Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared P Zimmerman]

Yeah, I think I misunderstood what was happening with the ico registration.  I 
thought it was using the ico to downsample the subject surface, but I see that 
this is an atlas space and I can do w/e calculations I need I this space and 
then register back to subject space after. 

Thanks for the help, I got it to work by doing mri_vol2surf to register to my 
subject surface and then mri_surf2surf to downsample.

-jared

> On Sep 29, 2016, at 12:34 PM, Douglas N Greve  
> wrote:
> 
> I don't understand what you mean. When you use ico (when it used to 
> work), it always went to fsaverage space. Do you want to decimate the 
> native space surfaces?
> 
> 
> On 09/29/2016 10:15 AM, Jared P Zimmerman wrote:
>> I want to project to the native subject surfaces though, not 
>> fsaverage.  If I use —trgsubject subjID would that work with the 
>> —icoorder flag?  Alternatively I guess I could project to fsaverage 
>> and then use mri_surf2surf to move back to the subject surface, but 
>> that seems like a roundabout way to do it and will probably add some 
>> unnecessary interpolation.
>> 
>> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder 
>> flags and I did successfully get output with 112745 vertices (is this 
>> FS7 space?  I would have expected ~164k vertices, is this with medial 
>> wall masked?) and I could try to resample that with mri_surf2surf.  I 
>> wasn’t able to do this before, but I didn’t use the flag —trgsubject 
>> or —trgicoorder flags, though I suspect I will run into the same 
>> problem trying doing this.  I’m not at my computer now but can try 
>> this later this afternoon though.
>> 
>> Thanks,
>> Jared
>> 
>>> On Sep 29, 2016, at 12:00 AM, Douglas Greve 
>>>  
>>> >> 
>>> wrote:
>>> 
>>> you can actually skip the ico thing and just use --trgsubject fsaverage6
>>> 
>>> 
>>> On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
 Thanks Doug,
 
 This does seem like it will do the right thing, but it’s failing 
 because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to 
 have an ico subject in my subjects_dir
 
 Should this normally be in the subjects_dir?  I don’t recall ever 
 seeing this made when I’ve run recon-all in the past.
 
 Thanks,
 Jared
 
 Here’s the full terminal output when I run the command:
 
 mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg 
 func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o 
 func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 
 --interp trilinear --noreshape --trgsubject ico --icoorder 6 
 --out_type mgh --surf-fwhm 6
 IcoOrder = 6, nIcoVtxs = 40962
 srcvol = /func_test/filtered_func_residuals.nii.gz
 srcreg = func_test/coreg/fs_ep2struct_fsl.dat
 srcregold = 0
 srcwarp unspecified
 surf = white
 hemi = lh
 trgsubject = ico
 surfreg = sphere.reg
 ProjFrac = 0.5
 thickness = thickness
 reshape = 0
 interp = trilinear
 float2int = round
 GetProjMax = 0
 INFO: float2int code = 0
 Done loading volume
 Reading surface /subjdir_test//subID/surf/lh.white
 Done reading source surface
 Reading thickness /subjdir_test//subID/surf/lh.thickness
 Done
 Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
 using old
 Done mapping volume to surface
 Number of source voxels hit = 11345
 Reading source surface registration
 subjdir_test//subID/surf/lh.sphere.reg
 Done loading source registration surface
 Reading icosahedron, order = 6, radius = 100
  Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
 Done loading target registration surface
 Mapping Surfaces (subID -> ico)
 surf2surf_nnfr: building source hash (res=16).
 Surf2Surf: Forward Loop (40962)
 
 surf2surf_nnfr: building target hash (res=16).
 Surf2Surf: Reverse Loop (112745)
 Reverse Loop had 72236 hits
 
> On Sep 28, 2016, at 3:34 PM, Douglas Greve 
>  
> >> 
> wrote:
> 
> You need to specify --trgsubject ico in mri_vol2surf
> 
> 
> On 9/28/16 3:01 PM, Jared Zimmerman wrote:
>> Hi All, forwarding this message along again as I'm still having 
>> some trouble getting this to work.  Basically I would like to 1) 
>> project processed residual time-series from the subject-space 
>> volume to the subject-space surface, 2) smooth on the surface, 3) 
>> down-sample to FS4 space.
>> 
>> To do this is have used bbregister to calculate the registration, 
>> then mri_vol2surf to project to the surface, but I am not sure the 
>> output of mri_vol2surf is what I 

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Douglas N Greve]

I don't understand what you mean. When you use ico (when it used to 
work), it always went to fsaverage space. Do you want to decimate the 
native space surfaces?


On 09/29/2016 10:15 AM, Jared P Zimmerman wrote:
> I want to project to the native subject surfaces though, not 
> fsaverage.  If I use —trgsubject subjID would that work with the 
> —icoorder flag?  Alternatively I guess I could project to fsaverage 
> and then use mri_surf2surf to move back to the subject surface, but 
> that seems like a roundabout way to do it and will probably add some 
> unnecessary interpolation.
>
> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder 
> flags and I did successfully get output with 112745 vertices (is this 
> FS7 space?  I would have expected ~164k vertices, is this with medial 
> wall masked?) and I could try to resample that with mri_surf2surf.  I 
> wasn’t able to do this before, but I didn’t use the flag —trgsubject 
> or —trgicoorder flags, though I suspect I will run into the same 
> problem trying doing this.  I’m not at my computer now but can try 
> this later this afternoon though.
>
> Thanks,
> Jared
>
>> On Sep 29, 2016, at 12:00 AM, Douglas Greve 
>> > wrote:
>>
>> you can actually skip the ico thing and just use --trgsubject fsaverage6
>>
>>
>> On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
>>> Thanks Doug,
>>>
>>> This does seem like it will do the right thing, but it’s failing 
>>> because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to 
>>> have an ico subject in my subjects_dir
>>>
>>> Should this normally be in the subjects_dir?  I don’t recall ever 
>>> seeing this made when I’ve run recon-all in the past.
>>>
>>> Thanks,
>>> Jared
>>>
>>> Here’s the full terminal output when I run the command:
>>>
>>> mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg 
>>> func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o 
>>> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 
>>> --interp trilinear --noreshape --trgsubject ico --icoorder 6 
>>> --out_type mgh --surf-fwhm 6
>>> IcoOrder = 6, nIcoVtxs = 40962
>>> srcvol = /func_test/filtered_func_residuals.nii.gz
>>> srcreg = func_test/coreg/fs_ep2struct_fsl.dat
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = white
>>> hemi = lh
>>> trgsubject = ico
>>> surfreg = sphere.reg
>>> ProjFrac = 0.5
>>> thickness = thickness
>>> reshape = 0
>>> interp = trilinear
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> Done loading volume
>>> Reading surface /subjdir_test//subID/surf/lh.white
>>> Done reading source surface
>>> Reading thickness /subjdir_test//subID/surf/lh.thickness
>>> Done
>>> Mapping Source Volume onto Source Subject Surface
>>> 1 0.5 0.5 0.5
>>> using old
>>> Done mapping volume to surface
>>> Number of source voxels hit = 11345
>>> Reading source surface registration
>>> subjdir_test//subID/surf/lh.sphere.reg
>>> Done loading source registration surface
>>> Reading icosahedron, order = 6, radius = 100
>>>   Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
>>> Done loading target registration surface
>>> Mapping Surfaces (subID -> ico)
>>> surf2surf_nnfr: building source hash (res=16).
>>> Surf2Surf: Forward Loop (40962)
>>>
>>> surf2surf_nnfr: building target hash (res=16).
>>> Surf2Surf: Reverse Loop (112745)
>>> Reverse Loop had 72236 hits
>>>
 On Sep 28, 2016, at 3:34 PM, Douglas Greve 
 > wrote:

 You need to specify --trgsubject ico in mri_vol2surf


 On 9/28/16 3:01 PM, Jared Zimmerman wrote:
> Hi All, forwarding this message along again as I'm still having 
> some trouble getting this to work.  Basically I would like to 1) 
> project processed residual time-series from the subject-space 
> volume to the subject-space surface, 2) smooth on the surface, 3) 
> down-sample to FS4 space.
>
> To do this is have used bbregister to calculate the registration, 
> then mri_vol2surf to project to the surface, but I am not sure the 
> output of mri_vol2surf is what I should be expecting.  The output 
> file has dimensions 112745 x 1 x 1 x 120 when I'm expecting ~40k 
> vertices for FS6 space and ~3k vertices for FS4 space, but 
> changing the --icoorder flag seems to have no effect on the number 
> of vertices in the output.
>
> I have loaded the output surface functional image into Matlab to 
> se that there is real time-series data in there, but I have no way 
> of knowing if it has mapped the data appropriately.  Additionally, 
> I've tried to use mri_surf2surf to downsample this data but have 
> not ben able to successfully get that to downsample the surface. 
>  The mri_surf2surf call I used is as follows:
>
> mri_surf2surf --srcsubject subjID --srcsurfval 
> 

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared P Zimmerman]

>  FS4 space, but changing the --icoorder flag
>>  seems to have no effect on the number of
>>  vertices in the output.
>> 
>>  I have loaded the output surface functional
>>  image into Matlab to se that there is real
>>  time-series data in there, but I have no way
>>  of knowing if it has mapped the data
>>  appropriately.  Additionally, I've tried to
>>  use mri_surf2surf to downsample this data but
>>  have not ben able to successfully get that to
>>  downsample the surface.  The mri_surf2surf
>>  call I used is as follows:
>> 
>>  mri_surf2surf --srcsubject subjID --srcsurfval
>>  /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh
>>  --trgsubject subjID --trgsurfval
>>  /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh
>>  --hemi lh --trgicoorder 4
>> 
>>  Any advice on how to achieve my goal of
>>  projecting to subject surfaces, smoothing and
>>  downsampling to FS4, as well as
>>  recommendations on how to visualize the
>>  surface functional data and confirm that the
>>  projections has worked properly would be much
>>  appreciated.  Additionally, what should the
>>  dimensions of a surface time series look like?
>>   I would have expected for have an nVertices x
>>  nFrames x 1 array instead of the nVertices x 1
>>  x 1 x nFrames array, is this correct?
>> 
>>  Thank you,
>>  Jared
>> 
>>  - Forwarded Message -
>>  From: "Jared Zimmerman"
>>  <jar...@mail.med.upenn.edu>
>>  To: freesurfer@nmr.mgh.harvard.edu
>>  Sent: Monday, September 19, 2016 8:46:17 PM
>>  Subject: [Freesurfer] Projecting processed 4D
>>  functional data to individual surfaces
>> 
>>  Hi All,
>> 
>>  I'm trying to project some processed
>>  resting-state data onto the surface to run
>>  some surface based parcellations, and I'm
>>  running into a bit of difficulty.  Basically
>>  I'm using bbregister to register my functional
>>  to the T1, then mri_vol2surf to project to the
>>  surface with the following pseudocode:
>> 
>>  bbregister --s subjID --mov
>>  /mov_dir/subjID_example_func_brain.nii.gz \
>>   --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
>>   --init-fsl --bold
>> 
>>  mri_vol2surf --src
>>  /mov_dir/filtered_func_residuals.nii.gz \
>>   --out
>>  /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh
>>  \
>>   --srcreg /coreg/fs_ep2struct_fsl.dat --hemi
>>  lh \
>>   --surf white --projfrac 0.5 --icoorder 6
>>  --fwhm 6 --out_type mgh --noreshape
>> 
>>  The registration looks pretty good after I run
>>  bbregister, but what I get out from the
>>  mri_vol2surf seems weird.  First of all, the
>>  dimensions are 112745 x 1 x 1 x 120, which
>>  seems odd. I'm forcing no reshaping, and from
>>  the help page it seems like the x-dim should
>>  be 40962 for icoorder=6.  I have 120 frames in
>>  my input data, so that seems to be right, but
>>  I'm not sure where this dimension is coming
>>  from.  I've also tried it with icoorder=4 and
>>  I get the same x-dim=112745 when I'm expecting
>>  2562.  I've also run these commands with
>>  various iterations e.g. reshaping, no
>>  smoothing, no projfrac, and I get the same
>>  thing every time.
>> 
>>  I'm also wondering how I should view these
>>  files to confirm that the surface projection
>>  has worked as I expect it if/when I am able to
>>  get the dimensions to be correct.  I cannot
>>  open any of the projected functional files in
>>  either freeview or tksurfer, so it will be
>>  helpful to know how I might be able to view
>>  these time-series on the surface after I've
>>  succeeded in projecting them to that space.
>> 
>>  Any advice would be much appreciated
>> 
>>  Thanks,
>>  Jared
>>  ___
>>  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-m

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Bruce Fischl]

ata and confirm that the
  projections has worked properly would be much
  appreciated.  Additionally, what should the
  dimensions of a surface time series look like?
   I would have expected for have an nVertices x
  nFrames x 1 array instead of the nVertices x 1
  x 1 x nFrames array, is this correct?


  Thank you,
  Jared

  - Forwarded Message -
  From: "Jared Zimmerman"
  <jar...@mail.med.upenn.edu>
  To: freesurfer@nmr.mgh.harvard.edu
  Sent: Monday, September 19, 2016 8:46:17 PM
  Subject: [Freesurfer] Projecting processed 4D
  functional data to individual surfaces

  Hi All,

  I'm trying to project some processed
  resting-state data onto the surface to run
  some surface based parcellations, and I'm
  running into a bit of difficulty.  Basically
  I'm using bbregister to register my functional
  to the T1, then mri_vol2surf to project to the
  surface with the following pseudocode:

  bbregister --s subjID --mov
  /mov_dir/subjID_example_func_brain.nii.gz \
   --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
   --init-fsl --bold

  mri_vol2surf --src
  /mov_dir/filtered_func_residuals.nii.gz \
   --out
  /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh
  \
   --srcreg /coreg/fs_ep2struct_fsl.dat --hemi
  lh \
   --surf white --projfrac 0.5 --icoorder 6
  --fwhm 6 --out_type mgh --noreshape


  The registration looks pretty good after I run
  bbregister, but what I get out from the
  mri_vol2surf seems weird.  First of all, the
  dimensions are 112745 x 1 x 1 x 120, which
  seems odd. I'm forcing no reshaping, and from
  the help page it seems like the x-dim should
  be 40962 for icoorder=6.  I have 120 frames in
  my input data, so that seems to be right, but
  I'm not sure where this dimension is coming
  from.  I've also tried it with icoorder=4 and
  I get the same x-dim=112745 when I'm expecting
  2562.  I've also run these commands with
  various iterations e.g. reshaping, no
  smoothing, no projfrac, and I get the same
  thing every time.

  I'm also wondering how I should view these
  files to confirm that the surface projection
  has worked as I expect it if/when I am able to
  get the dimensions to be correct.  I cannot
  open any of the projected functional files in
  either freeview or tksurfer, so it will be
  helpful to know how I might be able to view
  these time-series on the surface after I've
  succeeded in projecting them to that space.

  Any advice would be much appreciated


  Thanks,
  Jared
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  The information in this e-mail is intended
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  contains patient information, please contact
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The information in this e-mail is intended only for the person to whom
it is
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared P Zimmerman]

;>>> mri_surf2surf to downsample this data but have not ben able to 
>>>> successfully get that to downsample the surface.  The mri_surf2surf call I 
>>>> used is as follows:
>>>> 
>>>> mri_surf2surf --srcsubject subjID --srcsurfval 
>>>> /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh --trgsubject 
>>>> subjID --trgsurfval 
>>>> /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi lh 
>>>> --trgicoorder 4
>>>> 
>>>> Any advice on how to achieve my goal of projecting to subject surfaces, 
>>>> smoothing and downsampling to FS4, as well as recommendations on how to 
>>>> visualize the surface functional data and confirm that the projections has 
>>>> worked properly would be much appreciated.  Additionally, what should the 
>>>> dimensions of a surface time series look like?  I would have expected for 
>>>> have an nVertices x nFrames x 1 array instead of the nVertices x 1 x 1 x 
>>>> nFrames array, is this correct?
>>>> 
>>>> 
>>>> Thank you,
>>>> Jared
>>>> 
>>>> - Forwarded Message -
>>>> From: "Jared Zimmerman" <jar...@mail.med.upenn.edu 
>>>> <mailto:jar...@mail.med.upenn.edu>>
>>>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>> Sent: Monday, September 19, 2016 8:46:17 PM
>>>> Subject: [Freesurfer] Projecting processed 4D functional data to 
>>>> individualsurfaces
>>>> 
>>>> Hi All,
>>>> 
>>>> I'm trying to project some processed resting-state data onto the surface 
>>>> to run some surface based parcellations, and I'm running into a bit of 
>>>> difficulty.  Basically I'm using bbregister to register my functional to 
>>>> the T1, then mri_vol2surf to project to the surface with the following 
>>>> pseudocode:
>>>> 
>>>> bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \
>>>>  --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
>>>>  --init-fsl --bold
>>>> 
>>>> mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \
>>>>  --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \
>>>>  --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \
>>>>  --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh 
>>>> --noreshape
>>>> 
>>>> 
>>>> The registration looks pretty good after I run bbregister, but what I get 
>>>> out from the mri_vol2surf seems weird.  First of all, the dimensions are 
>>>> 112745 x 1 x 1 x 120, which seems odd. I'm forcing no reshaping, and from 
>>>> the help page it seems like the x-dim should be 40962 for icoorder=6.  I 
>>>> have 120 frames in my input data, so that seems to be right, but I'm not 
>>>> sure where this dimension is coming from.  I've also tried it with 
>>>> icoorder=4 and I get the same x-dim=112745 when I'm expecting 2562.  I've 
>>>> also run these commands with various iterations e.g. reshaping, no 
>>>> smoothing, no projfrac, and I get the same thing every time.
>>>> 
>>>> I'm also wondering how I should view these files to confirm that the 
>>>> surface projection has worked as I expect it if/when I am able to get the 
>>>> dimensions to be correct.  I cannot open any of the projected functional 
>>>> files in either freeview or tksurfer, so it will be helpful to know how I 
>>>> might be able to view these time-series on the surface after I've 
>>>> succeeded in projecting them to that space.
>>>> 
>>>> Any advice would be much appreciated
>>>> 
>>>> 
>>>> Thanks,
>>>> Jared
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>> <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

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Douglas Greve]

you can actually skip the ico thing and just use --trgsubject fsaverage6


On 9/28/16 7:06 PM, Jared P Zimmerman wrote:

Thanks Doug,

This does seem like it will do the right thing, but it’s failing 
because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have 
an ico subject in my subjects_dir


Should this normally be in the subjects_dir?  I don’t recall ever 
seeing this made when I’ve run recon-all in the past.


Thanks,
Jared

Here’s the full terminal output when I run the command:

mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg 
func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o 
func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 
--interp trilinear --noreshape --trgsubject ico --icoorder 6 
--out_type mgh --surf-fwhm 6

IcoOrder = 6, nIcoVtxs = 40962
srcvol = /func_test/filtered_func_residuals.nii.gz
srcreg = func_test/coreg/fs_ep2struct_fsl.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = ico
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Reading surface /subjdir_test//subID/surf/lh.white
Done reading source surface
Reading thickness /subjdir_test//subID/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 11345
Reading source surface registration
subjdir_test//subID/surf/lh.sphere.reg
Done loading source registration surface
Reading icosahedron, order = 6, radius = 100
  Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
Done loading target registration surface
Mapping Surfaces (subID -> ico)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (40962)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (112745)
Reverse Loop had 72236 hits

On Sep 28, 2016, at 3:34 PM, Douglas Greve > wrote:


You need to specify --trgsubject ico in mri_vol2surf


On 9/28/16 3:01 PM, Jared Zimmerman wrote:
Hi All, forwarding this message along again as I'm still having some 
trouble getting this to work.  Basically I would like to 1) project 
processed residual time-series from the subject-space volume to the 
subject-space surface, 2) smooth on the surface, 3) down-sample to 
FS4 space.


To do this is have used bbregister to calculate the registration, 
then mri_vol2surf to project to the surface, but I am not sure the 
output of mri_vol2surf is what I should be expecting.  The output 
file has dimensions 112745 x 1 x 1 x 120 when I'm expecting ~40k 
vertices for FS6 space and ~3k vertices for FS4 space, but changing 
the --icoorder flag seems to have no effect on the number of 
vertices in the output.


I have loaded the output surface functional image into Matlab to se 
that there is real time-series data in there, but I have no way of 
knowing if it has mapped the data appropriately.  Additionally, I've 
tried to use mri_surf2surf to downsample this data but have not ben 
able to successfully get that to downsample the surface.  The 
mri_surf2surf call I used is as follows:


mri_surf2surf --srcsubject subjID --srcsurfval 
/mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh 
--trgsubject subjID --trgsurfval 
/mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi lh 
--trgicoorder 4


Any advice on how to achieve my goal of projecting to subject 
surfaces, smoothing and downsampling to FS4, as well as 
recommendations on how to visualize the surface functional data and 
confirm that the projections has worked properly would be much 
appreciated.  Additionally, what should the dimensions of a surface 
time series look like?  I would have expected for have an nVertices 
x nFrames x 1 array instead of the nVertices x 1 x 1 x nFrames 
array, is this correct?



Thank you,
Jared

- Forwarded Message -
From: "Jared Zimmerman" >
To: freesurfer@nmr.mgh.harvard.edu 


Sent: Monday, September 19, 2016 8:46:17 PM
Subject: [Freesurfer] Projecting processed 4D functional data to 
individualsurfaces


Hi All,

I'm trying to project some processed resting-state data onto the 
surface to run some surface based parcellations, and I'm running 
into a bit of difficulty.  Basically I'm using bbregister to 
register my functional to the T1, then mri_vol2surf to project to 
the surface with the following pseudocode:


bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \
 --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
 --init-fsl --bold

mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \
 --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \
 --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \
 --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh 

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Douglas Greve]

You need to specify --trgsubject ico in mri_vol2surf


On 9/28/16 3:01 PM, Jared Zimmerman wrote:
> Hi All, forwarding this message along again as I'm still having some trouble 
> getting this to work.  Basically I would like to 1) project processed 
> residual time-series from the subject-space volume to the subject-space 
> surface, 2) smooth on the surface, 3) down-sample to FS4 space.
>
> To do this is have used bbregister to calculate the registration, then 
> mri_vol2surf to project to the surface, but I am not sure the output of 
> mri_vol2surf is what I should be expecting.  The output file has dimensions 
> 112745 x 1 x 1 x 120 when I'm expecting ~40k vertices for FS6 space and ~3k 
> vertices for FS4 space, but changing the --icoorder flag seems to have no 
> effect on the number of vertices in the output.
>
> I have loaded the output surface functional image into Matlab to se that 
> there is real time-series data in there, but I have no way of knowing if it 
> has mapped the data appropriately.  Additionally, I've tried to use 
> mri_surf2surf to downsample this data but have not ben able to successfully 
> get that to downsample the surface.  The mri_surf2surf call I used is as 
> follows:
>
> mri_surf2surf --srcsubject subjID --srcsurfval 
> /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh --trgsubject subjID 
> --trgsurfval /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi 
> lh --trgicoorder 4
>
> Any advice on how to achieve my goal of projecting to subject surfaces, 
> smoothing and downsampling to FS4, as well as recommendations on how to 
> visualize the surface functional data and confirm that the projections has 
> worked properly would be much appreciated.  Additionally, what should the 
> dimensions of a surface time series look like?  I would have expected for 
> have an nVertices x nFrames x 1 array instead of the nVertices x 1 x 1 x 
> nFrames array, is this correct?
>
>
> Thank you,
> Jared
>
> - Forwarded Message -
> From: "Jared Zimmerman" <jar...@mail.med.upenn.edu>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Monday, September 19, 2016 8:46:17 PM
> Subject: [Freesurfer] Projecting processed 4D functional data to individual   
> surfaces
>
> Hi All,
>
> I'm trying to project some processed resting-state data onto the surface to 
> run some surface based parcellations, and I'm running into a bit of 
> difficulty.  Basically I'm using bbregister to register my functional to the 
> T1, then mri_vol2surf to project to the surface with the following pseudocode:
>
> bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \
>   --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
>   --init-fsl --bold
>
> mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \
>   --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \
>   --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \
>   --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape
>
>
> The registration looks pretty good after I run bbregister, but what I get out 
> from the mri_vol2surf seems weird.  First of all, the dimensions are 112745 x 
> 1 x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help 
> page it seems like the x-dim should be 40962 for icoorder=6.  I have 120 
> frames in my input data, so that seems to be right, but I'm not sure where 
> this dimension is coming from.  I've also tried it with icoorder=4 and I get 
> the same x-dim=112745 when I'm expecting 2562.  I've also run these commands 
> with various iterations e.g. reshaping, no smoothing, no projfrac, and I get 
> the same thing every time.
>
> I'm also wondering how I should view these files to confirm that the surface 
> projection has worked as I expect it if/when I am able to get the dimensions 
> to be correct.  I cannot open any of the projected functional files in either 
> freeview or tksurfer, so it will be helpful to know how I might be able to 
> view these time-series on the surface after I've succeeded in projecting them 
> to that space.
>
> Any advice would be much appreciated
>
>
> Thanks,
> Jared
> ___
> 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

[Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared Zimmerman]

Hi All, forwarding this message along again as I'm still having some trouble 
getting this to work.  Basically I would like to 1) project processed residual 
time-series from the subject-space volume to the subject-space surface, 2) 
smooth on the surface, 3) down-sample to FS4 space.

To do this is have used bbregister to calculate the registration, then 
mri_vol2surf to project to the surface, but I am not sure the output of 
mri_vol2surf is what I should be expecting.  The output file has dimensions 
112745 x 1 x 1 x 120 when I'm expecting ~40k vertices for FS6 space and ~3k 
vertices for FS4 space, but changing the --icoorder flag seems to have no 
effect on the number of vertices in the output.  

I have loaded the output surface functional image into Matlab to se that there 
is real time-series data in there, but I have no way of knowing if it has 
mapped the data appropriately.  Additionally, I've tried to use mri_surf2surf 
to downsample this data but have not ben able to successfully get that to 
downsample the surface.  The mri_surf2surf call I used is as follows:

mri_surf2surf --srcsubject subjID --srcsurfval 
/mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh --trgsubject subjID 
--trgsurfval /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi 
lh --trgicoorder 4

Any advice on how to achieve my goal of projecting to subject surfaces, 
smoothing and downsampling to FS4, as well as recommendations on how to 
visualize the surface functional data and confirm that the projections has 
worked properly would be much appreciated.  Additionally, what should the 
dimensions of a surface time series look like?  I would have expected for have 
an nVertices x nFrames x 1 array instead of the nVertices x 1 x 1 x nFrames 
array, is this correct?


Thank you,
Jared

- Forwarded Message -
From: "Jared Zimmerman" <jar...@mail.med.upenn.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, September 19, 2016 8:46:17 PM
Subject: [Freesurfer] Projecting processed 4D functional data to individual 
surfaces

Hi All,

I'm trying to project some processed resting-state data onto the surface to run 
some surface based parcellations, and I'm running into a bit of difficulty.  
Basically I'm using bbregister to register my functional to the T1, then 
mri_vol2surf to project to the surface with the following pseudocode:

bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \
 --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
 --init-fsl --bold

mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ 
 --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \
 --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \
 --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape


The registration looks pretty good after I run bbregister, but what I get out 
from the mri_vol2surf seems weird.  First of all, the dimensions are 112745 x 1 
x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help page it 
seems like the x-dim should be 40962 for icoorder=6.  I have 120 frames in my 
input data, so that seems to be right, but I'm not sure where this dimension is 
coming from.  I've also tried it with icoorder=4 and I get the same 
x-dim=112745 when I'm expecting 2562.  I've also run these commands with 
various iterations e.g. reshaping, no smoothing, no projfrac, and I get the 
same thing every time.

I'm also wondering how I should view these files to confirm that the surface 
projection has worked as I expect it if/when I am able to get the dimensions to 
be correct.  I cannot open any of the projected functional files in either 
freeview or tksurfer, so it will be helpful to know how I might be able to view 
these time-series on the surface after I've succeeded in projecting them to 
that space.

Any advice would be much appreciated


Thanks,
Jared
___
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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
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared Zimmerman]

Hi All,

I'm trying to project some processed resting-state data onto the surface to run 
some surface based parcellations, and I'm running into a bit of difficulty.  
Basically I'm using bbregister to register my functional to the T1, then 
mri_vol2surf to project to the surface with the following pseudocode:

bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \
 --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
 --init-fsl --bold

mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ 
 --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \
 --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \
 --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape


The registration looks pretty good after I run bbregister, but what I get out 
from the mri_vol2surf seems weird.  First of all, the dimensions are 112745 x 1 
x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help page it 
seems like the x-dim should be 40962 for icoorder=6.  I have 120 frames in my 
input data, so that seems to be right, but I'm not sure where this dimension is 
coming from.  I've also tried it with icoorder=4 and I get the same 
x-dim=112745 when I'm expecting 2562.  I've also run these commands with 
various iterations e.g. reshaping, no smoothing, no projfrac, and I get the 
same thing every time.

I'm also wondering how I should view these files to confirm that the surface 
projection has worked as I expect it if/when I am able to get the dimensions to 
be correct.  I cannot open any of the projected functional files in either 
freeview or tksurfer, so it will be helpful to know how I might be able to view 
these time-series on the surface after I've succeeded in projecting them to 
that space.

Any advice would be much appreciated


Thanks,
Jared
___
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.