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 mat
Dear all,
I would like to display the ROI together with a statistical analysis
within this ROI on the surface in tksurfer. However, I somehow cannot
manage to view the two overlays at the same time. Is it because I use
freesurfer version 5.0?
Thank you!
Aga
_
Is the ROI a label?
On Aug 31, 2011, at 7:14 AM, "Burzynska, Aga"
wrote:
> Dear all,
> I would like to display the ROI together with a statistical analysis
> within this ROI on the surface in tksurfer. However, I somehow cannot
> manage to view the two overlays at the same time. Is it becaus
Hi Navid, it is still not clear what you want. Each surface coordinate
has an xyz. This space that this xyz is in is a peculiar space defined
by FS. You want to use a different xyz space. It could be scanner space.
It could be col-row-slice of your axial data. Or is it that you just
want to vis
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(
For surfval, you need to give it a file name eg, lh.curv, lh.thickness.
You'll also need a registration file (or indicate that it is a header
registration with --regheader subjectname)
doug
Antonella Cappelletti wrote:
> Hi all,
> I don't understand what's wrong with this command line:
> mri_su
You'll need to do this in steps.
1. Create a registration matrix R between your axial and conformed data:
tkregister2 --mov axial.nii --targ orig.mgz --regheader --reg
axial.reg.dat --noedit --s subjectname
2. Get the tkreg vox2ras matrix T from your axial:
mri_info --vox2ras axial.nii
3. Compu
Thanks, Koen. The issue is in my preliminary study this is the only subfield
that shows a significant difference. So do you think it would still be worth
reporting?
On Wed, Aug 31, 2011 at 1:41 AM, Koen Van Leemput
wrote:
> Hi Shashwath,
>
> The label "hippocampus" was used in the tail of the hip
If you pass it dicom, it will try to extract the bvalues, which is where
it is failing.
doug
Antonella Kis wrote:
> Dear Doug,
>
> Sorry but I still have a question about this error:
> I understood that dt_recon it takes original dicom images as input and
> it generates multiple NIFTI volumes th
That's almost right. Just specify the subject name and not the full
path. Also, you will need to supply bvals and bvects
dt_recon --i DTI_15.nii.gz --s NPI001 --o
/usr/local/freesurfer/NPI001/DTI_15
Antonella Kis wrote:
> Hi Doug,
>
> Thanks again for helping. So my question is then: I will p
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
It does not always work to extract them from the dicom. You should talk
to whoever set up your scans to get the bvals and bvects.
doug
Antonella Kis wrote:
> Hi Doug,
>
> Thanks again. From where I take the bvals and bvects. I was reading
> that if my DICOM files were acquired using a Siemens sc
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, Dougl
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
If they meet the requirements outlined in the help section (run with
--help).
Antonella Kis wrote:
> Dear Doug,
>
> I can get this values if I convert the dicom files with MRIcron. Can I
> use this values?
>
> Thanks.
> Antonella
>
> PS> Why when I ran the dt_recon I didn't get the fa.nii, adc.n
That registration appears to be ok. Remember, that is the boundary
between the cortical gray and white matter, not the edge of the brain or
skull, so it should be interior.
doug
noam Schneck wrote:
> Here are slices from the registration.
>
> On Wed, Aug 31, 2011 at 2:39 PM, Douglas N Greve
>
your data have 17 frames, but you bvals and bvects only have 16 values.
Antonella Kis wrote:
> Dear Doug,
>
> I used the mentioned bvals and bvecs but I am getting the following error:
>
> Loading y from /usr/local/freesurfer/NPI001/DTI_15/dwi-ec.nii
> Using DTI
> Loading BValues from bvals.dat
>
you need to find out what values need to go into you bvals and bvects
file to match what you acquired. I don't know what you acquired so I
can't help you. Sometimes the bval/bvect files dont include a bval=0
acquisition at the beginning, so check that first
Antonella Kis wrote:
> Hi Doug,
>
>
Can you send a pic?
noam Schneck wrote:
> Nevertheless when I use that register.dat to view a statmap on the
> anatomical space (which is the same registration from epi to t1 space)
> I have activation outside of the brain. I understand that BBR has
> aligned the images well, but it seems not t
Hi all:
Is there a way that can perform a test to compare the difference of
cortical thickness between groups (at least three) using ANOVA (analysis of
variance) in FS? If it is how can i do that?
Any suggestions will be appreciative___
Free
That actually looks fine to me too. When FEAT creates a mask of the
brain, it extends the mask out a bit to make sure that it does not cut
off any brain. Every voxel in the mask will get a zstat. If your raise
the threshold a bit, the stuff outside of the brain will probably drop away.
doug
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