Re: [Freesurfer] Projecting FA map onto fsaverge surface

2016-08-19 Thread Taha Abdullah 
Great! looks good, thanks for the help.

Enjoy your weekend!

On Fri, Aug 19, 2016 at 11:34 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> 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
>>  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/subjec
>> ts/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
>>
>>

Re: [Freesurfer] Projecting FA map onto fsaverge surface

2016-08-19 Thread Anastasia Yendiki 


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
 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).

Re: [Freesurfer] Projecting FA map onto fsaverge surface

2016-08-19 Thread Taha Abdullah 
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.mgh
>> -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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> is
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Projecting FA map onto fsaverge surface

2016-08-19 Thread Anastasia Yendiki 


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.mgh
 -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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