On Wed, Aug 31, 2011 at 2:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

You should not need to adjust the registration. The surface should follow the gray white boundary in the EPI (hard to see but there). Can you send a pic of the green surface on the EPI with the default registration (ie, without you making changes)?

noam Schneck wrote:

It is from an individual. I checked the registration, the green surface outline seems well within the movable EPI image. I can scale it down manually and than the zstat, with the scaled down register.dat, fits within the anatomical. Is this the only solution?

On Wed, Aug 31, 2011 at 2:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Is this a zmap from the individual run or the gfeat? If
individual, double check the registration with
tkregister2 --mov example_func.nii.gz --reg anat2exf.register.dat
--surfs
If from a gfeat, then you should use anat2std.register.dat, like

tkmedit bert orig.mgz -overlay zstat1.nii.gz -overlay-reg
anat2exf.register.dat -fthresh 2.3 -fmax 4.3 -aux brain.mgz -seg
aparc+aseg.mgz

doug

noam Schneck wrote:

Hi,
Here is the command line for viewing the zstat from a single
subject single run, in which I ran into the same problem. I've
also attached a screenshot of the tkmedit image: tkmedit bert
bert/mri/orig.mgz -overlay zstat1.nii.gz -overlay-reg
anat2exf.register.dat -fthresh 2.3 -fmax 4.3 -aux
bert/mri/brain.mgz -seg bert/mri/aparc+aseg.mgz
Thank you so much for your help,
Noam
On Wed, Aug 31, 2011 at 12:04 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

noam Schneck wrote:

Hi Doug

Here are more detailed versions of my first two questions.
1) I used tkmedit to look at the mean_func produced by
a gfeat
analysis of one subject's three functional runs
overlayed onto
the anatomical image produced by recon-all on that same
subject(bert/mri/orig.mgz). The registration matrix I
used was
the anat2std.dat that was produced by running
reg-feat2anat on
all three of the feat analyses from the individual
runs. When
I did this I saw that the mean_func image was outside the
boundaries of the anatomical image. Correspondingly, when I
overlayed the zstat.nii.gz from the gfeat analysis onto the
anatomical image I had activation outside of the anatomical
image brain.

What was the command line?

2) Originally, I ran BBR on a subject that I had run
Recon-all for. I used BBR to register the
example_func.nii.gz
to the bert/mri/orig.mgz. I had BBR output an fsl.mat.
I then
used ApplyXFM in fsl to apply BBR's fsl.mat to register the
example_func.nii.gz onto a T1 image that had been
created by
converting bert/mri/brainmask.mgz into niftii with
mri_convert. I tried it again, this time converting the
orig.mgz to niftii. In both cases the example_func in
T1 space
image produced by ApplyXFM is rotated about 90 degrees and
also inverted. This is viewed in fslview, I have
attached a
screenshot. The corresponding T1 images created by
mri_convert
are not. What can I do to allow me to use BBR's fsl.mat
within ApplyXFM?

Here is the header info for the T2*_T1 image attached
to this
email. sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 256
dim2 256
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.5000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.000000 -0.000000 -0.000000 128.678986
qto_xyz:2 -0.000000 0.000000 1.000000 -100.598366
qto_xyz:3 0.000000 -1.000000 0.000000 143.524200
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Superior-to-Inferior
qform_zorient Posterior-to-Anterior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.000000 -0.000000 0.000000 128.678986
sto_xyz:2 -0.000000 -0.000000 1.000000 -100.598366
sto_xyz:3 -0.000000 -1.000000 0.000000 143.524200
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Superior-to-Inferior
sform_zorient Posterior-to-Anterior
file_type NIFTI-1+
file_code 1
descrip FreeSurfer Jun 18 2008
aux_file Thank you,
Noam

On Mon, Aug 29, 2011 at 1:16 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

Hi Noam,

noam Schneck wrote:

Hi,

I am trying to use reg-feat2anat to register my Feat
analyses
to anatomical images and running into a number
of problems.
1) When I check the registration of the
mean_func to the
anatomical in tkregister2 it looks fine. But
when I overlay
the fsl statmaps onto the anatomical brain they
extend
outside
of boundaries of the anatomical brain.

Need more detail. What command are you using to
visualize?

2) Also, before using reg-feat2anat. I was
trying to do the
EPI_2_structural registration in FLIRT with the
fsl.mat
produced by BBR. When I try this the registered
image is
rotated 90 degrees from the original image. Why
does
that happen?

More detail needed. What program did you run? What
visualization
tool? This will align the anatomical in the
conformed space
to the
EPI, so make sure you're using the right anatomical.

3) I also noticed that if I look at the header
information for
an image in fslhd and mri_info the orientations are
flipped.
If the fslhd orientation is RAS it will be LPI
in mri_info.
Could this be related to what is happening in
question (2)?

Need more detail. What images are you looking at?

In general, you have to tell us specifically what
you are
doing.
It's going to be very hard to help with vague
descriptions.
doug

Best,
Noam
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