any ideas? Thanks!
Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > thanks Bruce - I had found that option for my fsaverage maps and it worked. > > What about if I am importing probability maps formed as .mnc and creating > overlays from them? The percentages seem to be very odd for min and max > threshold. > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > >> Hi Trisanna >> >> if you are using mri_average you can give it -p as the first argument and >> it will compute a percent at the end >> Bruce >> On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote: >> >> Hi Bruce >>> >>> Is there is a way to set the probability of an overlay between 0 and 1? >>> Would this have to be done when creating the overlay using mri_vol2surf? >>> >>> thanks >>> >>> Trisanna >>> >>> -- >>> Ph.D. CandidateMcGill University >>> Integrated Program in Neuroscience >>> Psychology >>> >>> >>> On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Trisanna >>> >>> the binaries that take mandatory command-line arguments (i.e. >>> without a -- or - in front of them) require all options to be >>> given before the mandatory arguments >>> >>> cheers >>> Bruce >>> >>> On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote: >>> >>> thanks, Bruce. Yes in the end through trial and >>> error I tried "mri_average -noconform input output" >>> and it worked. I was >>> surprised that I had to put the -noconform first as >>> normally one can put the argument anywhere in the >>> command. >>> >>> Best >>> >>> Trisanna >>> >>> -- >>> Ph.D. CandidateMcGill University >>> Integrated Program in Neuroscience >>> Psychology >>> >>> >>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> yes, your last file on the command line should >>> be the output file (the average) >>> >>> cheers >>> Bruce >>> >>> On Mon, 20 Jun 2016, Trisanna Sprung-Much >>> wrote: >>> >>> As a follow-up, here is the mri_info for one >>> of my overlays in the folder >>> and the output file that mri_average seems to >>> create (if I don't specify an >>> output and it re-writes my last file). The >>> dimensions are off: >>> Any ideas? >>> >>> Trisanna >>> >>> >>> Tgtrisanna@kaplan >>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f >>> sa >>> vee_left/aalf_lh$ mri_info >>> fsaverage_overlay_aalf_icbm-102_left.mgz >>> Volume information for >>> fsaverage_overlay_aalf_icbm-102_left.mgz >>> type: MGH >>> dimensions: 163842 x 1 x 1 >>> voxel sizes: 1.0000, 1.0000, 1.0000 >>> type: FLOAT (3) >>> fov: 163842.000 >>> dof: 0 >>> xstart: -81921.0, xend: 81921.0 >>> ystart: -0.5, yend: 0.5 >>> zstart: -0.5, zend: 0.5 >>> TR: 0.00 msec, TE: 0.00 msec, TI: >>> 0.00 msec, flip angle: 0.00 >>> degrees >>> nframes: 1 >>> PhEncDir: UNKNOWN >>> ras xform present >>> xform info: x_r = 1.0000, y_r = >>> 0.0000, z_r = 0.0000, c_r = >>> 0.5000 >>> : x_a = 0.0000, y_a = >>> 1.0000, z_a = 0.0000, c_a = >>> -17.5000 >>> : x_s = 0.0000, y_s = >>> 0.0000, z_s = 1.0000, c_s = >>> 18.5000 >>> >>> talairach xfm : >>> Orientation : RAS >>> Primary Slice Direction: axial >>> >>> voxel to ras transform: >>> 1.0000 0.0000 0.0000 >>> -81920.5000 >>> 0.0000 1.0000 0.0000 >>> -18.0000 >>> 0.0000 0.0000 1.0000 >>> 18.0000 >>> 0.0000 0.0000 0.0000 >>> 1.0000 >>> >>> voxel-to-ras determinant 1 >>> >>> ras to voxel transform: >>> 1.0000 -0.0000 -0.0000 >>> 81920.5000 >>> -0.0000 1.0000 -0.0000 >>> 18.0000 >>> -0.0000 -0.0000 1.0000 >>> -18.0000 >>> 0.0000 0.0000 0.0000 >>> 1.0000 >>> >>> >>> trisanna@kaplan >>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa >>> >>> verage_left/aalf_lh$ mri_info >>> fsaverage_overlay_aalf_icbm-350_left.mgz >>> Volume information for >>> fsaverage_overlay_aalf_icbm-350_left.mgz >>> type: MGH >>> dimensions: 256 x 256 x 256 >>> voxel sizes: 1.0000, 1.0000, 1.0000 >>> type: FLOAT (3) >>> fov: 256.000 >>> dof: 0 >>> xstart: -128.0, xend: 128.0 >>> ystart: -128.0, yend: 128.0 >>> zstart: -128.0, zend: 128.0 >>> TR: 0.00 msec, TE: 0.00 msec, TI: >>> 0.00 msec, flip angle: 0.00 >>> degrees >>> nframes: 1 >>> PhEncDir: UNKNOWN >>> ras xform present >>> xform info: x_r = -1.0000, y_r = >>> 0.0000, z_r = 0.0000, c_r = >>> 0.5000 >>> : x_a = 0.0000, y_a = >>> 0.0000, z_a = 1.0000, c_a = >>> -17.5000 >>> : x_s = 0.0000, y_s = >>> -1.0000, z_s = 0.0000, c_s = >>> 18.5000 >>> >>> talairach xfm : >>> Orientation : LIA >>> Primary Slice Direction: coronal >>> >>> -- >>> Ph.D. CandidateMcGill University >>> Integrated Program in Neuroscience >>> Psychology >>> >>> >>> On Mon, Jun 20, 2016 at 12:32 AM, Trisanna >>> Sprung-Much >>> <trisanna.sprung-m...@mail.mcgill.ca> wrote: >>> Hi Dr. Fischl >>> I ran the following mri_average and consistently get >>> this message. It >>> seems to be trying to read my output as one of the >>> input volumes. If I >>> don't specify an output it re-writes my last file in >>> the input folder >>> and when I try to open this it doesn't work at all. >>> >>> What exactly does MRIchangeType mean? >>> >>> >>> >>> (navigated to folder with all .mgz volumes want to >>> average) >>> mri_average *.mgz test.mgz --noconform >>> >>> 1 of 51: reading >>> fsaverage_overlay_aalf_icbm-102_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 2 of 51: reading >>> fsaverage_overlay_aalf_icbm-103_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 3 of 51: reading >>> fsaverage_overlay_aalf_icbm-104_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 4 of 51: reading >>> fsaverage_overlay_aalf_icbm-105_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 5 of 51: reading >>> fsaverage_overlay_aalf_icbm-106_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 6 of 51: reading >>> fsaverage_overlay_aalf_icbm-107_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 7 of 51: reading >>> fsaverage_overlay_aalf_icbm-108_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 8 of 51: reading >>> fsaverage_overlay_aalf_icbm-109_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 9 of 51: reading >>> fsaverage_overlay_aalf_icbm-110_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 10 of 51: reading >>> fsaverage_overlay_aalf_icbm-111_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 11 of 51: reading >>> fsaverage_overlay_aalf_icbm-112_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 12 of 51: reading >>> fsaverage_overlay_aalf_icbm-113_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 13 of 51: reading >>> fsaverage_overlay_aalf_icbm-114_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 14 of 51: reading >>> fsaverage_overlay_aalf_icbm-115_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 15 of 51: reading >>> fsaverage_overlay_aalf_icbm-116_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 16 of 51: reading >>> fsaverage_overlay_aalf_icbm-117_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 17 of 51: reading >>> fsaverage_overlay_aalf_icbm-118_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 18 of 51: reading >>> fsaverage_overlay_aalf_icbm-119_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 19 of 51: reading >>> fsaverage_overlay_aalf_icbm-120_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 20 of 51: reading >>> fsaverage_overlay_aalf_icbm-121_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 21 of 51: reading >>> fsaverage_overlay_aalf_icbm-122_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 22 of 51: reading >>> fsaverage_overlay_aalf_icbm-123_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 23 of 51: reading >>> fsaverage_overlay_aalf_icbm-124_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 24 of 51: reading >>> fsaverage_overlay_aalf_icbm-125_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 25 of 51: reading >>> fsaverage_overlay_aalf_icbm-126_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 26 of 51: reading >>> fsaverage_overlay_aalf_icbm-127_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 27 of 51: reading >>> fsaverage_overlay_aalf_icbm-131_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 28 of 51: reading >>> fsaverage_overlay_aalf_icbm-133_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 29 of 51: reading >>> fsaverage_overlay_aalf_icbm-134_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 30 of 51: reading >>> fsaverage_overlay_aalf_icbm-135_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 31 of 51: reading >>> fsaverage_overlay_aalf_icbm-137_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 32 of 51: reading >>> fsaverage_overlay_aalf_icbm-139_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 33 of 51: reading >>> fsaverage_overlay_aalf_icbm-140_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 34 of 51: reading >>> fsaverage_overlay_aalf_icbm-141_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 35 of 51: reading >>> fsaverage_overlay_aalf_icbm-142_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 36 of 51: reading >>> fsaverage_overlay_aalf_icbm-143_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 37 of 51: reading >>> fsaverage_overlay_aalf_icbm-144_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 38 of 51: reading >>> fsaverage_overlay_aalf_icbm-145_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 39 of 51: reading >>> fsaverage_overlay_aalf_icbm-146_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 40 of 51: reading >>> fsaverage_overlay_aalf_icbm-150_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 41 of 51: reading >>> fsaverage_overlay_aalf_icbm-158_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 42 of 51: reading >>> fsaverage_overlay_aalf_icbm-200_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 43 of 51: reading >>> fsaverage_overlay_aalf_icbm-201_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 44 of 51: reading >>> fsaverage_overlay_aalf_icbm-203_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 45 of 51: reading >>> fsaverage_overlay_aalf_icbm-204_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 46 of 51: reading >>> fsaverage_overlay_aalf_icbm-205_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 47 of 51: reading >>> fsaverage_overlay_aalf_icbm-209_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 48 of 51: reading >>> fsaverage_overlay_aalf_icbm-340_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 49 of 51: reading >>> fsaverage_overlay_aalf_icbm-347_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 50 of 51: reading >>> fsaverage_overlay_aalf_icbm-350_left.mgz... >>> embedding and interpolating volume >>> MRIchangeType: Building histogram >>> 51 of 51: reading test.mgz... >>> >>> mghRead(/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsaverage_l >>> >>> eft/aalf_lh/test.mgz, -1): could not open file >>> mri_average: MRIread(test.mgz) failed >>> >>> >>> -- >>> Ph.D. CandidateMcGill University >>> Integrated Program in Neuroscience >>> Psychology >>> >>> >>> On Sun, Jun 19, 2016 at 12:46 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> no problem. >>> >>> Bruce >>> On Sun, 19 Jun 2016, Trisanna Sprung-Much >>> wrote: >>> >>> thanks Dr. Fischl - I think sometimes my >>> emails don't get sent out on the >>> first try and so I resend - don't mean >>> to spam >>> everyone. >>> Don't know how I missed the mri_average >>> option >>> - I think I need vacation >>> too. >>> >>> thanks and have a lovely Sunday! >>> >>> Trisanna >>> >>> -- >>> Ph.D. CandidateMcGill University >>> Integrated Program in Neuroscience >>> Psychology >>> >>> >>> On Sun, Jun 19, 2016 at 11:22 AM, Bruce >>> Fischl >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Trisanna >>> >>> Doug is on vacation and his >>> response >>> time is likely to be pretty >>> slow. If any emails go unanswered >>> you >>> should repost them in a >>> week or two. >>> >>> As for this, if you overlays are >>> mapped >>> to fsaverage you can >>> just use mri_average to average >>> them. >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Sun, 19 Jun 2016, Trisanna >>> Sprung-Much wrote: >>> >>> Hi Doug >>> >>> So all of my overlays for >>> each >>> subject have been >>> registered to fsaverage >>> using mri_surf2surf. I am >>> now >>> wondering how I could >>> create an average in >>> "fsaverage space" using >>> these >>> overlays - I >>> understand that >>> mris_make_average_surface is >>> an >>> option but I cannot >>> seem to find whether >>> this works for overlays and >>> not >>> just surfaces >>> (white, pial). I want to >>> take >>> each subject overlay on >>> fsaverage >>> and average them >>> to get a probability map. >>> >>> thanks >>> >>> -- >>> Ph.D. CandidateMcGill >>> University >>> Integrated Program in >>> Neuroscience >>> Psychology >>> >>> >>> On Fri, Jun 17, 2016 at 5:48 >>> PM, >>> Trisanna >>> Sprung-Much >>> >>> <trisanna.sprung-m...@mail.mcgill.ca> >>> wrote: >>> Hi Doug >>> >>> So all of my sulci for each >>> subject have been >>> registered to fsaverage >>> using mri_surf2surf. I am >>> now >>> wondering how I could >>> create an average >>> of a sulcus using these >>> overlays - >>> I understand that >>> mris_make_average_surface is >>> an >>> option but I cannot >>> seem to find >>> whether this works for >>> overlays >>> and not just >>> surfaces (white, pial). I >>> want to take each subject >>> overlay >>> on fsaverage and >>> average them to get >>> a probability map for a >>> single >>> sulcus. >>> >>> thanks >>> >>> Trisanna >>> >>> -- >>> Ph.D. CandidateMcGill >>> University >>> Integrated Program in >>> Neuroscience >>> Psychology >>> >>> >>> On Wed, Jun 15, 2016 at 6:25 >>> PM, >>> Trisanna >>> Sprung-Much >>> >>> <trisanna.sprung-m...@mail.mcgill.ca> >>> wrote: >>> worked beautifully. >>> Thank >>> you! >>> >>> -- >>> Ph.D. CandidateMcGill >>> University >>> Integrated Program in >>> Neuroscience >>> Psychology >>> >>> >>> On Wed, Jun 15, 2016 at 4:41 >>> PM, >>> Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> Try surf2surf with >>> --mapmethod nnf >>> >>> On 06/15/2016 04:25 >>> PM, >>> Trisanna Sprung-Much >>> wrote: >>> > Hi Doug - yes they >>> do >>> actually, I was quite >>> pleased. I did some >>> trials >>> > with other subjects >>> and >>> the mri_vol2surf all >>> looks >>> good. Very similar >>> > to what I had in our >>> in-house software. >>> > >>> > Would things be >>> better if >>> I were to isolate >>> each >>> sulcus as a .label >>> > and then try the >>> mri_label2label? Someone >>> suggested perhaps the >>> > colours are >>> overlapping >>> with the overlay.... >>> > >>> > -- >>> > Ph.D. Candidate >>> > McGill University >>> > Integrated Program >>> in >>> Neuroscience >>> > Psychology >>> > >>> > >>> > On Wed, Jun 15, 2016 >>> at >>> 4:10 PM, Douglas N >>> Greve >>> > >>> <gr...@nmr.mgh.harvard.edu >>> >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> wrote: >>> > >>> > The problem is >>> probably that the >>> vol2surf >>> command did not >>> properly >>> > sample the >>> labels onto >>> the surface. Do >>> the >>> labels on subject >>> 00350 >>> > surfaces look >>> ok? >>> > >>> > On 06/15/2016 >>> 04:00 >>> PM, Trisanna >>> Sprung-Much >>> wrote: >>> > > thanks Dr. >>> Fischl >>> > > >>> > > So the command >>> seems >>> to have worked! I >>> have >>> copied what ran in my >>> > > terminal. When >>> I >>> open the test.mgz >>> overlay >>> on the fsaverage pial >>> > > surface, >>> things look >>> ok but a bit >>> funny. I >>> am wondering if there >>> is >>> > > anything I can >>> do to >>> the mri_surf2surf >>> command to improve the >>> > > registration >>> to >>> fsaverage? *See my >>> snapshots >>> attached.* >>> > > >>> > > >>> trisanna@kaplan:~$ >>> mri_surf2surf >>> --srcsubject 00350 >>> --sval >>> > > >>> >>> >>> >>> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz >>> > > --trgsubject >>> fsaverage --tval test.mgz >>> --hemi lh >>> > > srcsubject = >>> 00350 >>> > > srcval = >>> > >>> >>> >>> >>> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz >>> > > srctype = >>> > > trgsubject = >>> fsaverage >>> > > trgval = >>> test.mgz >>> > > trgtype = >>> > > srcsurfreg = >>> sphere.reg >>> > > trgsurfreg = >>> sphere.reg >>> > > srchemi = >>> lh >>> > > trghemi = >>> lh >>> > > frame = 0 >>> > > fwhm-in = 0 >>> > > fwhm-out = 0 >>> > > label-src = >>> (null) >>> > > label-trg = >>> (null) >>> > > >>> OKToRevFaceOrder = >>> 1 >>> > > Reading source >>> surface reg >>> > > >>> >>> >>> >>> /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg >>> > > Loading source >>> data >>> > > Reading target >>> surface reg >>> > > >>> >>> >>> >>> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg >>> > > Done >>> > > Mapping Source >>> Volume onto Source >>> Subject >>> Surface >>> > > >>> surf2surf_nnfr: >>> building source hash >>> (res=16). >>> > > Surf2Surf: >>> Forward >>> Loop (163842) >>> > > >>> > > >>> surf2surf_nnfr: >>> building target hash >>> (res=16). >>> > > Surf2Surf: >>> Reverse >>> Loop (166912) >>> > > Reverse Loop >>> had >>> 41306 hits >>> > > Surf2Surf: >>> Dividing >>> by number of hits >>> (163842) >>> > > INFO: nSrcLost >>> = 0 >>> > > nTrg121 = >>> 132490, >>> nTrgMulti = 31352, >>> MnTrgMultiHits = >>> 2.31749 >>> > > nSrc121 = >>> 137180, >>> nSrcLost = 0, >>> nSrcMulti = >>> 29732, MnSrcMultiHits >>> = >>> > > 2.28602 >>> > > Saving target >>> data >>> > > Saving to >>> test.mgz >>> > > >>> > > best >>> > > >>> > > Trisanna >>> > > >>> > > -- >>> > > Ph.D. >>> Candidate >>> > > McGill >>> University >>> > > Integrated >>> Program >>> in Neuroscience >>> > > Psychology >>> > > >>> > > >>> > > On Wed, Jun >>> 15, 2016 >>> at 12:13 PM, >>> Bruce >>> Fischl >>> > > >>> <fis...@nmr.mgh.harvard.edu >>> >>> <mailto:fis...@nmr.mgh.harvard.edu> >>> > >>> <mailto:fis...@nmr.mgh.harvard.edu >>> > >>> <mailto:fis...@nmr.mgh.harvard.edu>>> >>> wrote: >>> > > >>> > > Hi Trisanna >>> > > >>> > > you would only >>> use >>> those options of if >>> you >>> were transforming >>> > a surface >>> > > Bruce >>> > > >>> > > >>> > > On Wed, 15 Jun >>> 2016, >>> Trisanna >>> Sprung-Much >>> wrote: >>> > > >>> > > thanks Dr. >>> Fischl >>> > > >>> > > I assume >>> that for >>> surface overlays >>> one >>> cannot specify >>> > > --sval-xyz >>> and >>> --tval-xyz or the >>> command >>> will treat the >>> > input >>> > > as a surface >>> > > itself? >>> > > >>> > > best >>> > > >>> > > Trisanna >>> > > >>> > > >>> > > >>> > > >>> > > -- >>> > > Ph.D. >>> CandidateMcGill University >>> > > Integrated >>> Program >>> in Neuroscience >>> > > Psychology >>> > > >>> > > >>> > > On Wed, Jun >>> 15, >>> 2016 at 11:11 AM, >>> Bruce >>> Fischl >>> > > >>> <fis...@nmr.mgh.harvard.edu >>> > >>> <mailto:fis...@nmr.mgh.harvard.edu> >>> > > >>> <mailto:fis...@nmr.mgh.harvard.edu >>> > >>> <mailto:fis...@nmr.mgh.harvard.edu>>> >>> wrote: >>> > > Hi >>> Trisanna >>> > > >>> > > you >>> don't >>> need to inflate the >>> overlays. They can just >>> > > use the >>> existing >>> surface-based >>> (sphere.reg) registration. >>> > > >>> > > cheers >>> > > Bruce >>> > > On >>> Wed, 15 >>> Jun 2016, Trisanna >>> Sprung-Much wrote: >>> > > >>> > > >>> Hi >>> there >>> > > >>> So I >>> have sulcal labels >>> from >>> another software >>> > > (.mnc >>> format) from >>> which I am trying >>> to >>> generate some >>> > > >>> probability maps. I was >>> able >>> > > >>> to >>> convert the .mnc to >>> .mgz >>> surface overlay >>> > using >>> > > mri_vol2surf >>> for >>> my MRIs after >>> running all >>> MRIs in >>> > > >>> recon-all. So, now I >>> have >>> > > >>> all my >>> painted voxels as >>> surface overlays, as I >>> > > was >>> instructed to >>> do a few months >>> ago. >>> > > >>> > > >>> I was >>> told that the next >>> step >>> would be to use >>> > > >>> mri_surf2surf to >>> resample the >>> overlays to >>> fsaverage. >>> > > >>> > > >>> I am a >>> bit confused as I >>> would >>> think that >>> > the next >>> > > step would >>> be to >>> take the surface >>> overlays >>> and >>> > > >>> inflate them before I >>> register >>> > > >>> them >>> to fsaverage. I see >>> that >>> when recon-all >>> > runs, >>> > > it computes >>> the >>> registration of the >>> MRI >>> surface to >>> > > >>> fsaverage and saves it >>> as >>> > > >>> sphere.reg. Is there a >>> way I >>> can inflate my >>> > > surface >>> overlays >>> in a similar manner >> >> >> _______________________________________________ >> 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. >> >> >
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