Re: [Freesurfer] getting vertex numbers

[Bruce Fischl]

Hi Lars,

you want to do "custom fill" then click the "over statistical threshold " 
option. Can't remember the exact name...


cheers,
Bruce


On Wed, 18 Feb 2009, Lars M. Rimol wrote:


Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas ("blobs") on the cortical surface that are
above sig. threshold. I'd like to get a list of the vertex numbers for each
of these significant areas, which do not correspond to the parcellations in
FS. In other words, I'm not trying to combine the already excisting ROI's.

I've tried drawing labels (on fsaverage) and saving them, but without
success. I clicked on 'Make path' and tried to mark vertices around the
area, then I tried 'Custom fill' with various options, and 'Mark label',
'New label from marked' and 'save label'. But I only manage to save one or
at most 3-4 vertices.

I'm using FS v 4.0.5.


Any tip on how to do this would be appreciated!

Thank you!



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Re: [Freesurfer] volume changes

[Bruce Fischl]

what are the voxel sizes?

On Wed, 18 Feb 2009, Jared Price wrote:


Dear gurus,
when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz 
seg_edited_axial.nii to reslice from coronal to axial space we are seeing 
some significant volume changes in the segmentation.  Anyone know why or how 
to fix it.

Jared
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Re: [Freesurfer] recon-all error: libexpat.so.0

[krish]

All,

For Suse Enterprise ( SLED ) 10.2, the following solution seems to work (
for Narly as well ):

The library libexpat.so.0 Freesurfer is looking for is actually named
libexpat.so.1

- First check whether you have a libexpat.so.1
ls /usr/lib64/libexpat.so.1

- If so, create a symbolic link with the name libexpat.so.0 to that
cd /usr/lib64
ln -s libexpat.so.1 libexpat.so.0


-Krish

>
> Dear all,
>
> I installed freesurfer_Linux_centos4_x86_64-stable-pub-v4.2.0-full on
> SuSE Enterprise (SLED 10.2), and ran recon-all.  The process ran until
> near the end, and then terminated with the following error:
>
> *
> .
>
> Reporting on  49 segmentations
> #
> #...@# Cortical ribbon mask Fri Feb 13 15:31:16 CET 2009
> /home/narly/data/freesurfer/subjects/2_Lena/mri
>
>  mris_volmask --label_left_white 2 --label_left_ribbon 3
> --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> --save_distance 2_Lena
>
> mris_volmask.bin: error while loading shared libraries: libexpat.so.0:
> cannot open shared object file: No such file or directory
> **
>
> but I'm able to visualise the labels on the 3D volume using tksurfer (i.e.
> the output looks ok).
>
> Do I still need to install libexpat.so.0, and if so, how?
>
>
> thanks in advance,
> Narly.
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[Freesurfer] qdec for fMRI using categorical covariate?

[Dave Brohawn]

Hello,

I want to generate screenshots of group activation in an anatomical ROI on
the left and right hemisphere for two different groups of subjects at a
particular contrast and time point of our analysis.

We want to use race as a covariate (categorical, with whites and blacks
being the two racial groups), and the screenshots to reflect this
covariate being taken into account.

Many examples I have seen on the wiki and in freesurfer archives describe
cortical thickness studies, or use covariates that are continuous (age).

Is qdec the program I want to use, and how do I ensure it treats race as


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[Freesurfer] qdec for fMRI analysis with categorical covariate? (continued)

[Dave Brohawn]

as a categorical covariate?

Thank you,

Dave Brohawn


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[Freesurfer] control points

[Muhammad Ayaz]

Dear All,

I am in phase of learning freesurfer. I added control points using tkmedit
and ran recon-all -autorecon2-cp  and i get the following error.
"
Total Number of Modified Voxels = 854 (out of 716825: 0.119136)
sh: wm.mgz: Permission denied
Broken pipe
Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Feb 18 14:34:54 EST 2009

"

It says permission denied but I have permission to access and make changes
to data.

Regards

Ayaz
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Re: [Freesurfer] volume changes

[Jeff Dewey]

To answer your question more completely, we're trying to compare two 
files with the following headers:


Freesurfer segmentation:
height = 256
width = 256
depth = 256
nframe = 1
imnr0 = 1
imnr1 = 256
 xnum = 256
 ynum = 256
  fov = 256.00
thick = 1.00
xstart = -128.00
 xend = 128.00
ystart = -128.00
 yend = 128.00
zstart = -128.00
 zend = 128.00
 type = 0
xsize = 1.00
ysize = 1.00
zsize = 1.00
x ras = -1.00 0.00 0.00
y ras = 0.00 0.00 -1.00
z ras = 0.00 1.00 0.00
c ras = 0.00 -0.15 17.750004
det(xyz_ras) = -1.00
ras_good_flag = 1
brightness = 1
subject_name =
path_to_t1 =
fname_format =


Target image:
height = 256
width = 256
depth = 120
nframe = 1
imnr0 = 1
imnr1 = 120
 xnum = 256
 ynum = 256
  fov = 256.00
thick = 1.00
xstart = -128.00
 xend = 128.00
ystart = -128.00
 yend = 128.00
zstart = -60.00
 zend = 60.00
 type = 3
xsize = 0.976562
ysize = 0.976562
zsize = 1.30
x ras = 1.00 0.00 0.00
y ras = 0.00 -1.00 0.00
z ras = 0.00 0.00 1.00
c ras = 0.00 0.00 17.749996
det(xyz_ras) = -1.00
ras_good_flag = 1
brightness = 1
subject_name =
path_to_t1 =
fname_format =

It's also acceptable to convert the target image to the freesurfer 
output space, as long as structure volumes in the segmentation are 
preserved.


Thanks again,
Jeff


Bruce Fischl wrote:

what are the voxel sizes?

On Wed, 18 Feb 2009, Jared Price wrote:


Dear gurus,
when running mri_convert -rt nearest -ot nii -rl 001.mgz 
seg_edited.mgz seg_edited_axial.nii to reslice from coronal to axial 
space we are seeing some significant volume changes in the 
segmentation.  Anyone know why or how to fix it.

Jared
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[Freesurfer] - dt_recon and coregistration of DTI to anatomy

[Kjell Inge]

I am using Freesurfer and I am having difficulties in coregistration of a DTI 
volume to the anatomy image.  I have been running 

recon-all -i  -i  -s 2005_anatomy
 
followed by 

recon-all -autorecon1 -s 2005_anatomy

and then 

dt_recon --i dti/subj_539_dti.nii --b dti/aging_hds_2005_dti.bval 
dti/aging_hds_2005_dti.bvec --s 2005_anatomy --o outputdti

where "dti/subj_539_dti.nii" is my DTI volume, "aging_hds_2005_dti.bval" and 
"dti/aging_hds_2005_dti.bvec" are my bval and bvec files and  "2005_anatomy" is 
my subject folder. I have made an output folder inside  "2005_anatomy" named 
"outputdti" My bval and bvec files are attached below.

Everything runs smoothly with no error messages, and there is a bunch of files 
created in "outputdti".
Now, my questions are as follow:

1. How do I see the registered DTI (for instance the FA) visualized on the 
anatomy? Is the finally registered FA image inside the file "FA.nii" or do you 
have to run a transformation on that? If so, which transformation and how is 
that done? There are several files containing rigid transformations, the .reg 
files and the register.dat file.

When I check FA.nii it does NOT seem to be coregistered with my anatomical 
input image. What went wrong?

2. When I open the image "mask.nii" it is like a white box, no structures, is 
this really correct? Does this mean that the BET has not succeeded? However, 
when I open "brainmask.mgz"  by "tkmedit" it is certainly skullstripped. 

3. Does dt_recon really do a nonlinear registration? When looking through the 
script, I can only see that dt_recon uses flirt (inside "eddy_correct" on the 
"dwi.nii", producing "dwi-ec.nii" and inside "fslregister", applied to 
"lowb.nii") which is an affine registration tool.


I hope someone can solve my problems.

Erlend


bvec: 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 


bval: 0 0 0 0 0 -0.532213 -0.25014 0.633507 0.218922 0.41315 -0.734236 -0.93647 
0.333112 -0.103315 0.92654 -0.801489 0.916837 0.537756 0.213559 0.124139 
-0.27398 0.443315 -0.024171 -0.568365 -0.93093 0.825459 -0.472598 -0.504263 
-0.149336 0.694717 

0 0 0 0 0 0.104013 -0.721834 -0.753136 0.850393 -0.780294 -0.661804 0.054189 
-0.242859 -0.991677 0.372983 0.543143 -0.261948 0.438028 -0.664684 -0.051816 
0.960273 0.878048 0.368772 0.637098 -0.168158 -0.182178 -0.629557 -0.129265 
0.688743 0.344412 

0 0 0 0 0 -0.840197 0.64528 -0.177358 0.478441 0.469519 0.151371 0.346537 
0.911074 -0.076828 -0.04907 -0.250221 0.30132 -0.720382 -0.715952 -0.990911 
-0.053015 -0.180284 0.929206 0.520641 -0.324178 -0.534255 -0.616692 0.85382 
-0.709459 0.631465 


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[Freesurfer] mris_anatomical_stats segmentation fault

[Diana Wotruba]

Dear FS experts

I divided the fsaverage parcellations (aparc.a2005s) with an area threshold 
of 100mm2. Now I would like to get a stats file, using the following 
command:


mris_anatomical_stats -a aparc.a2005s_100.annot -t ?h.thickness -b -f 
001/stats/?h.aparc.a2005s_100.stats 001 ?h


I am getting the following error message:

"Segmentation fault" (after 1374 entries are read)


The same command works just fine with a parcellated .annot file I generated 
with a lower threshold (p.e. 150mm2).
 
Any help would be appreciated

Regards
Diana
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[Freesurfer] mris_divide_parcellation

[Jose Luis Cantero Lorente]

Dear FS Team,

I used mris_divide_parcellation to create a new parcelation with smaller 
regions, but all these regions seem to have a different size. I am interested 
to get smaller cortical parcellated regions, but all of them with the same 
area. How can I get it? Could I decide the area size?

Thank you in advance.

Best,
Jose

---
Jose Luis Cantero, Ph.D.
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cellular Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- Spain -

Phone: +34 954 977433
Fax: +34 954 349151
Email: jlcan...@upo.es
http://www.upo.es/neuroaging/es/

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Re: [Freesurfer] - dt_recon and coregistration of DTI to anatomy

[Douglas N Greve]

The answer is in the help, I think: dt_recon --help

doug

Kjell Inge wrote:
I am using Freesurfer and I am having difficulties in coregistration 
of a DTI volume to the anatomy image.  I have been running


recon-all -i  -i  -s 2005_anatomy
 
followed by


recon-all -autorecon1 -s 2005_anatomy

and then

dt_recon --i dti/subj_539_dti.nii --b dti/aging_hds_2005_dti.bval 
dti/aging_hds_2005_dti.bvec --s 2005_anatomy --o outputdti


where "dti/subj_539_dti.nii" is my DTI volume, 
"aging_hds_2005_dti.bval" and "dti/aging_hds_2005_dti.bvec" are my 
bval and bvec files and "2005_anatomy" is my subject folder. I have 
made an output folder inside "2005_anatomy" named "outputdti" My bval 
and bvec files are attached below.


Everything runs smoothly with no error messages, and there is a bunch 
of files created in "outputdti".

Now, my questions are as follow:

1. How do I see the registered DTI (for instance the FA) visualized on 
the anatomy? Is the finally registered FA image inside the file 
"FA.nii" or do you have to run a transformation on that? If so, which 
transformation and how is that done? There are several files 
containing rigid transformations, the .reg files and the register.dat 
file.


When I check FA.nii it does NOT seem to be coregistered with my 
anatomical input image. What went wrong?


2. When I open the image "mask.nii" it is like a white box, no 
structures, is this really correct? Does this mean that the BET has 
not succeeded? However, when I open "brainmask.mgz"  by "tkmedit" it 
is certainly skullstripped.


3. Does dt_recon really do a nonlinear registration? When looking 
through the script, I can only see that dt_recon uses flirt (inside 
"eddy_correct" on the "dwi.nii", producing "dwi-ec.nii" and inside 
"fslregister", applied to "lowb.nii") which is an affine registration 
tool.



I hope someone can solve my problems.

Erlend


bvec: 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 
1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 

bval: 0 0 0 0 0 -0.532213 -0.25014 0.633507 0.218922 0.41315 -0.734236 
-0.93647 0.333112 -0.103315 0.92654 -0.801489 0.916837 0.537756 
0.213559 0.124139 -0.27398 0.443315 -0.024171 -0.568365 -0.93093 
0.825459 -0.472598 -0.504263 -0.149336 0.694717 
0 0 0 0 0 0.104013 -0.721834 -0.753136 0.850393 -0.780294 -0.661804 
0.054189 -0.242859 -0.991677 0.372983 0.543143 -0.261948 0.438028 
-0.664684 -0.051816 0.960273 0.878048 0.368772 0.637098 -0.168158 
-0.182178 -0.629557 -0.129265 0.688743 0.344412 
0 0 0 0 0 -0.840197 0.64528 -0.177358 0.478441 0.469519 0.151371 
0.346537 0.911074 -0.076828 -0.04907 -0.250221 0.30132 -0.720382 
-0.715952 -0.990911 -0.053015 -0.180284 0.929206 0.520641 -0.324178 
-0.534255 -0.616692 0.85382 -0.709459 0.631465 



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Re: [Freesurfer] mris_divide_parcellation

[Douglas N Greve]

I'm surprised that the divisions are not roughly equal in area. How much 
different are they? You can also spec an area threshold instead of a 
number of subdivisions, but that just keeps dividing until all 
subdivisions are below that area. I don't think we have anything that 
will divide them into equal sizes, though I think bruce is working on 
something like that.


doug

Jose Luis Cantero Lorente wrote:

Dear FS Team,

I used mris_divide_parcellation to create a new parcelation with smaller 
regions, but all these regions seem to have a different size. I am interested 
to get smaller cortical parcellated regions, but all of them with the same 
area. How can I get it? Could I decide the area size?

Thank you in advance.

Best,
Jose

---
Jose Luis Cantero, Ph.D.
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cellular Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- Spain -

Phone: +34 954 977433
Fax: +34 954 349151
Email: jlcan...@upo.es
http://www.upo.es/neuroaging/es/

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Re: [Freesurfer] control points

[Douglas N Greve]

Do you have read and write permissions to that file?

Muhammad Ayaz wrote:

Dear All,

I am in phase of learning freesurfer. I added control points using tkmedit
and ran recon-all -autorecon2-cp  and i get the following error.
"
Total Number of Modified Voxels = 854 (out of 716825: 0.119136)
sh: wm.mgz: Permission denied
Broken pipe
Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Feb 18 14:34:54 EST 2009

"

It says permission denied but I have permission to access and make changes
to data.

Regards

Ayaz
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[Freesurfer] about segmentation

[Silvia biopanda]

Hi,
we are making changes in the aseg.mgz and we need to know how to erase
a wrong pixels. we read in the tutorial that the button three erases,
but it doesn't work.how can we do?
 cheers,
SK
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Re: [Freesurfer] mris_anatomical_stats segmentation fault

[Douglas N Greve]

are you replaceing the "?" with the actual hemisphere designation?

Diana Wotruba wrote:


Dear FS experts

I divided the fsaverage parcellations (aparc.a2005s) with an area 
threshold of 100mm2. Now I would like to get a stats file, using the 
following command:


mris_anatomical_stats -a aparc.a2005s_100.annot -t ?h.thickness -b -f 
001/stats/?h.aparc.a2005s_100.stats 001 ?h


I am getting the following error message:

"Segmentation fault" (after 1374 entries are read)


The same command works just fine with a parcellated .annot file I 
generated with a lower threshold (p.e. 150mm2).
 
Any help would be appreciated

Regards
Diana
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Re: [Freesurfer] qdec for fMRI using categorical covariate?

[Douglas N Greve]

Just create a race.levels file with "Black" and "White", then include 
"race" as a column in your qdec.table.dat. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis 
for more details.


doug


Dave Brohawn wrote:

Hello,

I want to generate screenshots of group activation in an anatomical ROI on
the left and right hemisphere for two different groups of subjects at a
particular contrast and time point of our analysis.

We want to use race as a covariate (categorical, with whites and blacks
being the two racial groups), and the screenshots to reflect this
covariate being taken into account.

Many examples I have seen on the wiki and in freesurfer archives describe
cortical thickness studies, or use covariates that are continuous (age).

Is qdec the program I want to use, and how do I ensure it treats race as


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Re: [Freesurfer] control points

[Muhammad Ayaz]

Yes i do have read and write permissios to these data set.

I just ran another subject from the data set and it ended at different
stage but again says permission denied.

#...@# Fix Topology lh Thu Feb 19 11:14:14 EST 2009

 cp ../surf/lh.orig.nofix ../surf/lh.orig


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated

cp: cannot create regular file `../surf/lh.inflated': Permission denied
Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Thu Feb 19 11:14:14 EST 2009


Ayaz


On Thu, February 19, 2009 11:40 am, Douglas N Greve wrote:
> Do you have read and write permissions to that file?
>
> Muhammad Ayaz wrote:
>> Dear All,
>>
>> I am in phase of learning freesurfer. I added control points using
>> tkmedit
>> and ran recon-all -autorecon2-cp  and i get the following error.
>> "
>> Total Number of Modified Voxels = 854 (out of 716825: 0.119136)
>> sh: wm.mgz: Permission denied
>> Broken pipe
>> Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64
>> x86_64 x86_64 GNU/Linux
>>
>> recon-all exited with ERRORS at Wed Feb 18 14:34:54 EST 2009
>>
>> "
>>
>> It says permission denied but I have permission to access and make
>> changes
>> to data.
>>
>> Regards
>>
>> Ayaz
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>>
>>
>>
>
>
>

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Re: [Freesurfer] control points

[Douglas N Greve]

can you do that copy by hand?

Muhammad Ayaz wrote:

Yes i do have read and write permissios to these data set.

I just ran another subject from the data set and it ended at different
stage but again says permission denied.

#...@# Fix Topology lh Thu Feb 19 11:14:14 EST 2009

 cp ../surf/lh.orig.nofix ../surf/lh.orig


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated

cp: cannot create regular file `../surf/lh.inflated': Permission denied
Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Thu Feb 19 11:14:14 EST 2009


Ayaz


On Thu, February 19, 2009 11:40 am, Douglas N Greve wrote:
  

Do you have read and write permissions to that file?

Muhammad Ayaz wrote:


Dear All,

I am in phase of learning freesurfer. I added control points using
tkmedit
and ran recon-all -autorecon2-cp  and i get the following error.
"
Total Number of Modified Voxels = 854 (out of 716825: 0.119136)
sh: wm.mgz: Permission denied
Broken pipe
Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Feb 18 14:34:54 EST 2009

"

It says permission denied but I have permission to access and make
changes
to data.

Regards

Ayaz
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Re: [Freesurfer] about segmentation

[Sita Kakunoori]

Make sure you are selecting the 'Edit segmentation tool' on the tkmedit 
tools window. You can also press the 'g' key to select the tool.


Sita.



On Thu, 19 Feb 2009, Silvia biopanda wrote:


Hi,
we are making changes in the aseg.mgz and we need to know how to erase
a wrong pixels. we read in the tutorial that the button three erases,
but it doesn't work.how can we do?
cheers,
SK
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Re: [Freesurfer] volume changes

[Bruce Fischl]

and how do you measure volume? Certainly the voxel count is bound to 
change since your voxel size is changing. The volume will certainly 
change as well.


cheers,
Bruce
On Thu, 19 Feb 2009, Jeff Dewey wrote:

To answer your question more completely, we're trying to compare two files 
with the following headers:


Freesurfer segmentation:
height = 256
width = 256
depth = 256
nframe = 1
imnr0 = 1
imnr1 = 256
xnum = 256
ynum = 256
 fov = 256.00
thick = 1.00
xstart = -128.00
xend = 128.00
ystart = -128.00
yend = 128.00
zstart = -128.00
zend = 128.00
type = 0
xsize = 1.00
ysize = 1.00
zsize = 1.00
x ras = -1.00 0.00 0.00
y ras = 0.00 0.00 -1.00
z ras = 0.00 1.00 0.00
c ras = 0.00 -0.15 17.750004
det(xyz_ras) = -1.00
ras_good_flag = 1
brightness = 1
subject_name =
path_to_t1 =
fname_format =


Target image:
height = 256
width = 256
depth = 120
nframe = 1
imnr0 = 1
imnr1 = 120
xnum = 256
ynum = 256
 fov = 256.00
thick = 1.00
xstart = -128.00
xend = 128.00
ystart = -128.00
yend = 128.00
zstart = -60.00
zend = 60.00
type = 3
xsize = 0.976562
ysize = 0.976562
zsize = 1.30
x ras = 1.00 0.00 0.00
y ras = 0.00 -1.00 0.00
z ras = 0.00 0.00 1.00
c ras = 0.00 0.00 17.749996
det(xyz_ras) = -1.00
ras_good_flag = 1
brightness = 1
subject_name =
path_to_t1 =
fname_format =

It's also acceptable to convert the target image to the freesurfer output 
space, as long as structure volumes in the segmentation are preserved.


Thanks again,
Jeff


Bruce Fischl wrote:

what are the voxel sizes?

On Wed, 18 Feb 2009, Jared Price wrote:


Dear gurus,
when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz 
seg_edited_axial.nii to reslice from coronal to axial space we are seeing 
some significant volume changes in the segmentation.  Anyone know why or 
how to fix it.

Jared
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Re: [Freesurfer] mris_divide_parcellation

[Bruce Fischl]

Hi Jose,

I have another tool that we haven't released that will do this more 
closely. You can't do that with mris_divide_parcellation since the units 
don't start with equal area (or multiples thereof)


cheers,
Bruce
On Thu, 19 Feb 2009, Jose 
Luis Cantero Lorente wrote:



Dear FS Team,

I used mris_divide_parcellation to create a new parcelation with smaller 
regions, but all these regions seem to have a different size. I am interested 
to get smaller cortical parcellated regions, but all of them with the same 
area. How can I get it? Could I decide the area size?

Thank you in advance.

Best,
Jose

---
Jose Luis Cantero, Ph.D.
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cellular Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- Spain -

Phone: +34 954 977433
Fax: +34 954 349151
Email: jlcan...@upo.es
http://www.upo.es/neuroaging/es/

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[Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

[Lloyd Elliott]

  I am trying to overlay surface information acquired with freesurfer  
on to the original MRI volume.  I tried reading lh.orig with  
[vertices,faces] =  freesurfer_read_surf('surf/lh.orig') and then  
transforming the vertices with the matrix:


vertices_affine = [vertices' ; ones(1,size(vertices,1))]  # append the  
affine coordinates

overlay = (rsb2vox*inv(M))  *  vertices_affine

where

M = xfm_read('mri/transforms/talairach.xfm')

and

rsb2vox = inv([
[-1 0 0 128 ;
 0 0 1 -128;
 0 -1 0 128;
 0 0 0 1]
])

  I was lead to believe that this is the correct procedure by reading  
the 'official' description of the coordinate systems on the freesurfer  
wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ).   
Unfortunately the scaling and translation is incorrect.  I've also  
tried other permutations of the above matrix multiplication without  
any luck.  Am I doing something incorrectly?


Thanks,
Lloyd Elliott
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[Freesurfer] cortical lesions with FS (T1+DIR sequences)

[Irene Mattisi]

Hi all, 
I'm using Freesurfer to calculate cortical atrophy in patients with multiple 
sclerosis. These patients usually have also cortical lesions that I can see 
with DIR sequences. 
My question is:  can I piece together the 2 sequences to see cortical lesions 
with FS? for FS we use a 3D fast-field echo (FFE) sequence: 120 contiguous 
axial slices with the off-centre positioned on zero, TR = 25 msec, TE = 4.6 
msec, flip angle = 30°, slice thickness = 1.2 mm, matrix size = 256x256. 
DIR sequence: repetition time (TR) = 15631 msec, echo time (TE) = 25 msec, 
inversion time (TI) = 3400 msec, delay = 325 msec, echo train length (ETL) = 
17, 50 contiguous axial slices with a thickness = 3 mm, a matrix size = 130 x 
256, and a field of view (FOV) = 250 x 200 mm.



Thanks, 

Irene Mattisi

Multiple Sclerosis Centre

Padua, Italy
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Re: [Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

[Douglas N Greve]

what are you trying to do? If you're trying to bring the surface coords 
into talairach (mni305) space, then you can use mri_surf2surf with the 
--sval-xyz-tal orig --taval-xyz options.


Lloyd Elliott wrote:
  I am trying to overlay surface information acquired with freesurfer 
on to the original MRI volume.  I tried reading lh.orig with 
[vertices,faces] =  freesurfer_read_surf('surf/lh.orig') and then 
transforming the vertices with the matrix:


vertices_affine = [vertices' ; ones(1,size(vertices,1))]  # append the 
affine coordinates

overlay = (rsb2vox*inv(M))  *  vertices_affine

where

M = xfm_read('mri/transforms/talairach.xfm')

and

rsb2vox = inv([
[-1 0 0 128 ;
 0 0 1 -128;
 0 -1 0 128;
 0 0 0 1]
])

  I was lead to believe that this is the correct procedure by reading 
the 'official' description of the coordinate systems on the freesurfer 
wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ).  
Unfortunately the scaling and translation is incorrect.  I've also 
tried other permutations of the above matrix multiplication without 
any luck.  Am I doing something incorrectly?


Thanks,
Lloyd Elliott
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Re: [Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

[Mishkin Derakhshan]

Hi Lloyd,
I dealt with the same problem at one time. My input volume was a minc
volume but I imagine the procedure should work for your input as well.

for native.mnc, which was your input into freesurfer, do this command:
mri_info --cras native.mnc
my output was
-2.35588 52.7907 24.8145

Then you can create the following transformation matrix:
1 0 0 -2.35588
0 1 0 52.7907
0 0 1 24.8145
0 0 0 1

You can then transform each co-ordinate point in your surface with the
above transformation matrix and then your surfaces will be in what the
MNI calls
world co-cordinate space (these are referred to as "scanner RAS" on the
freesurfer wiki coordinate page).

Overlaying this new surface with my native.mnc worked for me.
mishkin

On Thu, Feb 19, 2009 at 5:17 PM, Douglas N Greve
 wrote:
> what are you trying to do? If you're trying to bring the surface coords into
> talairach (mni305) space, then you can use mri_surf2surf with the
> --sval-xyz-tal orig --taval-xyz options.
>
> Lloyd Elliott wrote:
>>
>>  I am trying to overlay surface information acquired with freesurfer on to
>> the original MRI volume.  I tried reading lh.orig with [vertices,faces] =
>>  freesurfer_read_surf('surf/lh.orig') and then transforming the vertices
>> with the matrix:
>>
>> vertices_affine = [vertices' ; ones(1,size(vertices,1))]  # append the
>> affine coordinates
>> overlay = (rsb2vox*inv(M))  *  vertices_affine
>>
>> where
>>
>> M = xfm_read('mri/transforms/talairach.xfm')
>>
>> and
>>
>> rsb2vox = inv([
>> [-1 0 0 128 ;
>>  0 0 1 -128;
>>  0 -1 0 128;
>>  0 0 0 1]
>> ])
>>
>>  I was lead to believe that this is the correct procedure by reading the
>> 'official' description of the coordinate systems on the freesurfer wiki (
>> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ).  Unfortunately
>> the scaling and translation is incorrect.  I've also tried other
>> permutations of the above matrix multiplication without any luck.  Am I
>> doing something incorrectly?
>>
>> Thanks,
>> Lloyd Elliott
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>>
>>
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