Hi Bruce and team
I have a ROI mask in analyze (img_hdr) format obtained from MR spectroscopic
group analysis using a different registration (talairach based). I want to
use this ROI as a label to extract thickness measures on a group of
subjects. How can I do this?
If I use mri_vol2surf will I b
I tried all the solutions listed on the help page but they don't work. My
graphics card is an Intel Mobile 4 Series Chipset Integrated Graphics
Controller. How do I update the drivers?
Jon
> have you tried updating your video drivers? Freeview doesn't currently
> have any tools for tracing on
Dear Freesurfer users,
Thank you for your previous help and advice. I am still having difficulty
creating reasonable-looking surface overlay files from the functional data in
volume format, and would be grateful for any further help.
I have a functional image in volume format (originally writ
Hello All,
I would like to clarify the following.I couldn't find the answers i was looking
for in the archives so here are my questions;
1) In some of our subjects the WM/GM interface is identified correctly but the
pial surface falls short of some voxels which i want to manually edit them
i
Hi:
I have three MRIs of the same patient took during different months... I need
to compare the hippocampus volume fof the three exams (for example), the
cortical thickness, etc... How can I do such computation ?...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Sa
Hi Venkateswaran",
1. We'll need to see some examples to understand why it is happening.
2. We published some #s in our original PNAS paper, and there are certainly
plenty of published thickness studies around. You'll want to match a bunch
of things, including sequence and age for sure.
3. You s
I want to use contrast files that are outputs from SPM (in IMG HDR format)
to overlay on inflated surfaces.
But if I use bbregister and choose T1 as the image type, the regisration
achieved is poor (image attached)
Is this the correct way of doing this or am I missing something?
Commands used:
Hi Lena,
bbregister tool performs within-subject, cross-modal registration. I
think poor registration is probably because you are using fsaverage.
Sita.
On Fri, 12 Feb 2010, Lena Palaniyappan wrote:
>
>
>
> On 12/02/2010 16:47, "Lena Palaniyappan"
> wrote:
>
>> I want to use contrast files
Hi:
How can I execute a freesurfer command at a specificed time/day ?...
Any Ubuntu trick ?...
Sincerely,
--
Gonzalo Rojas Costa
Advanced Medical Image Processing Laboratory
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel:
Hi Lena,
why do you want to use the contrast files and not the EPIs themselves?
And why would the contrast by T1 weighted? In this context T1 means the
stuff inside the surface (e.g. white matter) is brighter than the stuff
outside the surface (e.g. gray matter). If the reverse is true then you
I don't have an Ubuntu system handy (I have CentOS everywhere) but "atrun"
should do the trick. Look at the manual page for atrun ("man atrun") for
details.
--
Henry Mensch / Systems and Storage Manager
Center for Imaging of Neurodegenerative Diseases
VA Medical Center, San Francisco CA USA
if you are doing within-subject then why use the contrast images instead
of the volumes themselves? And if the VBM is derived from the same
anatomicals as the FS surfaces aren't they already in register?
On Fri, 12
Feb 2010, Lena Palaniyappan wrote:
> Bruce & Sita - many thanks for your comment
Bumping this back up to the list. Could someone please address?
To be more concise, during longitudinal processing, where are wm/gm edits made?
On the cross-sectional runs, to the base, or on the .long. runs themselves?
Thanks.
-Derin
Begin forwarded message:
> From: Derin Cobia
> Date:
I want to extract wm volumes using wmparc for parcellations contained in
Destrieux 2009 atlas but when I inspect my wmparc stats file, most of the
volumes that I am interested in are reported as zero. What should I do to
read these volumes?
Many thanks
Lena
__
edits should be made to the cross-sectional subjects and the base
subjects. edits do not need to be made to the longitudinal runs, as
they will be transferred from the cross-sectional subject run. the base
subject does not get edits transferred from the composing set of
cross-sectional subjects b
Hi:
I have three MRIs of the same patient taken at different
dates/years... I need to compare the hippocampus volume (for example)
between the three MRI... I want to compare also the cortical thickness
between the three MRI... How can I do such computation ?...
Sincerely,
Gonzalo Rojas
freesurfer has what is called the 'longitudinal' processing stream which
is intended for exactly this purpose. you will need v4.5.0 of
freesurfer, as that version of recon-all contains the hooks to do this
type of analysis.
for complete details on how this works, see:
https://surfer.nmr.mgh.harva
I am trying to derive wmparc volumes for a2009s which are by default not
available in wmparc (segments read empty) _ is this because Desikan/Killiany
atlas is used in wmparc by default?
So I decided to run
Mri_aparc2aseg for each subject using
mri_aparc2aseg --s --annot aparc.a2009s --o mri/wmpa
Hi,
We are about to start processing data from several projects using FreeSurfer,
and I wanted to find out if the next version is coming out in the near future.
I know Nick had asked if anyone wanted Tiger builds about a month ago, which
has me thinking a new version is on the horizon, and
Hi Derin,
this is how I see it:
The base might need edits and if it does, they should be made. As you
say, the surfaces of the longitudinal runs are initialized with the
surface of the base, so, if it is not correct, this will pollute all
time points.
Another reason to edit the base is that wm e
Hello,
I want to measure the volume of my groups' cortex, n=139, mostly males. I
am using fs 3.0.5.
>From the aseg.stats file, lh + rh white matter is 548,000 and gray matter is
487,000, for a ratio of 1.1. I know the aseg.stats file is not a good place
to go for gray matter volume, as it is usu
Hi Jeff,
usually the aseg overestimates the gray matter, I think because the
manual segmentations it is based on also overestimate (they label voxels
that are mostly CSF as gray), so I don't find the direction of the effect
surprising. Both methods use partial volume correction to account for
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