Hi Bruce,
(4) open in mricon t1_zero and use roi1 as overlay...anyway -rl option
is what I was looking for! :D Thank you New pipiline is:
(command line:)
(a) mri_convert t1.mgz t1.nii.gz
(b) for roiX -> mri_convert roiX.mgz roiX.nii.gz -rl t1.mgz (it works
with t1.nii.gz also )
Thank you
Dear All,
I want to calculate the volume of WM, GM and CSF. First of all I have converted
the .mri files to .mgz files. I have checked the ReconAllDevTable page to get
the recon-all switches to calculate the volume of GM, WM and CFS.
I want to use the following switches to calculate the volume,
Dear Freesurfers,
I'm exploring the relationship among cortical thickness, aging and some
cognitive variables in a sample of healthy elders, and I want to test this
relationship regardless sex and years of education.
I think is easy to make contrasts to explore separately the correlation
between
Hi Nick,
Unfortunately doesn't help. When I remove the folder
qdec_project_archive from /tmp, and then try to Load Project File, a
new qdec_project_archive is created, but it only contains those four
folders/files that I mentioned in previous email. No qdec.table.dat.
Is it the same qdec.table.da
glad it worked out :)
On Wed, 20 Jul 2011, r.nava...@itab.unich.it wrote:
> Hi Bruce,
>
> (4) open in mricon t1_zero and use roi1 as overlay...anyway -rl option is
> what I was looking for! :D Thank you New pipiline is:
>
> (command line:)
> (a) mri_convert t1.mgz t1.nii.gz
> (b) for roiX ->
Hi Iven,
is there a reason you don't want to just run recon-all -all? It's more
time for the computer, but no more for you and will give you a lot more
measures
cheers
Bruce
On Wed, 20 Jul
2011, Fellhauer, Iven wrote:
> Dear All,
>
> I want to calculate the volume of WM, GM and CSF. First
Hi,
I see that some stats files are more reliable than others for certain types
of data, for instance I read that aseg isn't that reliable for WM/GM.
Which files I should use to find cortical thickness (whole-brain and each
hemisphere), GM/WM volumes (cortical) and whole brain volume?
What's the
Hi Gonzalo, that contrast will not do the conjunction. You can do a
conjunction explicitly by running mri_concat on the sig.mgh files for
the age contrast and the cognitive measure contrast. Use the --conjunct
option.
doug
Gonzalo Sanchez Benavides wrote:
> Dear Freesurfers,
>
> I'm exploring t
Hi Folks,
I noticed in the multiecho portion of the freesurfer wiki that it says
custom multiecho sequences are available from Martinos for use.
I was wondering who I might contact for information on obtaining sequences
for our 3T Siemens scanner as I hoped to test these out with freesurfer.
Thank
Hi Brian,
Meet Andre who I believe can help you.
Allison
On Wed, 20 Jul 2011, Brian C. Schweinsburg, Ph.D. wrote:
> Hi Folks,
> I noticed in the multiecho portion of the freesurfer wiki that it says
> custom multiecho sequences are available from Martinos for use.
> I was wondering who I might c
Yes, that should work. You will need a registration matrix to give to
mri_compute_volume_fractions. You can get this from tkregister2:
tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat
when you run this, hit the compare button to make sure that the mrs box
falls on the pa
Hi Doug,
Ok. Thank you! :)
Andreia
Citando Douglas N Greve :
> Yes, that should work. You will need a registration matrix to give to
> mri_compute_volume_fractions. You can get this from tkregister2:
>
> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat
>
> when you run t
Hi all,
I was wondering if anyone had any idea if it was possible to combine
together ROIs from the separate hemispheres into one ROI (for example LH V1
and RH V1) and then perform a functional ROI analysis on it. I know how to
combine ROIs (through labels_union) and how to do a functional ROI an
Hi Michael,
if cerebellar gray matter is not something you are terribly interested in
quantifying then you are fine.
cheers
Bruce
On Wed, 20 Jul 2011, Murray, Michael wrote:
Hi all,
We've using version 5.1 to conduct a longitudinal study involving over 150
subjects with up to three ti
Hi Martina,
is the x server running in 32 bit color mode? Sometimes using VNC I find
it selects 8 bit color if the connection isn't that fast.
cheers
Bruce
On Wed, 20 Jul
2011, Martina Ly wrote:
Hello freesurfer community,
I am viewing an inflated image generated by tksurfer using the comm
If it is, you can try running the skullstrip step a second time.
On Jul 20, 2011, at 7:14 PM, Bruce Fischl wrote:
> Hi Michael,
>
> if cerebellar gray matter is not something you are terribly interested in
> quantifying then you are fine.
>
> cheers
> Bruce
>
> On Wed, 20 Jul 2011, Murray, M
update: node on cluster had failing memory chip!
cheers,
satra
On Mon, Jul 18, 2011 at 4:16 PM, Satrajit Ghosh wrote:
> hi all,
>
> i'm trying to rerun some subjects processed with 5.0 with 5.1 and am
> getting the following error on all the subjects.
>
> simply executing recon-all -s subjid
Not our fault! The best kind of problem :)
On Jul 20, 2011, at 8:36 PM, Satrajit Ghosh wrote:
> update: node on cluster had failing memory chip!
>
> cheers,
>
> satra
>
>
> On Mon, Jul 18, 2011 at 4:16 PM, Satrajit Ghosh wrote:
> hi all,
>
> i'm trying to rerun some subjects processed wi
Hello,
I have a subject with three timepoints I am putting through the longitudinal
stream in fs 5.0.0. After the base template was created, I edited some of
the pial surfaces on the base. Now when I run the command:
"recon-all -base subject -autorecon2-pial -autorecon3", it says:
"ERROR: /mnt/f
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