Hi Doug,
Thanks for your response. I did run bbregister to register the EPI to T1, but
it did not resample the EPI to T1 space, just generated a register.dof6.dat
file, which is expected according to the help document. Also, the help
document of bbregister doesn’t indicate resampling or sort
Hi Pedro
I can't tell - you need to click around in the images and see what you
think
Bruce
On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote:
Thanks, Bruce.
I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs.
Expert opts would be -seg-wlo and -seg-ghi? Which values wo
Thanks, Bruce.
I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs.
Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable?
Do they depend on scanning characteristics or do you have a sort of standard
parameters for the software?
Regards,
Pedro
Dear FreeSurfer experts,
I drew a label that crosses the cortical and subcortical boundary. But
FreeSurfer still allows me to obtain statistics using this label for a given
subject, for example, area, volume, and thickness.
I am wondering if these statistics are valid since it crosses cortical
can you check mri_segmet and mris_make_surfaces and see if the
auto-detected intensity parameters are reasonable? Things like max gray
at csf border and such. If not, you can set them explicitly using the
expert opts - this usually works
Bruce
On Wed, 18 Feb 2015, Pedro Rosa - Gmail
wrote:
Hi Ajay
if it covers the whoe brain you might be ok, try it and see how it goes
Bruce
On
Wed, 18 Feb 2015, Ajay Kurani wrote:
Hello Freesurfer experts,
I have a question regarding the use of the -T2 and -FLAIR flags in
freesurfer. I have 2
scans: 1 whole brain MPRAGE and 1 partial brain
Yes - sorry this is probably easier with images.
The files I'm visualizing are the sig.mgh (uncorrected) and
cache.th13.abs.sig.ocn. mgh (cluster corrected) respectively, overlayed on an
fsaverage brain. I am visualizing using tksurfer.
When I run mri_glmfit, I get the "example_sig" output (se
On 2/18/15 4:38 PM, sabin khadka wrote:
Hi FS Users-
After using FSFAST's preproc-sess command (I get the output files:
fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz,
fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell
how well the EPIs are mapping onto th
I don't think I understand. What files are you visualizing? What is your
command to visualize?
On 2/18/15 3:42 PM, Hirsch, Gabriella wrote:
Hi FS experts,
I had a quick question I was hoping someone could help me with; I used
the group analysis tutorial
(https://surfer.nmr.mgh.harvard.edu
Yes, if you've run the T1 through recon-all, then you can use bbregister
to create a registration between the two. It will also resample to the
T1 space, but you can also use mri_vol2vol to do so too.
doug
On 2/18/15 5:43 PM, Xiaomin Yue wrote:
Hi,
I like to transfer a epi file to a T1 spa
Hi Mark,
I had a somewhat similar issue in the temporal lobe, which was due to the gray
matter being darker than what FreeSurfer assumes. This caused the gray-pial
boundary to be placed closer to the white surface than it should be.
For me the solution (suggested by Bruce) was to call mris_make
Hi,
I like to transfer a epi file to a T1 space. Is it possible?
Thanks,
Xiaomin
On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve"
wrote:
We don't have anything to do this directly. However, we do have this tool:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
See if that meets your ne
Hello Freesurfer experts,
I have a question regarding the use of the -T2 and -FLAIR flags in
freesurfer. I have 2 scans: 1 whole brain MPRAGE and 1 partial brain FLAIR
(bottom of cerebellum/brainstem gets cut off on some subjects). I wanted
to see if freesurfer would still be able to run corre
Hi FS Users-
After using FSFAST's preproc-sess command (I get the output files:
fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz,
fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell how well
the EPIs are mapping onto the common space (I am assuming fsaverage in
Merci bien :).
On Wed, Feb 18, 2015 at 2:54 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats,
> because that will give you a robust maximum (i.e., if there are a couple of
> voxels that are outliers with a ver
Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats,
because that will give you a robust maximum (i.e., if there are a couple
of voxels that are outliers with a very high value it won't take them into
account, which is probably a good idea here). Then use 20% of that robust
Hi FS experts,
I had a quick question I was hoping someone could help me with; I used the
group analysis tutorial
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) to
analyse two groups of subjects.
I ran the mri_glmfit command, as well as the clusterwise correction
Hi FreeSurfer,
I want to study the treatment effect on group pf 20 patients in 2 time
points ( 6 month to 2 years) , I have also 2 time points from controls ( 2
to 3 years) . I ran longitudinal pile line and looked at the rate using
qdec and the results shows positive significance from zero , does
Thank you very much Anastasia,
May I please check with you if what I am thinking of doing sounds correct?
I would use fslstats in FSL with the flag -R which gives me the maximum
value. For Forceps major I get a value of 200, 20% of this value would be
40, so then in the path.pd.nii.gz image I thres
Hi FreeSurfer,
What would be the best way to compare the patient group before and after
treatment with a control group? Should one use the tp1 and tp2 registered
to the template from longitudinal analysis and compare those with the
control group?
Best regards,
Amirhossein Manzouri
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