Re: [Freesurfer] mri_cvs_register for EPI
Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below: I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject - template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? The file ddescritions are detailed if you run mri_cvs_register --help. For your purposes you do not need to use the --nocleanup option. The final ransformation that you will need is called final*norm.m3z In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ * --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.affine.mgz el_reg_tocvs_avg35_inMNI152_aseg.mgz el_reg_tocvs_avg35_inMNI152.mgz final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log transform.txt These comments are wrt to an older version of the code. We do not use the tm3d format any more. I will update the wiki. In my particular case, which images should be entered as arguments to --template and --subject ? template is always your target (atlas space where you are registering TO) and subject is the moving image that you are registering. 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI - anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. You will need the m3z file from cvs and the rigid registration that you get from BBR. Lilla ___ 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.
Re: [Freesurfer] mri_cvs_register for EPI
Hello Lilla, thank you the clarifications. I managed to get mri_vol2vol running, but I have one remaining obstacle - when I use the CVS template as target volume, the EPIs get resampled to 1mm isotropic voxels. I need to get a 3x3x3mm resolution. I tried to use mri_convert -vs 3 3 3 norm.mgz norm333.mgz on the template and then use norm333.mgz in the mri_vol2vol commandline (mri_vol2vol --targ /home/marcel/freesurfer/subjects/cvs_avg35_inMNI152/mri/norm333.mgz --m3z final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg register.dof6.dat --mov onevol.nii.gz --o fmri_cvs333.nii.gz), but the fmri_cvs333.nii.gz volume produced by this command is empty. One option is to resample the normalized EPI in CVS template space, but interpolating the image twice is not a very good idea... Can you think of any solutions to this issue? Best regards, Marcel 2013/8/8 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below: I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject - template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? The file ddescritions are detailed if you run mri_cvs_register --help. For your purposes you do not need to use the --nocleanup option. The final ransformation that you will need is called final*norm.m3z In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ * --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.**affine.mgz el_reg_tocvs_avg35_inMNI152_**aseg.mgz el_reg_tocvs_avg35_inMNI152.**mgz final_CVSmorphed_tocvs_avg35_**inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_**inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_**inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_**inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_**inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_**inMNI152.mri_cvs_register.**1308031447.log transform.txt These comments are wrt to an older version of the code. We do not use the tm3d format any more. I will update the wiki. In my particular case, which images should be entered as arguments to --template and --subject ? template is always your target (atlas space where you are registering TO) and subject is the moving image that you are registering. 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI - anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. You will need the m3z file from cvs and the rigid registration that you get from BBR. Lilla 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/**compliancelinehttp://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 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
Re: [Freesurfer] mri_cvs_register for EPI
Hi Marcel, We have encountered this problem before, but we have not come up with the perfect solution yet. As you dais, either the volume gets resampled twice or the high res tranformation needs to be downsampled. Neither of these is ideal, but I am planning on implementing applying the morph and downsampling as one step in the near future. Lilla On Thu, 8 Aug 2013, Marcel Falkiewicz wrote: Hello Lilla, thank you the clarifications. I managed to get mri_vol2vol running, but I have one remaining obstacle - when I use the CVS template as target volume, the EPIs get resampled to 1mm isotropic voxels. I need to get a 3x3x3mm resolution. I tried to use mri_convert -vs 3 3 3 norm.mgz norm333.mgz on the template and then use norm333.mgz in the mri_vol2vol commandline (mri_vol2vol --targ /home/marcel/freesurfer/subjects/cvs_avg35_inMNI152/mri/norm333.mgz --m3z final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg register.dof6.dat --mov onevol.nii.gz --o fmri_cvs333.nii.gz), but the fmri_cvs333.nii.gz volume produced by this command is empty. One option is to resample the normalized EPI in CVS template space, but interpolating the image twice is not a very good idea... Can you think of any solutions to this issue? Best regards, Marcel 2013/8/8 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below: I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject - template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? The file ddescritions are detailed if you run mri_cvs_register --help. For your purposes you do not need to use the --nocleanup option. The final ransformation that you will need is called final*norm.m3z In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ * --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.affine.mgz el_reg_tocvs_avg35_inMNI152_aseg.mgz el_reg_tocvs_avg35_inMNI152.mgz final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log transform.txt These comments are wrt to an older version of the code. We do not use the tm3d format any more. I will update the wiki. In my particular case, which images should be entered as arguments to --template and --subject ? template is always your target (atlas space where you are registering TO) and subject is the moving image that you are registering. 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI - anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. You will need the m3z file from cvs and the rigid registration that you get from BBR. Lilla 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
Re: [Freesurfer] mri_cvs_register for EPI
Thank you Lilla, this explains my case. The accuracy of mri_cvs_register is legendary and incorporating this into standard fMRI processing pipeline is most desirable:) Could you please inform the group once this feature is implemented? Thank you! Best regards, Marcel 2013/8/8 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Marcel, We have encountered this problem before, but we have not come up with the perfect solution yet. As you dais, either the volume gets resampled twice or the high res tranformation needs to be downsampled. Neither of these is ideal, but I am planning on implementing applying the morph and downsampling as one step in the near future. Lilla On Thu, 8 Aug 2013, Marcel Falkiewicz wrote: Hello Lilla, thank you the clarifications. I managed to get mri_vol2vol running, but I have one remaining obstacle - when I use the CVS template as target volume, the EPIs get resampled to 1mm isotropic voxels. I need to get a 3x3x3mm resolution. I tried to use mri_convert -vs 3 3 3 norm.mgz norm333.mgz on the template and then use norm333.mgz in the mri_vol2vol commandline (mri_vol2vol --targ /home/marcel/freesurfer/**subjects/cvs_avg35_inMNI152/**mri/norm333.mgz --m3z final_CVSmorph_tocvs_avg35_**inMNI152.m3z --noDefM3zPath --reg register.dof6.dat --mov onevol.nii.gz --o fmri_cvs333.nii.gz), but the fmri_cvs333.nii.gz volume produced by this command is empty. One option is to resample the normalized EPI in CVS template space, but interpolating the image twice is not a very good idea... Can you think of any solutions to this issue? Best regards, Marcel 2013/8/8 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below: I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject - template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? The file ddescritions are detailed if you run mri_cvs_register --help. For your purposes you do not need to use the --nocleanup option. The final ransformation that you will need is called final*norm.m3z In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ * --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.**affine.mgz el_reg_tocvs_avg35_inMNI152_**aseg.mgz el_reg_tocvs_avg35_inMNI152.**mgz final_CVSmorphed_tocvs_avg35_**inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_**inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_**inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_**inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_**inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_**inMNI152.mri_cvs_register.**1308031447.log transform.txt These comments are wrt to an older version of the code. We do not use the tm3d format any more. I will update the wiki. In my particular case, which images should be entered as arguments to --template and --subject ? template is always your target (atlas space where you are registering TO) and subject is the moving image that you are registering. 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI - anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. You will need the m3z file
[Freesurfer] mri_cvs_register for EPI
Hello, I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject - template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ - --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.affine.mgz el_reg_tocvs_avg35_inMNI152_aseg.mgz el_reg_tocvs_avg35_inMNI152.mgz final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log transform.txt In my particular case, which images should be entered as arguments to --template and --subject ? 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI - anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. Sorry for the lenghty post, but I'm quite new to freesurfer and I'm a bit confused:) Best regards, Marcel ___ 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.
