Apologies.
forwarded it on now
Thanks a million
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty
Hi Erik
can you cc the list so that others (like Doug!) can respond?
thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Hi Bruce,
Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear.
I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify,
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ?
So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage.
Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic.
Thanks again
best regards
Erik
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampa
l
subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
e
register.dat file automatically so created this using the bbregister tool
and
registered B0 image to my orig.mgz. I then used this dat to align my aseg
to
my diffusion space image and it worked well. The issue is when I try to us
e
it to transform my hippocampal subfield volumes to diffusion space. They j
ust
don't line up. Is this due to the different FOV for the subfields? Can any
one
advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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.
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image?
I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader
this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface.
but I might not understand what is going on ... doug
On 04/02/2014 03:03 PM, Erik O'Hanlon wrote:
Apologies.
forwarded it on now
Thanks a million
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty
Hi Erik
can you cc the list so that others (like Doug!) can respond?
thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Hi Bruce,
Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear.
I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify,
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ?
So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage.
Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic.
Thanks again
best regards
Erik
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampa
l
subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
e
register.dat file automatically so created this using the bbregister tool
and
registered B0 image to my orig.mgz. I then used this dat to align my aseg
to
my diffusion space image and it worked well. The issue is when I try to us
e
it to transform my hippocampal subfield volumes to diffusion space. They j
ust
don't line up. Is this due to the different FOV for the subfields? Can any
one
advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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
Hi Doug,
Thanks for that, I will give that a shot and see how it looks.
As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen.
Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see
Much appreciated.
best regards
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image?
I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader
this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface.
but I might not understand what is going on ... doug
On 04/02/2014 03:03 PM, Erik O'Hanlon wrote:
Apologies.
forwarded it on now
Thanks a million
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty
Hi Erik
can you cc the list so that others (like Doug!) can respond?
thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Hi Bruce,
Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear.
I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify,
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ?
So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage.
Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic.
Thanks again
best regards
Erik
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampa
l
subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
e
register.dat file automatically so created this using the bbregister tool
and
registered B0 image to my orig.mgz. I then used this dat to align my aseg
to
my diffusion space image and it worked well. The issue is when I try to us
e
it to transform my hippocampal subfield volumes to diffusion space. They j
ust
don't line up. Is this due to the different FOV for the subfields? Can any
one
advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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
-- 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: 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
Hi Doug,
I managed to get the subfield volumes aligned at last. I used bbregister to get the dat file for the No_diff2orig transform. Then used tkregister2 to get the dat for my subfield volume to orig. Used mdi_vol2vol to align my subfield vol to the orig.mgz. Finally aligned the subfieldaligned_orig file to the No_diff image using mdi_vol2vol with the regsiterNodiff2orig.dat file and the --inv flag. I know it's probably not the best way to do it but it all aligns nicely.
Thanks for the pointers
Cheers
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohanlon@rcsi.ie] Sent: 03 April 2014 10:23 To: Freesurfer support list Subject: Re: [Freesurfer] FW: registration difficulty
Hi Doug,
Thanks for that, I will give that a shot and see how it looks.
As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen.
Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see
Much appreciated.
best regards
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image?
I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader
this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface.
but I might not understand what is going on ... doug
On 04/02/2014 03:03 PM, Erik O'Hanlon wrote:
Apologies.
forwarded it on now
Thanks a million
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty
Hi Erik
can you cc the list so that others (like Doug!) can respond?
thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Hi Bruce,
Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear.
I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify,
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ?
So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage.
Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic.
Thanks again
best regards
Erik
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampa
l
subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
e
register.dat file automatically so created this using the bbregister tool
and
registered B0 image to my orig.mgz. I then used this dat to align my aseg
to
my diffusion space image and it worked well. The issue is when I try to us
e
it to transform my hippocampal subfield volumes to diffusion space. They j
ust
don't line up. Is this due to the different FOV for the subfields? Can any
one
advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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
-- 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: 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
First run this tkregister2 --mov hipposubfield.mgz --reg hsf.reg.dat --s subject --regheader --fstarg
It will bring up the tkregister2 GUI and just double check that the subfields are where they need to be. Hit "Save Reg" and exit. In the future, you can run the tkregister2 command with --noedit and it will not bring the GUI up (and will save the registration). hipposubfield.mgz is the HSF segmentation.
Now run
mri_matrix_multiple -im register.dof6.dat -iim hsf.reg.dat -om func2hsf.reg.dat
where register.dof6.dat is the registration between the functional and anatomical
Check that it looks ok
tkregister2 --mov func.nii.gz --targ hipposubfield.mgz --reg func2hsf.reg.dat
I'm not sure what your final plans are, but you can use func2hsf.reg.dat with mri_vol2vol (similar to the tkregister2 cmd above)
doug
On 04/03/2014 05:23 AM, Erik O'Hanlon wrote:
Hi Doug,
Thanks for that, I will give that a shot and see how it looks.
As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen.
Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see
Much appreciated.
best regards
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image?
I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader
this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface.
but I might not understand what is going on ... doug
On 04/02/2014 03:03 PM, Erik O'Hanlon wrote:
Apologies.
forwarded it on now
Thanks a million
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty
Hi Erik
can you cc the list so that others (like Doug!) can respond?
thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Hi Bruce,
Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear.
I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify,
should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ?
So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage.
Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic.
Thanks again
best regards
Erik
Hi Erik
so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go).
cheers Bruce
On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
Dear FS experts,
I am running my first FS analysis and I'm trying to register my hippocampa
l
subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
e
register.dat file automatically so created this using the bbregister tool
and
registered B0 image to my orig.mgz. I then used this dat to align my aseg
to
my diffusion space image and it worked well. The issue is when I try to us
e
it to transform my hippocampal subfield volumes to diffusion space. They j
ust
don't line up. Is this due to the different FOV for the subfields? Can any
one
advise how to get these volumes to transform correctly?
Any help would be greatly appreciated.
Thanks
Erik
Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher
[IMAGE]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.ie
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