Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them give me an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced, Gabriel
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them give me an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced, Gabriel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have used both for the output of mni152reg:
mri_vol2vol --mov /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --targ /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat --inv --o /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz
and
mri_vol2vol --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat --o /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz
I also have tried these two commands with the output matrix of bbregister s001_register.dat
----- Mensaje original ----- De: Douglas Greve greve@nmr.mgh.harvard.edu Fecha: Jueves, 27 de Marzo de 2014, 4:11 am Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu
>
What is your vol2vol command line?
> >
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
> Dear FS experts, > >
I've been dealing with the conversion to MNI152 of some volumetric labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed.
> >
I've tried bbregister and mni152reg commands, both of them give me an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it.
> >
Any help will be really appreciated.
> >
Many thanks in advanced, Gabriel
> > _______________________________________________ > 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
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.
<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
The first one should be correct. How are you visualizing it? What is the command line?
On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
I have used both for the output of mni152reg:
mri_vol2vol --mov /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --targ /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat --inv --o /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz
and
mri_vol2vol --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat --o /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz
I also have tried these two commands with the output matrix of bbregister s001_register.dat
----- Mensaje original ----- De: Douglas Greve greve@nmr.mgh.harvard.edu Fecha: Jueves, 27 de Marzo de 2014, 4:11 am Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some volumetric
labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them give me
an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced, Gabriel
_______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu <javascript:main.compose('new', 't=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
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.
<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have tried several thing like opening on MriCroN and tkregister as:
tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg /root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat
----- Mensaje original ----- De: Douglas N Greve greve@nmr.mgh.harvard.edu Fecha: Jueves, 27 de Marzo de 2014, 5:54 pm Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu
The first one should be correct. How are you visualizing it? What is the command line?
On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
I have used both for the output of mni152reg:
mri_vol2vol --mov /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
targ
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--inv --o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz>
and
mri_vol2vol --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
mov
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz>
I also have tried these two commands with the output matrix of bbregister s001_register.dat
----- Mensaje original ----- De: Douglas Greve greve@nmr.mgh.harvard.edu Fecha: Jueves, 27 de Marzo de 2014, 4:11 am Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some
volumetric
labels of my subjects extracted with mris_extract_label in FS
v.5.1
but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them
give me
an example to check at the registrations using tktegister2,
when I
use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they
appear
to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced, Gabriel
_______________________________________________ > Freesurfer
mailing list >Freesurfer@nmr.mgh.harvard.edu <javascript:main.compose('new', 't=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
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.
<font size="3">--------------------------<br />PhD.
student Gabriel
González-Escamilla<br />Laboratory of Functional
Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br
/>University
Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 -
Seville<br
/>- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
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
<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
try tkmedit -f MNI152 -aux aseg.mgz
On 03/27/2014 01:18 PM, Gabriel Gonzalez Escamilla wrote:
I have tried several thing like opening on MriCroN and tkregister as:
tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg /root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat
----- Mensaje original ----- De: Douglas N Greve greve@nmr.mgh.harvard.edu Fecha: Jueves, 27 de Marzo de 2014, 5:54 pm Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu
The first one should be correct. How are you visualizing it? What is the command line?
On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
I have used both for the output of mni152reg:
mri_vol2vol --mov /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
targ
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--inv --o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz>
and
mri_vol2vol --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
mov
/root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
--o
/root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz>
I also have tried these two commands with the output matrix of bbregister s001_register.dat
----- Mensaje original ----- De: Douglas Greve greve@nmr.mgh.harvard.edu Fecha: Jueves, 27 de Marzo de 2014, 4:11 am Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu
What is your vol2vol command line?
On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I've been dealing with the conversion to MNI152 of some
volumetric
labels of my subjects extracted with mris_extract_label in FS
v.5.1
but, I've been unable to succeed.
I've tried bbregister and mni152reg commands, both of them
give me
an example to check at the registrations using tktegister2,
when I
use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they
appear
to be rotated, I don't know how is it possible or how to fix it.
Any help will be really appreciated.
Many thanks in advanced, Gabriel
_______________________________________________ > Freesurfer
mailing list >Freesurfer@nmr.mgh.harvard.edu <javascript:main.compose('new', 't=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
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.
<font size="3">--------------------------<br />PhD.
student Gabriel
González-Escamilla<br />Laboratory of Functional
Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br
/>University
Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 -
Seville<br
/>- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
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
<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Gabriel Gonzalez Escamilla