Register marsbar nii to freesurfer fs average

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Re: [Freesurfer] beta

Koolschijn, Cédric

12 Dec 2012 12 Dec '12

10:24 a.m.

Dear FS-experts,

I'm trying to follow the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to get volumetric stats etc on a functional ROI derived from marsbar. The tutorial looks all clear to me, however, I have already problems at the first step.

If I want to view the ROI I see a big orange square instead of the specific region. This almost fills the whole brain.

command:

tkmedit -f avg152T1.nii -overlay DLPFC.nii -fthresh 0.5

I created the DLPFC.nii in MarsBar (v. 0.42): "ROI definition" > "Export" > "Export ROI to image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as DLPFC.nii

If I view the ROI on marsbar it looks good. Did I miss some prior step, or is something else wrong?

Thanks in advance!

Best wishes, Cédric

------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E P.C.M.P.Koolschijn@uva.nl W http://home.medewerker.uva.nl/p.c.m.p.koolschijn/ ------------------------------------------------------------

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Douglas N Greve

13 Dec 13 Dec

1:01 p.m.

Hi Cedric, when you view it marsbar, are you viewing it on avg152T1.nii? Do avg152T1.nii and DLPFC.nii have the same geometry? To check, look at the qform matrix with: mri_info --vox2ras avg152T1.nii mri_info --vox2ras DLPFC.nii and make sure that they have the same number of rows, cols, slices

doug

On 12/12/2012 10:24 AM, Koolschijn, Cédric wrote:

...

Dear FS-experts,

I'm trying to follow the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to get volumetric stats etc on a functional ROI derived from marsbar. The tutorial looks all clear to me, however, I have already problems at the first step.

If I want to view the ROI I see a big orange square instead of the specific region. This almost fills the whole brain.

command: tkmedit -f avg152T1.nii -overlay DLPFC.nii -fthresh 0.5 I created the DLPFC.nii in MarsBar (v. 0.42): "ROI definition" > "Export" > "Export ROI to image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as DLPFC.nii

If I view the ROI on marsbar it looks good. Did I miss some prior step, or is something else wrong?

Thanks in advance!

Best wishes, Cédric

P.C.M.P. Koolschijn (Cédric), PhD Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands /E /P.C.M.P.Koolschijn@uva.nl /W/ http://home.medewerker.uva.nl/p.c.m.p.koolschijn/

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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Koolschijn, Cédric

22 Jan 22 Jan

9:16 a.m.

New subject: dimension mismatch: Cortical Thickness of a Volume-defined ROI

Hi Doug and other FS-experts,

I succesfully applied the registration step of the Cortical Thickness of a Volume-defined ROI wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness However, I'm having troubles at the end.

3) Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface overlay. This works perfectly: (fsaverage dir)

mri_vol2surf --mov ../../Parietal_Sup_L152.nii --reg ../../test.register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fs.average.parietal.mgh --reshape

Then viewing: tksurfer fsaverage lh inflated -overlay lh.fsaverage.parietal.mgh -fthresh 0.5 Is also perfect.

The problem arises in step 4/5. First:

4) Map your subject thickness data to the fsaverage subject. Do this for all your subjects. mri_surf2surf --s BT1P0392_9_1 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape

srcsubject = BT1P0392_9_1 srcval = lh.thickness srctype = trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh 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 /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//BT1P0392_9_1/surf/lh .sphere.reg Loading source data Reading target surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//fsaverage/surf/lh.sp here.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 (144750) Reverse Loop had 31554 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141619, nTrgMulti = 22223, MnTrgMultiHits = 2.41988 nSrc121 = 107010, nSrcLost = 0, nSrcMulti = 37740, MnSrcMultiHits = 2.34197 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh

Here all is well. But then: 5) Run mri_segstats, using the subject-ROI surface, to get the thickness data for your ROI.

mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt

$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt sysname Linux hostname corleone01univ.nl machine x86_64 user cedric Loading /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7

If I then follow the suggestion to use the --reshape-factor 7 and re-run steps 4 and 5, I keep on getting the same error message " ERROR: dimension mismatch between input volume and seg".

Do you have any ideas what is going (wr)on(g)?

Many thanks, Cédric

Douglas N Greve

10:25 a.m.

New subject: dimension mismatch: Cortical Thickness of a Volume-defined ROI

Hi Cedric, try it with --noreshape. If you're using mgh format, then reshaping is not necessary. doug On 01/22/2013 09:16 AM, Koolschijn, Cédric wrote:

...

Hi Doug and other FS-experts,

I succesfully applied the registration step of the Cortical Thickness of a Volume-defined ROI wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness However, I'm having troubles at the end.

Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI

surface overlay. This works perfectly: (fsaverage dir)

mri_vol2surf --mov ../../Parietal_Sup_L152.nii --reg ../../test.register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fs.average.parietal.mgh --reshape

Then viewing: tksurfer fsaverage lh inflated -overlay lh.fsaverage.parietal.mgh -fthresh 0.5 Is also perfect.

The problem arises in step 4/5. First:

Map your subject thickness data to the fsaverage subject. Do this for

all your subjects. mri_surf2surf --s BT1P0392_9_1 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape

srcsubject = BT1P0392_9_1 srcval = lh.thickness srctype = trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh 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 /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//BT1P0392_9_1/surf/lh .sphere.reg Loading source data Reading target surface reg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy//fsaverage/surf/lh.sp here.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 (144750) Reverse Loop had 31554 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141619, nTrgMulti = 22223, MnTrgMultiHits = 2.41988 nSrc121 = 107010, nSrcLost = 0, nSrcMulti = 37740, MnSrcMultiHits = 2.34197 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh

Here all is well. But then: 5) Run mri_segstats, using the subject-ROI surface, to get the thickness data for your ROI.

mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt

$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --seg /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh --in lh.thickness.fsaverage.mgh --sum segstats-Parietal.txt sysname Linux hostname corleone01univ.nl machine x86_64 user cedric Loading /home/cedric/data/Anatomy_BD/freesurfer/Brain_Anatomy/fsaverage/surf/lh.fs. average.Parietal.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7

If I then follow the suggestion to use the --reshape-factor 7 and re-run steps 4 and 5, I keep on getting the same error message " ERROR: dimension mismatch between input volume and seg".

Do you have any ideas what is going (wr)on(g)?

Many thanks, Cédric

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Douglas N Greve
Koolschijn, Cédric