Hi Taha - Once you've mapped from the volume onto the white surface, you
should be able to display it on the inflated surface, and also to get
thickness statistics (thickness is just the distance between corresponding
points on the white and pial surface). You don't need to do anything to
map from white to inflated within an individual.
Best,
a.y
On Fri, 19 Aug 2016, Taha Abdullah wrote:
Excellent! Thank you for the quick advice, I tried this initially but I was
using the wrong xfm format.
Since I have the FA map in subject ?h.white space, I have done the same with the
tract endings too. I am having some difficulties conceptually, in terms of
projecting the end points onto either the subject specfic or fsaverage inflated
surface. I assumed using mri_surf2surf would be sufficient to transform the
endpts from subject surface ?h.white space to the inflated surface, but it is a
scalar data file. Once the endpts are projected onto the inflated surface it
seems straightforward to extract the thickness values for further analysis.
Essentially replicating the attached image from Sølsnesa 2015. If you have any
suggestions that would be much appreciated. Thank you very much!
Best,
Taha
On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Taha - Trying getting a .dat registration file from bbregister
and using that as the input to mri_vol2surf. There's a multimodal
tutorial on the freesurfer wiki that might be of help.
Best,
a.y
On Thu, 18 Aug 2016, Taha Abdullah wrote:
Hello All,
I am trying to project FA map (dtifit_FA.nii.gz) and the
endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface
space.
I was following instructions on
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html,
under FreeSurfer
Registration, to create the various xfms files.
Next, I registered the FA map to subject conformed space
using flirt
* flirt -in dtifit_FA.nii.gz -ref
../../mri/orig.nii.gz -applyxfm -init
./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
Then, I used mri_vol2surf to project the registered FA
map onto fsaverage surface with the following command.
* mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1
--cortex --hemi rh --trgsubject fsaverage --regheader
taha_brain
--reg ./xfms_taha/fa2freesurfer.mat --o
FA_2fsavg_surf.mgh
Upon viewing in freeview the fsavg rh.white surface and
fa2FS.nii.gz (FA map in FreeSurfer space) did not allign
properly. I have tried some variations wtihout any luck.
I used the following command line for freeview.
* freeview
-f/usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m
gh -v fa2FS.nii.gz
* Attached are some pics of the FA confomred map and
fsaverage.rh.white surface
Do I need a xfm file for taliarch allignment? Any advice
or insight would be greatly appreciated.
Thanks in advance,
Taha
Terminal output: from mri_vol2surf
srcvol = fa2FS.nii.gz
srcreg = ./xfms_taha/fa2freesurfer.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using
/usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz
as target reference.
Loading label
/usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface
/usr/local/freesurfer/subjects/taha_brain/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 6 6 6
using old
Done mapping volume to surface
Number of source voxels hit = 81606
Reading source surface registration
/usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration
/usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (taha_brain -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (143161)
Reverse Loop had 26084 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 107182, nSrcLost = 0, nSrcMulti = 35979,
MnSrcMultiHits = 2.29979
nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits =
2.24882
Masking with
/usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Writing to FA_2fsavg_surf.mgh
Dim: 163842 1 1
--
Taha Abdullah
Department of Physiology
Northwestern University Feinberg School of Medicine
Masters of Science Physiology and Biophysics, Georgetown
University 2015
Work: (312)-503-0413
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--
Taha Abdullah
Department of Physiology
Northwestern University Feinberg School of Medicine
Masters of Science Physiology and Biophysics, Georgetown University 2015
Work: (312)-503-0413
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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
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