Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat **** WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 **** The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view?
doug
On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat
WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast.
-Kathleen
On 8/19/10 2:39 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view?
doug
On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat
WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
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.
That warning in and of itself is not critical, but it does suggest that the initial registration failed. I assume the registration still looks bad? Does this happen on a bunch of data sets or just this one? There are a couple of more steps. First, you can run with --init-fsl and check the initial registration to verify that it is way off. To do this, run with --init-reg-out and check that registration with tkregister2. If that is bad, you can can try two things. First, if you have spm and matlab, you can use --init-spm. Second, you can tweak the initial registration by hand to get it "close" (ie, within 5mm and 5deg), then use --init-reg
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast.
-Kathleen
On 8/19/10 2:39 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view?
doug
On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat
WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
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.
Thanks. The tkregister2 check gives some new information. The initial registration is not very bad when checked in tkregister2. Also, the final registration is perfectly acceptable when checked in tkregister2, so my original question needs clarification.
What I want to do is to use the register.dat file to create an anatomical registered to a functional. I want the actual registered anatomical data as a saved file. In the past, I applied these lines to a dataset that didn't produce the G-W contrast warning. Also, this fmri dataset was collected in the same scan session as the anatomical. bbregister --mov epi.template_{$S}.nii --bold --s {$S} --init-fsl --reg register_{$S}.dat mri_vol2vol --reg register_{$S}.dat --mov epi.template_{$S}.nii --fstarg --inv --no-resample --o {$S}_Anat_in_Func_noresamp.nii
The output, {$S}_Anat_in_Func_noresamp.nii, aligned well with the fmri volume epi.template_{$S}.nii with no other registration needed.
Now I am applying these lines to several different datasets. All of them do produce the G-W contrast warning, and they were not collected in the same scan sessions as their surface anatomicals. In each case, the output, {$S}_Anat_in_Func_noresamp.nii, is very far from the fmri volume epi.template_{$S}.nii. This is strange, since in these same datasets the register_{$S}.dat produces a good alignment between epi.template_{$S}.nii and {$S}/mri/orig.mgz when viewed in tkregister2.
Thanks very much for your help on this, Kathleen
On 8/20/10 11:32 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That warning in and of itself is not critical, but it does suggest that the initial registration failed. I assume the registration still looks bad? Does this happen on a bunch of data sets or just this one? There are a couple of more steps. First, you can run with --init-fsl and check the initial registration to verify that it is way off. To do this, run with --init-reg-out and check that registration with tkregister2. If that is bad, you can can try two things. First, if you have spm and matlab, you can use --init-spm. Second, you can tweak the initial registration by hand to get it "close" (ie, within 5mm and 5deg), then use --init-reg
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast.
-Kathleen
On 8/19/10 2:39 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view?
doug
On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat
WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Why are you using --no-resample? This will keep the anatomical in the 256^3 space (it just changes the header).
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
Thanks. The tkregister2 check gives some new information. The initial registration is not very bad when checked in tkregister2. Also, the final registration is perfectly acceptable when checked in tkregister2, so my original question needs clarification.
What I want to do is to use the register.dat file to create an anatomical registered to a functional. I want the actual registered anatomical data as a saved file. In the past, I applied these lines to a dataset that didn't produce the G-W contrast warning. Also, this fmri dataset was collected in the same scan session as the anatomical. bbregister --mov epi.template_{$S}.nii --bold --s {$S} --init-fsl --reg register_{$S}.dat mri_vol2vol --reg register_{$S}.dat --mov epi.template_{$S}.nii --fstarg --inv --no-resample --o {$S}_Anat_in_Func_noresamp.nii
The output, {$S}_Anat_in_Func_noresamp.nii, aligned well with the fmri volume epi.template_{$S}.nii with no other registration needed.
Now I am applying these lines to several different datasets. All of them do produce the G-W contrast warning, and they were not collected in the same scan sessions as their surface anatomicals. In each case, the output, {$S}_Anat_in_Func_noresamp.nii, is very far from the fmri volume epi.template_{$S}.nii. This is strange, since in these same datasets the register_{$S}.dat produces a good alignment between epi.template_{$S}.nii and {$S}/mri/orig.mgz when viewed in tkregister2.
Thanks very much for your help on this, Kathleen
On 8/20/10 11:32 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That warning in and of itself is not critical, but it does suggest that the initial registration failed. I assume the registration still looks bad? Does this happen on a bunch of data sets or just this one? There are a couple of more steps. First, you can run with --init-fsl and check the initial registration to verify that it is way off. To do this, run with --init-reg-out and check that registration with tkregister2. If that is bad, you can can try two things. First, if you have spm and matlab, you can use --init-spm. Second, you can tweak the initial registration by hand to get it "close" (ie, within 5mm and 5deg), then use --init-reg
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast.
-Kathleen
On 8/19/10 2:39 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view?
doug
On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat
WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Aha. OK, omitting -no-resample, as below, outputs a well registered, but downsampled, anatomical file. What should I change to output a well registered anatomical file with the same dimension and voxel size as the original anatomical? If this was in the mri_vol2vol help, it was not clear to me.
mri_vol2vol --reg register_{$S}.dat --mov epi.template_{$S}.nii --fstarg --inv --o {$S}_Anat_in_Func_noresamp.nii
Thanks! -Kathleen
On 8/23/10 11:44 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Why are you using --no-resample? This will keep the anatomical in the 256^3 space (it just changes the header).
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
Thanks. The tkregister2 check gives some new information. The initial registration is not very bad when checked in tkregister2. Also, the final registration is perfectly acceptable when checked in tkregister2, so my original question needs clarification.
What I want to do is to use the register.dat file to create an anatomical registered to a functional. I want the actual registered anatomical data as a saved file. In the past, I applied these lines to a dataset that didn't produce the G-W contrast warning. Also, this fmri dataset was collected in the same scan session as the anatomical. bbregister --mov epi.template_{$S}.nii --bold --s {$S} --init-fsl --reg register_{$S}.dat mri_vol2vol --reg register_{$S}.dat --mov epi.template_{$S}.nii --fstarg --inv --no-resample --o {$S}_Anat_in_Func_noresamp.nii
The output, {$S}_Anat_in_Func_noresamp.nii, aligned well with the fmri volume epi.template_{$S}.nii with no other registration needed.
Now I am applying these lines to several different datasets. All of them do produce the G-W contrast warning, and they were not collected in the same scan sessions as their surface anatomicals. In each case, the output, {$S}_Anat_in_Func_noresamp.nii, is very far from the fmri volume epi.template_{$S}.nii. This is strange, since in these same datasets the register_{$S}.dat produces a good alignment between epi.template_{$S}.nii and {$S}/mri/orig.mgz when viewed in tkregister2.
Thanks very much for your help on this, Kathleen
On 8/20/10 11:32 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That warning in and of itself is not critical, but it does suggest that the initial registration failed. I assume the registration still looks bad? Does this happen on a bunch of data sets or just this one? There are a couple of more steps. First, you can run with --init-fsl and check the initial registration to verify that it is way off. To do this, run with --init-reg-out and check that registration with tkregister2. If that is bad, you can can try two things. First, if you have spm and matlab, you can use --init-spm. Second, you can tweak the initial registration by hand to get it "close" (ie, within 5mm and 5deg), then use --init-reg
doug
Hansen, Kathleen (NIH/NIMH) [F] wrote:
Thanks for the suggestions. It is whole-brain epi data. Unfortunately, it was not acquired at the same time as the anatomical. Just for the heck of it I tried substituting --init-header for --init-fsl anyway, and got the same warning about negative G-W contrast.
-Kathleen
On 8/19/10 2:39 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
It may have been the initialization that failed. Was the epi acquired at the same time as the anatomical? If so, you might be able to run it with --init-header. Also, is this whole brain or partial field of view?
doug
On 8/19/10 1:50 PM, Hansen, Kathleen (NIH/NIMH) [F] wrote:
Hello,
The following command has produced a very wrong registration and a warning:
bbregister --mov epi.template.strange_G-W_contrast.nii --bold --s D06 --init-fsl --reg register.strange_G-W_contrast.dat
WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1
The file epi.template.strange_G-W_contrast.nii is BOLD fmri data, not T1-weighted data. As far as I can tell, it is a typical BOLD fmri volume. Any ideas?
Thank you, Kathleen
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Hansen, Kathleen (NIH/NIMH) [F]