Re: [Freesurfer] Non-rigid registration approaches
External Email - Use Caution Hi Douglas, I applied a non-rigid registration to my nifti files using another software (IRTK) and then tried to run dt_recon in Freesurfer. Dt_recon is failing during Fitting Tensors and the error message it is displaying is "ERROR: DTIstructFromBFiles(): dimension mismatch" the error message goes on to say that my bvecs file has 99 rows while my bvals file has 11 rows. I've looked at my bvecs and bvals files: the bvecs has 33 rows and 3 columns, and the bvals has 33 rows and 1 column. Can you tell me what the problem is? Is there a way to get past this error? -Hedyeh Date: Tue, 24 Apr 2018 13:20:20 -0400 From: Douglas Greve Subject: Re: [Freesurfer] Non-rigid registration approaches To: Message-ID: <52506cd6-286b-21a0-859a-1cda85557...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sorry, I don' know what to tell you. On 4/21/18 5:34 PM, Hedyeh Javaheri wrote: > > > Thanks for your reply Douglas, > > I am trying co-register the Diffusion data onto the original > structural MRIs. I have tried bbregister and mri_vol2vol but the > results are not great. I realized that the diffusion data have a lot > of distortions, so the rigid and/or affine co-registration is not > sufficient. Do you recommend performing a non-rigid registration in > this case? If you do, do you know of any ways to do that within > Freesurfer? > > > Thanks > > -Hedyeh ___ 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] Non-rigid registration approaches
Sorry, I don' know what to tell you. On 4/21/18 5:34 PM, Hedyeh Javaheri wrote: Thanks for your reply Douglas, I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion data have a lot of distortions, so the rigid and/or affine co-registration is not sufficient. Do you recommend performing a non-rigid registration in this case? If you do, do you know of any ways to do that within Freesurfer? Thanks -Hedyeh - Date: Tue, 17 Apr 2018 11:49:04 -0400 From: Douglas Greve <mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Non-rigid registration approaches To: <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <763da2ef-359a-9f44-9b54-1f96acb3b...@mgh.harvard.edu <mailto:763da2ef-359a-9f44-9b54-1f96acb3b...@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: > Hello all, > > I am performing DTI analysis and wanted to know if Freesurfer has a > tool for non-rigid registration. > I performed recon-all and dt_recon on my subject and then used the > register.dat file that was generated by dt_recon to convert the > dt_recon output files back into the space of my orig.nii file from the > recon-all output. Now I need to register the files in the orig.nii > space back onto the T1 MRI that is in native space. > > I have tried using? mri_vol2vol to get the files in the orig.nii > (recon-all) space into the T1 native space without using a > registration file (I used --regheader) and now the registration matrix > of my file is the same as the native space, but when I use rview to > visualize the registration there are flaws. I've also tried this > co-registration using tkregister2 to create a registration file called > register.native.dat, and then used mri_vol2vol with > register.native.dat; and the results were the same as when I used > mri_vol2vol with --regheader. > > Is there a tool to do actual manual registration in Freesurfer? Using > tkregister2 I cannot perform localized changes; and the global changes > it is capable of do not improve on the coregistration. > > Here is a breakdown of what I have done: > > subject in Native space to Freesurfer conformed space using recon-all, > output: orig.nii > subject in Native space to other Freesurfer space using dt_recon, > output: lowb.nii and register.dat > From the other Freesufer space to Freesurfer conformed space using > register.dat, output: lowb2orig.nii > attempting to convert from Freesurfer conformed space to Native space: > ? ? ? ? ? ? ? ? ? using mri_vol2vol and --regheader --> poor registration > ? ? ? ? ? ? ? ? ? using tkregister2 to make register.native.dat, then > mri_vol2vol and ?register.native.dat --> poor registration > > I am running Freesurfer version 6 on Windows. > > Thanks in advance! > -Hedyeh Javaheri ___ 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.
Re: [Freesurfer] Non-rigid registration approaches
External Email - Use Caution Thanks for your reply Douglas, I am trying co-register the Diffusion data onto the original structural MRIs. I have tried bbregister and mri_vol2vol but the results are not great. I realized that the diffusion data have a lot of distortions, so the rigid and/or affine co-registration is not sufficient. Do you recommend performing a non-rigid registration in this case? If you do, do you know of any ways to do that within Freesurfer? Thanks -Hedyeh - Date: Tue, 17 Apr 2018 11:49:04 -0400 From: Douglas Greve Subject: Re: [Freesurfer] Non-rigid registration approaches To: Message-ID: <763da2ef-359a-9f44-9b54-1f96acb3b...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: > Hello all, > > I am performing DTI analysis and wanted to know if Freesurfer has a > tool for non-rigid registration. > I performed recon-all and dt_recon on my subject and then used the > register.dat file that was generated by dt_recon to convert the > dt_recon output files back into the space of my orig.nii file from the > recon-all output. Now I need to register the files in the orig.nii > space back onto the T1 MRI that is in native space. > > I have tried using? mri_vol2vol to get the files in the orig.nii > (recon-all) space into the T1 native space without using a > registration file (I used --regheader) and now the registration matrix > of my file is the same as the native space, but when I use rview to > visualize the registration there are flaws. I've also tried this > co-registration using tkregister2 to create a registration file called > register.native.dat, and then used mri_vol2vol with > register.native.dat; and the results were the same as when I used > mri_vol2vol with --regheader. > > Is there a tool to do actual manual registration in Freesurfer? Using > tkregister2 I cannot perform localized changes; and the global changes > it is capable of do not improve on the coregistration. > > Here is a breakdown of what I have done: > > subject in Native space to Freesurfer conformed space using recon-all, > output: orig.nii > subject in Native space to other Freesurfer space using dt_recon, > output: lowb.nii and register.dat > From the other Freesufer space to Freesurfer conformed space using > register.dat, output: lowb2orig.nii > attempting to convert from Freesurfer conformed space to Native space: > ? ? ? ? ? ? ? ? ? using mri_vol2vol and --regheader --> poor registration > ? ? ? ? ? ? ? ? ? using tkregister2 to make register.native.dat, then > mri_vol2vol and ?register.native.dat --> poor registration > > I am running Freesurfer version 6 on Windows. > > Thanks in advance! > -Hedyeh Javaheri ___ 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] Non-rigid registration approaches
Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: Hello all, I am performing DTI analysis and wanted to know if Freesurfer has a tool for non-rigid registration. I performed recon-all and dt_recon on my subject and then used the register.dat file that was generated by dt_recon to convert the dt_recon output files back into the space of my orig.nii file from the recon-all output. Now I need to register the files in the orig.nii space back onto the T1 MRI that is in native space. I have tried using mri_vol2vol to get the files in the orig.nii (recon-all) space into the T1 native space without using a registration file (I used --regheader) and now the registration matrix of my file is the same as the native space, but when I use rview to visualize the registration there are flaws. I've also tried this co-registration using tkregister2 to create a registration file called register.native.dat, and then used mri_vol2vol with register.native.dat; and the results were the same as when I used mri_vol2vol with --regheader. Is there a tool to do actual manual registration in Freesurfer? Using tkregister2 I cannot perform localized changes; and the global changes it is capable of do not improve on the coregistration. Here is a breakdown of what I have done: subject in Native space to Freesurfer conformed space using recon-all, output: orig.nii subject in Native space to other Freesurfer space using dt_recon, output: lowb.nii and register.dat From the other Freesufer space to Freesurfer conformed space using register.dat, output: lowb2orig.nii attempting to convert from Freesurfer conformed space to Native space: using mri_vol2vol and --regheader --> poor registration using tkregister2 to make register.native.dat, then mri_vol2vol and register.native.dat --> poor registration I am running Freesurfer version 6 on Windows. Thanks in advance! -Hedyeh Javaheri ___ 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] Non-rigid registration approaches
Hello all, I am performing DTI analysis and wanted to know if Freesurfer has a tool for non-rigid registration. I performed recon-all and dt_recon on my subject and then used the register.dat file that was generated by dt_recon to convert the dt_recon output files back into the space of my orig.nii file from the recon-all output. Now I need to register the files in the orig.nii space back onto the T1 MRI that is in native space. I have tried using mri_vol2vol to get the files in the orig.nii (recon-all) space into the T1 native space without using a registration file (I used --regheader) and now the registration matrix of my file is the same as the native space, but when I use rview to visualize the registration there are flaws. I've also tried this co-registration using tkregister2 to create a registration file called register.native.dat, and then used mri_vol2vol with register.native.dat; and the results were the same as when I used mri_vol2vol with --regheader. Is there a tool to do actual manual registration in Freesurfer? Using tkregister2 I cannot perform localized changes; and the global changes it is capable of do not improve on the coregistration. Here is a breakdown of what I have done: subject in Native space to Freesurfer conformed space using recon-all, output: orig.nii subject in Native space to other Freesurfer space using dt_recon, output: lowb.nii and register.dat >From the other Freesufer space to Freesurfer conformed space using register.dat, output: lowb2orig.nii attempting to convert from Freesurfer conformed space to Native space: using mri_vol2vol and --regheader --> poor registration using tkregister2 to make register.native.dat, then mri_vol2vol and register.native.dat --> poor registration I am running Freesurfer version 6 on Windows. Thanks in advance! -Hedyeh Javaheri ___ 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.
