again. Thanks for your help Doug.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
No, you should not need to do that much adjustment. Is this a full or partial volume?
It could be that your nifti volume is oriented incorrectly. To check this,
tkmedit -f example_func.nii
Make sure that the different cardinal views are oriented correctly.
doug
Stacy Chu wrote:
Thanks, I actually ended up finding that SagMir button and after playing
around
with it I got it to fit the surface. By lowering the intensity and
comparing
the fit between the two hemi's in the sagittal view it became obvious
which
one
fit better. The orientation was initialy completely upside down and
flipped
the
wrong way. Is it very uncommon to need to adjust so much? What could be
the
reason? I am using nifti.
Stacy
Quoting Doug Greve greve@nmr.mgh.harvard.edu:
You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti?
Stacy Chu wrote:
>Hi all, > >I used > >reg-feat2anat --feat > >
istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
>--subject > > > >
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
>and then > >reg-feat2anat --feat > >
istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
>--subject > > > >
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
>--manual > >to register and edit the registration of a functional to its anatomical > > > > > > volume.
>The initial registration came out pretty bad and I think I need to do a >left-right flip. I see that I can rotate/translate/resize using > > > > > > tkregister2,
>but I can't figure out how to make a flip. Does anyone know the best > >
way
> >
to
> > do
>that? If the registration looks so bad do I need to change something in > > > >
the
>command for my initial registration process? Thanks! > >Best, > >Stacy > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > >_______________________________________________ >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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
This message was sent using IMP, the Internet Messaging Program.
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Stacy Chu