Hello,
I am new to freesurfer. I have been looking for an answer to this issue for days.
I ran bbregister to align a dti scan to a t1 struc.
It worked beautifully.
I am trying to register a very abnormal looking dataset to the t1 using the registration parameters created during the first bbregister (dti to t1).
I have been unable to figure this out, but it seems like it must be a common procedure. Any advice would be greatly appreciated.
I don't know what you are trying to do. Can you elaborate?
On 04/19/2017 07:26 PM, Jacobson, Aaron wrote:
Hello,
I am new to freesurfer. I have been looking for an answer to this issue for days.
I ran bbregister to align a dti scan to a t1 struc.
It worked beautifully.
I am trying to register a very abnormal looking dataset to the t1 using the registration parameters created during the first bbregister (dti to t1).
I have been unable to figure this out, but it seems like it must be a common procedure. Any advice would be greatly appreciated.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Absolutely, thanks for looking into this.
I have 3 datasets:
1. T1 anatomical 2. DTI 3. Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data
I want to register the unusual dataset (#3) to the T1 anatomical.
Since the unusual dataset cannot be read successfully by bbregister, I registered the DTI to the anatomical and I would like to use the registration parameters from that registration (DTI to t1) to register the unusual dataset to the T1.
Is this a possibility?
Aaron D. Jacobson Technical Operations Manager UCSD Center for Functional MRI 9500 Gilman Drive La Jolla CA 92093-0677
On 4/20/17, 8:09 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
I don't know what you are trying to do. Can you elaborate?
On 04/19/2017 07:26 PM, Jacobson, Aaron wrote: > Hello, > > I am new to freesurfer. I have been looking for an answer to this > issue for days. > > I ran bbregister to align a dti scan to a t1 struc. > > It worked beautifully. > > I am trying to register a very abnormal looking dataset to the t1 > using the registration parameters created during the first bbregister > (dti to t1). > > I have been unable to figure this out, but it seems like it must be a > common procedure. Any advice would be greatly appreciated. > > > _______________________________________________ > 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
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.
Yes, when using mri_vol2vol or mri_vol2surf, spec the unusual data set as the --mov but pass the bbregister registration to the --reg flag.
On 04/20/2017 11:41 AM, Jacobson, Aaron wrote:
Absolutely, thanks for looking into this.
I have 3 datasets:
- T1 anatomical
- DTI
- Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data
I want to register the unusual dataset (#3) to the T1 anatomical.
Since the unusual dataset cannot be read successfully by bbregister, I registered the DTI to the anatomical and I would like to use the registration parameters from that registration (DTI to t1) to register the unusual dataset to the T1.
Is this a possibility?
Aaron D. Jacobson Technical Operations Manager UCSD Center for Functional MRI 9500 Gilman Drive La Jolla CA 92093-0677
On 4/20/17, 8:09 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
I don't know what you are trying to do. Can you elaborate? On 04/19/2017 07:26 PM, Jacobson, Aaron wrote: > Hello, > > I am new to freesurfer. I have been looking for an answer to this > issue for days. > > I ran bbregister to align a dti scan to a t1 struc. > > It worked beautifully. > > I am trying to register a very abnormal looking dataset to the t1 > using the registration parameters created during the first bbregister > (dti to t1). > > I have been unable to figure this out, but it seems like it must be a > common procedure. Any advice would be greatly appreciated. > > > _______________________________________________ > 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 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
Thanks a lot! That worked well! The registration is not perfect, but it is much better than the original.
I used the command:
mri_vol2vol --mov PathTo/UnusualData.nii.gz --targ PathTo/orig.nii.gz --interp nearest --o PathTo/UnusualData_toT1reg.nii.gz --reg PathTo/dti2t1.dat
Is there anything you would suggest that I run differently?
Aaron D. Jacobson Technical Operations Manager UCSD Center for Functional MRI 9500 Gilman Drive La Jolla CA 92093-0677
On 4/20/17, 8:42 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Yes, when using mri_vol2vol or mri_vol2surf, spec the unusual data set as the --mov but pass the bbregister registration to the --reg flag.
On 04/20/2017 11:41 AM, Jacobson, Aaron wrote: > Absolutely, thanks for looking into this. > > I have 3 datasets: > > 1. T1 anatomical > 2. DTI > 3. Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data > > I want to register the unusual dataset (#3) to the T1 anatomical. > > Since the unusual dataset cannot be read successfully by bbregister, I registered the DTI to the anatomical and I would like to use the registration parameters from that registration (DTI to t1) to register the unusual dataset to the T1. > > Is this a possibility? > > Aaron D. Jacobson > Technical Operations Manager > UCSD Center for Functional MRI > 9500 Gilman Drive > La Jolla CA 92093-0677 > > > > On 4/20/17, 8:09 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: > > I don't know what you are trying to do. Can you elaborate? > > > On 04/19/2017 07:26 PM, Jacobson, Aaron wrote: > > Hello, > > > > I am new to freesurfer. I have been looking for an answer to this > > issue for days. > > > > I ran bbregister to align a dti scan to a t1 struc. > > > > It worked beautifully. > > > > I am trying to register a very abnormal looking dataset to the t1 > > using the registration parameters created during the first bbregister > > (dti to t1). > > > > I have been unable to figure this out, but it seems like it must be a > > common procedure. Any advice would be greatly appreciated. > > > > > > _______________________________________________ > > 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 > > > 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
That command looks right. If the unusual volume was derived in a voxel-for-voxel way from the DTI, then its registration should be just as good
On 04/20/2017 12:11 PM, Jacobson, Aaron wrote:
Thanks a lot! That worked well! The registration is not perfect, but it is much better than the original.
I used the command:
mri_vol2vol --mov PathTo/UnusualData.nii.gz --targ PathTo/orig.nii.gz --interp nearest --o PathTo/UnusualData_toT1reg.nii.gz --reg PathTo/dti2t1.dat
Is there anything you would suggest that I run differently?
Aaron D. Jacobson Technical Operations Manager UCSD Center for Functional MRI 9500 Gilman Drive La Jolla CA 92093-0677
On 4/20/17, 8:42 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
Yes, when using mri_vol2vol or mri_vol2surf, spec the unusual data set as the --mov but pass the bbregister registration to the --reg flag. On 04/20/2017 11:41 AM, Jacobson, Aaron wrote: > Absolutely, thanks for looking into this. > > I have 3 datasets: > > 1. T1 anatomical > 2. DTI > 3. Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data > > I want to register the unusual dataset (#3) to the T1 anatomical. > > Since the unusual dataset cannot be read successfully by bbregister, I registered the DTI to the anatomical and I would like to use the registration parameters from that registration (DTI to t1) to register the unusual dataset to the T1. > > Is this a possibility? > > Aaron D. Jacobson > Technical Operations Manager > UCSD Center for Functional MRI > 9500 Gilman Drive > La Jolla CA 92093-0677 > > > > On 4/20/17, 8:09 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: > > I don't know what you are trying to do. Can you elaborate? > > > On 04/19/2017 07:26 PM, Jacobson, Aaron wrote: > > Hello, > > > > I am new to freesurfer. I have been looking for an answer to this > > issue for days. > > > > I ran bbregister to align a dti scan to a t1 struc. > > > > It worked beautifully. > > > > I am trying to register a very abnormal looking dataset to the t1 > > using the registration parameters created during the first bbregister > > (dti to t1). > > > > I have been unable to figure this out, but it seems like it must be a > > common procedure. Any advice would be greatly appreciated. > > > > > > _______________________________________________ > > 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 > > > 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
freesurfer@nmr.mgh.harvard.edu
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Jacobson, Aaron