Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
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.
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
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.
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
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
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.
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
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don't see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don't see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don't see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 Doug,
I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then?
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 6/17/14 4:09 AM, Yang, Daniel wrote:
Hi Doug,
I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then?
It is used mostly in FSFAST
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don't see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think I just ran something like
bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl
Maybe I tweeked it manually
On 6/17/14 1:10 PM, Yang, Daniel wrote:
Hi Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don't see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 Doug,
Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl
And obtained the following:
fsaverage 1.000000 1.000000 0.150000 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round
Which is a little bit different from mni152.register.dat:
fsaverage 1.000000 1.000000 0.150000 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister
I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions:
1. Why are the two different? Is one better than the one, or the difference is trivial? Is it okay to use the one I generated myself? What “tweaks” were done in mni152.register.dat?
2. I see that there are multiple options in bbregister. For example, is it better to use --nearest?
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 7:15 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
I think I just ran something like
bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl
Maybe I tweeked it manually
On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
They look pretty similar. I doubt that there will be much practical difference.
On 6/17/14 3:08 PM, Yang, Daniel wrote:
Hi Doug,
Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl
And obtained the following:
fsaverage 1.000000 1.000000 0.150000 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round
Which is a little bit different from mni152.register.dat:
fsaverage 1.000000 1.000000 0.150000 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister
I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions:
- Why are the two different? Is one better than the one, or the
difference is trivial? Is it okay to use the one I generated myself? What "tweaks" were done in mni152.register.dat?
- I see that there are multiple options in bbregister. For example,
is it better to use --nearest?
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 7:15 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
I think I just ran something like
bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl
Maybe I tweeked it manually
On 6/17/14 1:10 PM, Yang, Daniel wrote:
Hi Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz One question: I don't see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I think this is a 1mm file? Best, Daniel On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)? Best, Daniel On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edu <mailto:yung-jui.yang@yale.edu>> wrote: Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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
Thanks! Does bbregister use orig.mgz in --s? If yes, I guess I should use MNI152_T1_1mm.nii.gz instead, since it has skull, like $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz.
Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 10:51 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
They look pretty similar. I doubt that there will be much practical difference.
On 6/17/14 3:08 PM, Yang, Daniel wrote: Hi Doug,
Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl
And obtained the following:
fsaverage 1.000000 1.000000 0.150000 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round
Which is a little bit different from mni152.register.dat:
fsaverage 1.000000 1.000000 0.150000 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister
I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions:
1. Why are the two different? Is one better than the one, or the difference is trivial? Is it okay to use the one I generated myself? What “tweaks” were done in mni152.register.dat?
2. I see that there are multiple options in bbregister. For example, is it better to use --nearest?
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 7:15 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
I think I just ran something like
bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl
Maybe I tweeked it manually
On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
bbregister uses the surfaces. Whether you use 1mm or 2mm depends on what you want to do with it and is not related to the resolution of the anatomical
On 6/17/14 5:58 PM, Yang, Daniel wrote:
Thanks! Does bbregister use orig.mgz in --s? If yes, I guess I should use MNI152_T1_1mm.nii.gz instead, since it has skull, like $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz.
Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 10:51 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
They look pretty similar. I doubt that there will be much practical difference.
On 6/17/14 3:08 PM, Yang, Daniel wrote:
Hi Doug,
Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl
And obtained the following:
fsaverage 1.000000 1.000000 0.150000 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round
Which is a little bit different from mni152.register.dat:
fsaverage 1.000000 1.000000 0.150000 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister
I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions:
- Why are the two different? Is one better than the one, or the
difference is trivial? Is it okay to use the one I generated myself? What "tweaks" were done in mni152.register.dat?
- I see that there are multiple options in bbregister. For example,
is it better to use --nearest?
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 7:15 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
I think I just ran something like
bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl
Maybe I tweeked it manually
On 6/17/14 1:10 PM, Yang, Daniel wrote:
Hi Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space?
> mri_binarize --i > ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o > right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: > It appears that Email in Plaint Text makes the command line look > ugly. Here is a cleaner view. These two should provide the right > amygdala as the anatomical ROI in MNI152 2mm space. > > mri_binarize --i > ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o > right_amygdala.mgz --match 54 > mri_vol2vol --mov right_amygdala.mgz --targ > ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz ---reg > ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat > --o right_amygdala.nii.gz > > If you run them, you will see what they do. They work for me. > > Again, my next question is, where can I find reg.1mm.mni152.dat? > Or how can I generate one? > > Thanks! > > On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edu > mailto:greve@nmr.mgh.harvard.edu> wrote: > > > Sorry, what are you trying to do with that vol2vol command? > The command > line is surely wrong ... > > > On 6/16/14 5:57 AM, Yang, Daniel wrote: > > Thanks! I see that mri_binarize + mri_vol2vol is what I > wanted. > > I am able to obtain, for example, the right amygdala, > using the following > commands: > > mri_binarize --i > ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz > --o right_amygdala.mgz --match 54 > mri_vol2vol --mov right_amygdala.mgz --targ > ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg > ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat > --o > right_amygdala.nii.gz > rm right_amygdala.mgz > > > One question: I don't see a file like > reg.1mm.mni152.dat. How do I obtain > a similar file in MNI152 1mm space, based on > ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <-- I > think this is a > 1mm file? > > Best, > Daniel > > On 6/15/14, 10:58 PM, "Bruce Fischl" > <fischl@nmr.mgh.harvard.edu > mailto:fischl@nmr.mgh.harvard.edu> wrote: > > mri_vol2vol with the transforms/talairach.xfm as the > transform should do > the trick. Make sure that the resample type is > nearest neighbor > > Cheers > Bruce > > On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" > <yung-jui.yang@yale.edu > mailto:yung-jui.yang@yale.edu> > wrote: > > Hi Bruce, > > Sorry, I wasn¹t clear. It¹s great to know that > the FreeSurfer is very > flexible. I meant to obtain the aseg individual > label files in MNI152 > space as NIfTI files, for example, the different > parts of the CC. > > Could you please point me to the right > direction, as to what tool I > should > use for this purpose (preferably a command line > tool, rather than a > visualization tool)? > > Best, > Daniel > > On 6/15/14, 10:16 PM, "Bruce Fischl" > <fischl@nmr.mgh.harvard.edu > mailto:fischl@nmr.mgh.harvard.edu> > wrote: > > Hi Daniel > Any of our tools can write nifti if you give > the output volume the > extension .nii or .nii.gz > > > Cheers > Bruce > > On Jun 15, 2014, at 5:54 PM, "Yang, > Daniel" <yung-jui.yang@yale.edu > mailto:yung-jui.yang@yale.edu> > wrote: > > Dear all, > > While it is possible to obtain NIfTI > files for cortical parcellation > using mri_annotation2label, I am running > if it is possible to obtain > NIfTI files associated with aseg parts? > > Thanks! > Daniel > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto: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 > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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
Thanks, then I guess I should use $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz, rather than $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz, since the surface has no skull...
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
bbregister uses the surfaces. Whether you use 1mm or 2mm depends on what you want to do with it and is not related to the resolution of the anatomical
On 6/17/14 5:58 PM, Yang, Daniel wrote: Thanks! Does bbregister use orig.mgz in --s? If yes, I guess I should use MNI152_T1_1mm.nii.gz instead, since it has skull, like $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz.
Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 10:51 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
They look pretty similar. I doubt that there will be much practical difference.
On 6/17/14 3:08 PM, Yang, Daniel wrote: Hi Doug,
Thanks! I ran this: bbregister --mov $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 1mmreg.dat --init-fsl
And obtained the following:
fsaverage 1.000000 1.000000 0.150000 9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 1.294338703155518e+00 -7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 -1.810301017761230e+01 -4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 -1.897199630737305e+01 0 0 0 1 round
Which is a little bit different from mni152.register.dat:
fsaverage 1.000000 1.000000 0.150000 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister
I am curious about this transformation because I want to transform BrainVoyager Talairach brain template to another common space. Two questions:
1. Why are the two different? Is one better than the one, or the difference is trivial? Is it okay to use the one I generated myself? What “tweaks” were done in mni152.register.dat?
2. I see that there are multiple options in bbregister. For example, is it better to use --nearest?
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 7:15 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
I think I just ran something like
bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl
Maybe I tweeked it manually
On 6/17/14 1:10 PM, Yang, Daniel wrote: Hi Doug,
Could you show us the full command of performing such a registration? Very curious! Thanks.
Best, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, June 17, 2014 at 4:30 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug
Thanks! Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction
On 6/16/14 6:16 PM, Yang, Daniel wrote: Hi Doug,
The way you are referring is to convert from MNI152 to MNI305? But I wanted to do the opposite. You can see that the right_amygdala.mgz I have as the input is already in the MNI305 space? mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 If I use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat, the product does not look right.
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec --interp nearest
doug
On 6/16/14 3:13 PM, Yang, Daniel wrote: Hi Doug,
I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm space. The code posted below, for example, generate the right amygdala in the MNI152 2mm space.
I am a little bit confused why my code is viewed as not doing sensible things. In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.
Could you tell me which part is wrong?
Thanks, Daniel
From: Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subcortical segment NIFTI files
Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense
doug
On 6/16/14 1:38 PM, Yang, Daniel wrote: It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space.
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz
If you run them, you will see what they do. They work for me.
Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I generate one?
Thanks!
On 6/16/14, 3:51 AM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ...
On 6/16/14 5:57 AM, Yang, Daniel wrote: Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.
I am able to obtain, for example, the right amygdala, using the following commands:
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mgz --targ ${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o right_amygdala.nii.gz rm right_amygdala.mgz
One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain a similar file in MNI152 1mm space, based on ${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz <― I think this is a 1mm file?
Best, Daniel
On 6/15/14, 10:58 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor
Cheers Bruce
On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Hi Bruce,
Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC.
Could you please point me to the right direction, as to what tool I should use for this purpose (preferably a command line tool, rather than a visualization tool)?
Best, Daniel
On 6/15/14, 10:16 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz
Cheers Bruce
On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu> wrote:
Dear all,
While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts?
Thanks! Daniel
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Yang, Daniel