[Freesurfer] roi from icbm152 to fsaverage inflated surface
Dear Freesurfers,
Using FreeSurfer 4.5.0, I am trying to map a binary *.nii roi-mask (defined in
${LABEL}) that has been outlined on the icbm-152 template in mni space to the
inflated surface model of fsaverage.
The approach below gives me a solution that looks very trustworthy, however,
I'd like to verify with the experts whether it is 100% accurate.
These are the commands I am using:
# to map the label to the fsaverage target
mri_label2vol --seg ${LABEL} --temp fsaverage/mri/orig.mgz --reg
${FREESURFER_HOME}/average/mni152.register.dat --invertmtrx -fillthresh 0.5 --o
${LABEL%.nii}_fsa.nii
# to intersect it with the wm surface, and then map it to the sphere (note that
identity.dat has been generate prior to running the command).
mri_vol2surf --src ${LABEL%.nii}_fsa.nii --reg identity.dat --hemi lh --surf
white --interp nearest --surfreg sphere.reg --icoorder 7 --out
${LABEL%.nii}_fsasurf_lh.mgh
# to convert the mgh to ascii
mris_convert -c ${LABEL%.nii}_fsasurf_lh.mgh fsaverage/surf/lh.white
{LABEL%.nii}_fsasurf_lh.asc
Many thanks,
Boris
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[Freesurfer] display results on fsaverage / calculate area
Hello Freesurfer-experts, I just analyzed some FreeSurfer cortical thickness data that have been surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage). For the visualization and reporting of my findings, I have a two questions: 1. Is there anything that conceptually speaks against showing my results on non-inflated surfaces of fsaverage, such as the white matter surface, the pial surface, or even a mid-surface model? 2. I have a couple of ROIs defined on the surface of fsaverage and want to report the surface area of a given ROI in mm^2. Should I calculate the area of a ROI directly from the given surface of fsaverage, or to take the area computations from ?h.pial.avg.area.mgh/?h.white.avg.area.mgh which represent the averages of the individuals that went into fsaverage. I am asking because I was slightly unclear of the wiki-instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface suggests to use ?h.pial.avg.area.mgh; on the other hand, the more recently edited http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage says that "The surface area of the new average subject (fsaverage) is that of a typical subject" I am using freesurfer 4.5.0. Hope my questions make sense and thank you very much for answering them, Boris --- Boris Bernhardt, PhD Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, 04103 Leipzig, Germany p: +(49) 341 9940 2658 e: bernha...@cbs.mpg.de http://www.cbs.mpg.de/~bernhardt ___ 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] display results on fsaverage / calculate area
Hi Bruce, Thanks a lot for your reply. > 2. The surface area of fsaverage is less than any individual, so you > *definitely* don't want to use it. You should map the ROI back to individuals > and compute it in the native space. I have two follow-up questions: 1) Do .pial.avg.area.mgh and/or .white.avg.area.mgh then store the mean native space surface areas for the individuals that were used to create fsaverage, and can I use these values to approximate the surface area of my ROIs then? 2) Do the avg.area files also exists somewhere for the half-thickness mid-surface? If not, does it make sense to approximate the mid-thickness surface area at each vertex by taking the mean of the corresponding pial.avg.area and white.avg.area entries? Many thanks, Boris > > cheers > Bruce > > > On Wed, 11 May 2011, Boris Bernhardt wrote: > >> Hello Freesurfer-experts, >> >> I just analyzed some FreeSurfer cortical thickness data that have been >> surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage). >> >> For the visualization and reporting of my findings, I have a two questions: >> >> 1. Is there anything that conceptually speaks against showing my results on >> non-inflated surfaces of fsaverage, such as the white matter surface, the >> pial surface, or even a mid-surface model? >> >> 2. I have a couple of ROIs defined on the surface of fsaverage and want > to report the surface area of a given ROI in mm^2. Should I calculate the > area of a ROI directly from the given surface of fsaverage, or to take the > area computations from ?h.pial.avg.area.mgh/?h.white.avg.area.mgh which > represent the averages of the individuals that went into fsaverage. >> >> I am asking because I was slightly unclear of the wiki-instructions: >> https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface >> suggests to use ?h.pial.avg.area.mgh; >> >> on the other hand, the more recently edited >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage >> says that "The surface area of the new average subject (fsaverage) is that >> of a typical subject" >> >> I am using freesurfer 4.5.0. >> >> Hope my questions make sense and thank you very much for answering them, >> Boris >> >> >> >> >> --- >> Boris Bernhardt, PhD >> Max Planck Institute for Human Cognitive and Brain Sciences >> Stephanstr. 1a, 04103 Leipzig, Germany >> >> p: +(49) 341 9940 2658 >> e: bernha...@cbs.mpg.de >> http://www.cbs.mpg.de/~bernhardt >> >> > > > 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. > --- Boris Bernhardt Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, 04103 Leipzig, Germany p: +(49) 341 9940 2658 e: bernha...@cbs.mpg.de http://www.cbs.mpg.de/~bernhardt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] display results on fsaverage / calculate area
Hi Bruce and Doug, thank you both so much for your help. >> You could generate it yourself easily enough >> though. For now I am taking the geometric average between pial and white surface coordinates. Is that the right way to do it, or is there a more precise way? Also: If I decided to represent the stuff on the mid-surface, would it then also make sense to also take the average of pial.avg.area.mgh white.avg.area.mgh as the area estimation at each vertex? Many thanks, Boris On 2011-05-12, at 4:08 PM, Douglas Greve wrote: > Yes, the avg.area files have the average over the input subjects at each > vertex. I've used it to overcome this problem. > doug > > On 5/12/11 8:04 AM, Bruce Fischl wrote: >> Hi Boris, >> >> 1. Doug can say for sure, but I believe so. >> 2. No. The mid surface doesn't correspond to any boundary in the image and >> so we are always hesitant to provide any morphometric measures for it. We >> are working on a more explicit estimation of the location of layer IV, but >> that is a future direction. You could generate it yourself easily enough >> though. >> >> cheers >> Bruce >> >> >> On Thu, 12 May 2011, Boris Bernhardt >> wrote: >> >>> Hi Bruce, >>> >>> Thanks a lot for your reply. >>> >>>> 2. The surface area of fsaverage is less than any individual, so you >>>> *definitely* don't want to use it. You should map the ROI back to >>>> individuals and compute it in the native space. >>> I have two follow-up questions: >>> >>> >>> 1) Do .pial.avg.area.mgh and/or .white.avg.area.mgh then store the mean >> native space surface areas for the individuals that were used to create >> fsaverage, and can I use these values to approximate the surface area of my >> ROIs then? >>> 2) Do the avg.area files also exists somewhere for the half-thickness >>> mid-surface? If not, does it make sense to approximate the mid-thickness >>> surface area at each vertex by taking the mean of the corresponding >>> pial.avg.area and white.avg.area entries? >>> >>> Many thanks, >>> Boris >>> >>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Wed, 11 May 2011, Boris Bernhardt wrote: >>>> >>>>> Hello Freesurfer-experts, >>>>> >>>>> I just analyzed some FreeSurfer cortical thickness data that have been >>>>> surface-resampled to fsaverage (using mris_surf2surf with -s fsaverage). >>>>> >>>>> For the visualization and reporting of my findings, I have a two >>>>> questions: >>>>> >>>>> 1. Is there anything that conceptually speaks against showing my results >>>>> on non-inflated surfaces of fsaverage, such as the white matter surface, >>>>> the pial surface, or even a mid-surface model? >>>>> >>>>> 2. I have a couple of ROIs defined on the surface of fsaverage and want >>>> to report the surface area of a given ROI in mm^2. Should I calculate the >>>> area of a ROI directly from the given surface of fsaverage, or to take the >>>> area computations from ?h.pial.avg.area.mgh/?h.white.avg.area.mgh which >>>> represent the averages of the individuals that went into fsaverage. >>>>> I am asking because I was slightly unclear of the wiki-instructions: >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/GroupAverageSurface >>>>> suggests to use ?h.pial.avg.area.mgh; >>>>> >>>>> on the other hand, the more recently edited >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage >>>>> says that "The surface area of the new average subject (fsaverage) is >>>>> that of a typical subject" >>>>> >>>>> I am using freesurfer 4.5.0. >>>>> >>>>> Hope my questions make sense and thank you very much for answering them, >>>>> Boris >>>>> >>>>> >>>>> >>>>> >>>>> --- >>>>> Boris Bernhardt, PhD >>>>> Max Planck Institute for Human Cognitive and Brain Sciences >>>>> Stephanstr. 1a, 04103 Leipzig, Germany >>>>> >>>>> p: +(49) 341 9940 2658 >>>>> e: bernha...@cbs.mpg.de >>>>> http://www.cbs.mpg.de/~bernhardt >>>>> >>>>> >>>> &
Re: [Freesurfer] display results on fsaverage / calculate area
Hi, > No no, to take the average of the areas is not the same as take the average > of the coordinates, because the areas depend quadratically on linear > distances. An average of the areas would not necessarily represent a surface > at the middle, most likely representing an (invisible) surface that would be > closer to the white in some places and closer to the pial in others, > depending on local folding. > Hope this helps! yes - that helps and clarifies things. Thank you all for your help and patience, Boris On 2011-05-12, at 11:57 PM, Anderson Winkler wrote: > Hi Boris, > >> For now I am taking the geometric average between pial and white surface >> coordinates. >> Is that the right way to do it, or is there a more precise way? > > To obtain a surface that lies in the geometric middle between white and pial > surfaces, it is correct to take the average of the coordinates. This surface > is not guaranteed to coincide with any biologically meaningful cortical > layer, but it has advantages over pial or white for not > over/under-representing gyri or sulci. > >> Also: If I decided to represent the stuff on the mid-surface, would it then >> also make sense to also take the average of pial.avg.area.mgh >> white.avg.area.mgh as the area estimation at each vertex? > > No no, to take the average of the areas is not the same as take the average > of the coordinates, because the areas depend quadratically on linear > distances. An average of the areas would not necessarily represent a surface > at the middle, most likely representing an (invisible) surface that would be > closer to the white in some places and closer to the pial in others, > depending on local folding. > > Hope this helps! > > All the best, > > Anderson ___ 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.
