So, currently I am using white and using projfrac-max 0 1 .01, and it is giving me a very clean image with maybe only .1% of the vertices incorrect. Seems to be the best so far.
In general, sometimes we have to use 3-D grids instead of FS grids to get deeper sources, and then we make 3-D nii volumes showing activity. I was interested in taking those volumes and projecting them onto a surface so i can view them on tksurfer.
In this case, i used a common map, made actually out of freesurfer (aparc+aseg) because I thought it would make it easy to see when I get the right answer.
I will attach a picture of the latest tomorrow morning when I get back in the office.
Thank you so much for your help, Omer Tal
Don't use orig, use white (or leave blank), that will help some. What are you trying to accomplish? doug
Omer Tal wrote:
Hey Doug,
I did play w/ that (tried 0.5 and 1) and the result if much better (see attached image) but there are still some regions where either no value is assigned or white matter voxels comes up. Are there any other suggestions you might have?
- is there a better --surf to use than orig?
- should I attempt to use the optimal projection function (not much
notes on using mri_compute_volume_fractions)?
Thank you for your continuous support, Omer Tal
the way you have it set up, it is sampling on the gray/white boundary ("white" surface). You can sample midway into the ribbon with --projfrac 0.5 doug
Omer Tal wrote:
Hey Doug,
Attached is a picture showing the resulting surface file. Note that the red regions correspond to the number 2 (white matter) and the yellow regions correspond to numbers between 1000 and 1035 (gray matter). If the conversion would be completed correctly, only numbers between the 1000 and 1035 should come up on the surface.
Thank you for your time and help, Omer Tal
can you post a picture?
Omer Tal wrote:
Hey Doug,
Tried, no change unfortunately.
Here is the output, just in the case: mri_vol2surf --src aparc+aseg.nii --surf orig --ref orig.mgz --regheader 111123 --hemi lh --o test.mgh srcvol = aparc+aseg.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = orig hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/otal/raweegmeg/structuralDB//111123/mri/orig.mgz as target reference. Reading surface /home/otal/raweegmeg/structuralDB//111123/surf/lh.orig Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 100537 Writing to test.mgh Dim: 157373 1 1
Thank you, Omer Tal
> Hi Omer, > Try removing "--srcreg identity" > doug > > Omer Tal wrote: > > > >> Hey Doug, >> >> Test.nii is a volume nii (1x1x1mm) with values of interest per >> voxel, >> created using the header from brain_T1.nii which was simply >> created >> by >> using mri_convert from the subject's original brain.mgz. The *.nii >> file >> loads fine and matches the subject as expected. It is when trying >> to >> go >> back to surface, that things seem to get messy. >> >> Thank you very much for your time, >> Omer Tal >> Keck Center for Functional MRI, UCSD >> >> >> >> >> >>> What is test.nii? How was it derived? >>> >>> Omer Tal wrote: >>> >>> >>> >>> >>>> Hey all, >>>> >>>> I am running into a bit of a problem converting back from a >>>> volume >>>> into >>>> a >>>> surface and was hoping someone would have some insight. >>>> >>>> I have an .nii volume for a given subject, and I want to convert >>>> it >>>> into >>>> a >>>> surface mgh file, so i can view it on tksurfer. Since its the >>>> same >>>> exact >>>> subject, I figured it should be relatively easy, but in the >>>> resulting >>>> surface all the white matter and gray matter voxels are mixed >>>> together >>>> (looks like tiger pattern on tksurfer) in the entire brain. I >>>> would >>>> point >>>> out though that the gray matter voxels do show up in the correct >>>> location >>>> (i.e. a motor gray voxel in my volume still ends up in the motor >>>> cortex >>>> in >>>> the mgh file), its just that they are surrounded with vertices >>>> which >>>> have >>>> white matter values. >>>> >>>> Any advice? >>>> >>>> Code: mri_vol2surf --src test nii --srcreg identity --ref T1.mgz >>>> --regheader test_subj --hemi lh --o test.mgh >>>> >>>> Thank you very much for your help, >>>> Omer Tal >>>> Keck Center for Functional MRI, UCSD >>>> >>>> _______________________________________________ >>>> 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 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> 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
-- 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
Hey Doug,
Here is the picture I get using the following line of code: mri_vol2surf --src aparc+aseg.nii --surf white --ref orig.mgz --regheader 111123 --hemi lh --o test.mgh --projfrac-max 0 1 0.01
In this case it makes sense i keep the max since the higher numbers correspond to gray matter voxels, but in general since my activity will be spread throughout the 3-D grid, I would probably want to use --projfrac-avg is my guess. Also, it seems as if smoothing might be a useful step to add as well (--surf-fwhm 5) when using real data (not a fake atlas).
Please let me know if you have any other useful tips I should take into consideration.
Thank you for helping me so much with this matter, Omer Tal Keck Center for Functional MRI, UCSD
So, currently I am using white and using projfrac-max 0 1 .01, and it is giving me a very clean image with maybe only .1% of the vertices incorrect. Seems to be the best so far.
In general, sometimes we have to use 3-D grids instead of FS grids to get deeper sources, and then we make 3-D nii volumes showing activity. I was interested in taking those volumes and projecting them onto a surface so i can view them on tksurfer.
In this case, i used a common map, made actually out of freesurfer (aparc+aseg) because I thought it would make it easy to see when I get the right answer.
I will attach a picture of the latest tomorrow morning when I get back in the office.
Thank you so much for your help, Omer Tal
Don't use orig, use white (or leave blank), that will help some. What are you trying to accomplish? doug
Omer Tal wrote:
Hey Doug,
I did play w/ that (tried 0.5 and 1) and the result if much better (see attached image) but there are still some regions where either no value is assigned or white matter voxels comes up. Are there any other suggestions you might have?
- is there a better --surf to use than orig?
- should I attempt to use the optimal projection function (not much
notes on using mri_compute_volume_fractions)?
Thank you for your continuous support, Omer Tal
the way you have it set up, it is sampling on the gray/white boundary ("white" surface). You can sample midway into the ribbon with --projfrac 0.5 doug
Omer Tal wrote:
Hey Doug,
Attached is a picture showing the resulting surface file. Note that the red regions correspond to the number 2 (white matter) and the yellow regions correspond to numbers between 1000 and 1035 (gray matter). If the conversion would be completed correctly, only numbers between the 1000 and 1035 should come up on the surface.
Thank you for your time and help, Omer Tal
can you post a picture?
Omer Tal wrote:
> Hey Doug, > > Tried, no change unfortunately. > > > Here is the output, just in the case: > mri_vol2surf --src aparc+aseg.nii --surf orig --ref orig.mgz > --regheader > 111123 --hemi lh --o test.mgh > srcvol = aparc+aseg.nii > srcreg unspecified > srcregold = 0 > srcwarp unspecified > surf = orig > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Computing registration from header. > Using /home/otal/raweegmeg/structuralDB//111123/mri/orig.mgz as > target > reference. > Reading surface > /home/otal/raweegmeg/structuralDB//111123/surf/lh.orig > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 100537 > Writing to test.mgh > Dim: 157373 1 1 > > Thank you, > Omer Tal > > > > > >> Hi Omer, >> Try removing "--srcreg identity" >> doug >> >> Omer Tal wrote: >> >> >> >>> Hey Doug, >>> >>> Test.nii is a volume nii (1x1x1mm) with values of interest per >>> voxel, >>> created using the header from brain_T1.nii which was simply >>> created >>> by >>> using mri_convert from the subject's original brain.mgz. The >>> *.nii >>> file >>> loads fine and matches the subject as expected. It is when trying >>> to >>> go >>> back to surface, that things seem to get messy. >>> >>> Thank you very much for your time, >>> Omer Tal >>> Keck Center for Functional MRI, UCSD >>> >>> >>> >>> >>> >>>> What is test.nii? How was it derived? >>>> >>>> Omer Tal wrote: >>>> >>>> >>>> >>>> >>>>> Hey all, >>>>> >>>>> I am running into a bit of a problem converting back from a >>>>> volume >>>>> into >>>>> a >>>>> surface and was hoping someone would have some insight. >>>>> >>>>> I have an .nii volume for a given subject, and I want to >>>>> convert >>>>> it >>>>> into >>>>> a >>>>> surface mgh file, so i can view it on tksurfer. Since its the >>>>> same >>>>> exact >>>>> subject, I figured it should be relatively easy, but in the >>>>> resulting >>>>> surface all the white matter and gray matter voxels are mixed >>>>> together >>>>> (looks like tiger pattern on tksurfer) in the entire brain. I >>>>> would >>>>> point >>>>> out though that the gray matter voxels do show up in the >>>>> correct >>>>> location >>>>> (i.e. a motor gray voxel in my volume still ends up in the >>>>> motor >>>>> cortex >>>>> in >>>>> the mgh file), its just that they are surrounded with vertices >>>>> which >>>>> have >>>>> white matter values. >>>>> >>>>> Any advice? >>>>> >>>>> Code: mri_vol2surf --src test nii --srcreg identity --ref >>>>> T1.mgz >>>>> --regheader test_subj --hemi lh --o test.mgh >>>>> >>>>> Thank you very much for your help, >>>>> Omer Tal >>>>> Keck Center for Functional MRI, UCSD >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> 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
-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Omer Tal