Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this:
mris_preproc --out lh-zstat1.mgz target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat
My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the target surface?
Thanks, Eric
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
Yes, it is possible. As long as the registration looks good in tkmedit/tkregister2, then it should accurately map to the surface, even a to a different target surface. What are you using to view the surface? One thing you should check though is whether it mapping as expected to the subject's own surface. You can do this with
tksurfer subjname lh inflated -overlay zstat1.nii.gz -overlay-reg register.dat
doug
emoulton@mclean.harvard.edu wrote:
Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this:
mris_preproc --out lh-zstat1.mgz –target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat
My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the –target surface?
Thanks, Eric
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Mapping to the subject's own surface looks promising, but I'm ultimately not seeing what I think should be correct. Let me give you some examples of how I've reached this observation. Note that anat2exf.register.dat is the same for all the command lines listed below.
Statistical image overlaid on the subject's orig.mgz brain. tkmedit SUBJ1 orig.mgz lh.white -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This looks as expected...partial brain statistical map overlying the full brain in the correct area.
Statistical image overlaid on a "group average" surface-based full brain tksurfer average lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This seems to match well with the image displayed using tkmedit.
Statistical image overlaid on the subject's surface-based full brain tksurfer SUBJ1 lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat Not OK - Statistical values are spread across the entire full brain.
After I run "mris_preproc --out lh-zstat1.mgz --target average --hemi lh --mean --iv zstat1.nii.gz anat2exf.register.dat", the output looks incorrect when viewing the result with the following:
tksurfer average lh inflated -overlay lh-zstat1.mgz The statistics have spread to fill the surface. Including the flag - overlay-reg anat2exf.register.dat with this tksurfer command line offers the same incorrect result.
I hope that this will help us to correct this registration issue. Any catches as to what might be wrong?
Thanks, Eric
On Nov 21, 2006, at 5:17 PM, Doug Greve wrote:
Yes, it is possible. As long as the registration looks good in tkmedit/tkregister2, then it should accurately map to the surface, even a to a different target surface. What are you using to view the surface? One thing you should check though is whether it mapping as expected to the subject's own surface. You can do this with
tksurfer subjname lh inflated -overlay zstat1.nii.gz -overlay-reg register.dat
doug
emoulton@mclean.harvard.edu wrote:
Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this:
mris_preproc --out lh-zstat1.mgz –target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat
My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the –target surface?
Thanks, Eric
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
Hmm, there's something fishy here. If the tkmedit command worked, then the 2nd tksurfer cmd (onto SUBJ1) should have worked. The first tksurfer command should NOT have worked as the registration would not be correct for for the average subject. Are you sure you did not reverse these? Which version of mris_preproc are you running? Run with --version to check.
doug
On Wed, 22 Nov 2006, Eric Moulton wrote:
Mapping to the subject's own surface looks promising, but I'm ultimately not seeing what I think should be correct. Let me give you some examples of how I've reached this observation. Note that anat2exf.register.dat is the same for all the command lines listed below.
Statistical image overlaid on the subject's orig.mgz brain. tkmedit SUBJ1 orig.mgz lh.white -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This looks as expected...partial brain statistical map overlying the full brain in the correct area.
Statistical image overlaid on a "group average" surface-based full brain tksurfer average lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This seems to match well with the image displayed using tkmedit.
Statistical image overlaid on the subject's surface-based full brain tksurfer SUBJ1 lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat Not OK - Statistical values are spread across the entire full brain.
After I run "mris_preproc --out lh-zstat1.mgz --target average --hemi lh --mean --iv zstat1.nii.gz anat2exf.register.dat", the output looks incorrect when viewing the result with the following:
tksurfer average lh inflated -overlay lh-zstat1.mgz The statistics have spread to fill the surface. Including the flag - overlay-reg anat2exf.register.dat with this tksurfer command line offers the same incorrect result.
I hope that this will help us to correct this registration issue. Any catches as to what might be wrong?
Thanks, Eric
On Nov 21, 2006, at 5:17 PM, Doug Greve wrote:
Yes, it is possible. As long as the registration looks good in tkmedit/tkregister2, then it should accurately map to the surface, even a to a different target surface. What are you using to view the surface? One thing you should check though is whether it mapping as expected to the subject's own surface. You can do this with
tksurfer subjname lh inflated -overlay zstat1.nii.gz -overlay-reg register.dat
doug
emoulton@mclean.harvard.edu wrote:
Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this:
mris_preproc --out lh-zstat1.mgz ?target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat
My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the ?target surface?
Thanks, Eric
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
With your assurance, I found my problem; the partial brain lines up fine the with full brain using both tkmedit and tksurfer for the individual when using the anat2exf.dat conversion matrix. I was expecting a more "hard-cut" at the edge of the partial brain as viewed with tksurfer. As an aside, my mris_preproc version is 1.18.2.1.
This actually brings me to the next question regarding partial brain statistical images: when I perform a group analysis on partial brain statistical images, should the entire average surface-based brain contain statistics (sig.mgz)? Depending on the subject, the extent of brain acquired is different, but does the GLM (using mri_glmfit) calculate the statistics even where only a subset of subjects have data? When FSL analyzes such data, it performs the GLM on a mask that corresponds only to the areas that overlap in all the subjects. Is there an equivalent mask that can be generated in Freesurfer to mask out the statistics that are based on a subset of subjects?
I have used mris_preproc to generate cope images (contrast of parameter estimates) for each subject in average space (which appear to be correct). I've run mri_concat to "compile" the subjects' results together, run mri_glmfit, and have resulting statistics that encompass the entire surface of the average.
Thanks, Eric
On Nov 22, 2006, at 7:03 PM, Doug Greve wrote:
Hmm, there's something fishy here. If the tkmedit command worked, then the 2nd tksurfer cmd (onto SUBJ1) should have worked. The first tksurfer command should NOT have worked as the registration would not be correct for for the average subject. Are you sure you did not reverse these? Which version of mris_preproc are you running? Run with --version to check.
doug
On Wed, 22 Nov 2006, Eric Moulton wrote:
Mapping to the subject's own surface looks promising, but I'm ultimately not seeing what I think should be correct. Let me give you some examples of how I've reached this observation. Note that anat2exf.register.dat is the same for all the command lines listed below.
Statistical image overlaid on the subject's orig.mgz brain. tkmedit SUBJ1 orig.mgz lh.white -overlay zstat1.nii.gz -overlay- reg anat2exf.register.dat OK - This looks as expected...partial brain statistical map overlying the full brain in the correct area.
Statistical image overlaid on a "group average" surface-based full brain tksurfer average lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This seems to match well with the image displayed using tkmedit.
Statistical image overlaid on the subject's surface-based full brain tksurfer SUBJ1 lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat Not OK - Statistical values are spread across the entire full brain.
After I run "mris_preproc --out lh-zstat1.mgz --target average -- hemi lh --mean --iv zstat1.nii.gz anat2exf.register.dat", the output looks incorrect when viewing the result with the following:
tksurfer average lh inflated -overlay lh-zstat1.mgz The statistics have spread to fill the surface. Including the flag - overlay-reg anat2exf.register.dat with this tksurfer command line offers the same incorrect result.
I hope that this will help us to correct this registration issue. Any catches as to what might be wrong?
Thanks, Eric
On Nov 21, 2006, at 5:17 PM, Doug Greve wrote:
Yes, it is possible. As long as the registration looks good in tkmedit/tkregister2, then it should accurately map to the surface, even a to a different target surface. What are you using to view the surface? One thing you should check though is whether it mapping as expected to the subject's own surface. You can do this with tksurfer subjname lh inflated -overlay zstat1.nii.gz -overlay-reg register.dat doug emoulton@mclean.harvard.edu wrote:
Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this: mris_preproc --out lh-zstat1.mgz ?target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the ?target surface? Thanks, Eric Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
If you want to exlude data from points that do not have representation from all subjects, run mri_glmfit with --prune (the mask in the output dir will show you the points that it kept/removed).
doug
On Mon, 27 Nov 2006, Eric Moulton wrote:
With your assurance, I found my problem; the partial brain lines up fine the with full brain using both tkmedit and tksurfer for the individual when using the anat2exf.dat conversion matrix. I was expecting a more "hard-cut" at the edge of the partial brain as viewed with tksurfer. As an aside, my mris_preproc version is 1.18.2.1.
This actually brings me to the next question regarding partial brain statistical images: when I perform a group analysis on partial brain statistical images, should the entire average surface-based brain contain statistics (sig.mgz)? Depending on the subject, the extent of brain acquired is different, but does the GLM (using mri_glmfit) calculate the statistics even where only a subset of subjects have data? When FSL analyzes such data, it performs the GLM on a mask that corresponds only to the areas that overlap in all the subjects. Is there an equivalent mask that can be generated in Freesurfer to mask out the statistics that are based on a subset of subjects?
I have used mris_preproc to generate cope images (contrast of parameter estimates) for each subject in average space (which appear to be correct). I've run mri_concat to "compile" the subjects' results together, run mri_glmfit, and have resulting statistics that encompass the entire surface of the average.
Thanks, Eric
On Nov 22, 2006, at 7:03 PM, Doug Greve wrote:
Hmm, there's something fishy here. If the tkmedit command worked, then the 2nd tksurfer cmd (onto SUBJ1) should have worked. The first tksurfer command should NOT have worked as the registration would not be correct for for the average subject. Are you sure you did not reverse these? Which version of mris_preproc are you running? Run with --version to check.
doug
On Wed, 22 Nov 2006, Eric Moulton wrote:
Mapping to the subject's own surface looks promising, but I'm ultimately not seeing what I think should be correct. Let me give you some examples of how I've reached this observation. Note that anat2exf.register.dat is the same for all the command lines listed below.
Statistical image overlaid on the subject's orig.mgz brain. tkmedit SUBJ1 orig.mgz lh.white -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This looks as expected...partial brain statistical map overlying the full brain in the correct area.
Statistical image overlaid on a "group average" surface-based full brain tksurfer average lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat OK - This seems to match well with the image displayed using tkmedit.
Statistical image overlaid on the subject's surface-based full brain tksurfer SUBJ1 lh inflated -overlay zstat1.nii.gz -overlay-reg anat2exf.register.dat Not OK - Statistical values are spread across the entire full brain.
After I run "mris_preproc --out lh-zstat1.mgz --target average --hemi lh --mean --iv zstat1.nii.gz anat2exf.register.dat", the output looks incorrect when viewing the result with the following:
tksurfer average lh inflated -overlay lh-zstat1.mgz The statistics have spread to fill the surface. Including the flag - overlay-reg anat2exf.register.dat with this tksurfer command line offers the same incorrect result.
I hope that this will help us to correct this registration issue. Any catches as to what might be wrong?
Thanks, Eric
On Nov 21, 2006, at 5:17 PM, Doug Greve wrote:
Yes, it is possible. As long as the registration looks good in tkmedit/tkregister2, then it should accurately map to the surface, even a to a different target surface. What are you using to view the surface? One thing you should check though is whether it mapping as expected to the subject's own surface. You can do this with tksurfer subjname lh inflated -overlay zstat1.nii.gz -overlay-reg register.dat doug emoulton@mclean.harvard.edu wrote:
Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this: mris_preproc --out lh-zstat1.mgz ?target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the ?target surface? Thanks, Eric Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
emoulton＠mclean.harvard.edu -
Eric Moulton