Hi,
Thanks Marcos for your reply. My problem is that asegstats2table does not
output values for eTIV. I do not manage to figure out why.
But maybe your script could work. Anyone knows what is the corresponding
FieldName Index for eTIV?? I checked a aseg.stats file and did not find it.
Thanks a l
Hi Doug,
I´m a bit unsure about polynomial fitting with qdec.
So I want to demonstrate linear, quadratic and cubic effects of age on lGI.
You wrote:
If you need to test all 3, then you'll have to use mri_glmfit with and FSGD
file.
I want to be sure if it is correct to demonstrate:
1. age linea
Hi Krista
I've never seen that happen before. Can you upload this subject and we
will take a look?
thanks
Bruce
On Wed, 2 Oct 2013, krista kelly wrote:
Hi Bruce,
I've tried twice to post this to the freesurfer mail list but it hasn't
worked, I'm assuming because of the attached pictures. I'
Hi, Eugenio,
I have already sent the log files to you. And would you please give me a hint
what is the right command for computing subfields with high-res T2? Thank you
very much!!
-Irene
From: Juan Eugenio Iglesias
To: Irene Lee
Cc: "freesurfer@nmr.mgh.
Hi again, Irene,
On 10/03/2013 09:39 AM, Irene Lee wrote:
Hi, Eugenio,
I have already sent the log files to you.
Sorry, I should have been more specific. I meant
[subject_dir]/scripts/recon-all.log and
[subject_dir]/scripts/hippo-subfields.log
And would you please give me a hint what is t
Hi Doug,
when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii
that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I
get different -log10(p) values than the ones that come out of mri_glmfit. I
am not sure why this is happening.
In principle, I just want pcc maps
Hi Tricia,
try
recon-all -long subject001 subject001_base -localGI
Best, Martin
On 09/28/2013 01:53 PM, Tricia Merkley wrote:
Hi,
Is it possible to run the LGI on data that has already been
longitudinally processed?
For example, when I try to run:
recon-all -s subject001.long.subject001_b
Hi Dani,
etiv is in the header, not in the table where the individual strucures
are) and looks like this:
# Measure IntraCranialVol, ICV, Intracranial Volume, 1736177.143497, mm^3
asegstats2table grabs it also.
Best, Martin
On 10/03/2013 04:54 AM, Daniel Ferreira wrote:
Hi,
Thanks Marcos
Hio
We want to compute the LGI index, using our local computing cluster. the
cluster does not have matlab or it's image processing toolbox on the computing
nodes. Which matlab .m files does the LGI computation use?
Thanks
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, P
Hi Freesurfer Experts,
I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
trouble getting the pial surface to go all the way through the grey matter.
Please see screenshot attached. These data were acquired with a surface
coil and the grey matter varies a lot in intensity. I
Hi Caspar
try putting control points in the white matter where the pial surface
doesn't get out far enough.
cheers
Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
> Hi Freesurfer Experts,
> I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
> trouble getting the p
Thanks, Bruce. The problem is fairly extensive. There is no way to do
normalize grey matter intensity (the white surface looks pretty good)?
Caspar
On Thursday, October 3, 2013, Bruce Fischl wrote:
> Hi Caspar
>
> try putting control points in the white matter where the pial surface
> doesn't get
is the WM in those regions already close to 110? No, there is no way to
normalize GM intensity (it has too much biological variability over the
brain)
On Thu, 3 Oct 2013, Caspar M.
Schwiedrzik wrote:
> Thanks, Bruce. The problem is fairly extensive. There is no way to do
> normalize grey matte
On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> when I run a two-tailed t-test against 0 in Matlab on the Rs in
> pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from
> ffxdof.dat, I get different -log10(p) values than the ones that come
> out of mri_glmfit.
I do
the white matter is mostly between 100 and 110 in these regions. at least
in the center of the wm, the voxels are almost all 110.
caspar
2013/10/3 Bruce Fischl
> is the WM in those regions already close to 110? No, there is no way to
> normalize GM intensity (it has too much biological variabil
h. Can you tell us more about the acquisition?
On Thu, 3 Oct 2013,
Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least in
the center of the wm, the voxels are almost all 110.
caspar
2013/10/3 Bruce Fischl
is the WM in those region
Hi Doug,
I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and
then ran a t-test against 0 over the 4th dimension. I converted the
resulting p-values to -log10 and then compared them to the output of
mri_glmfit, namely sig.vol.
This was the mri_glmfit command:
mri_glmfit \
--surf
This was a fairly regular MPRAGE, unfortunately not very well optimized for
contrast. However, the main issue seems to be that the data were acquired
with a surface coil here. That made some of the brain extremely bright
(close to the coil) and some of the brain pretty dark (far away from the
coil)
what resolution?
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
This was a fairly regular MPRAGE, unfortunately not very well optimized for
contrast. However, the main issue seems to be that the data were acquired
with a surface coil here. That made some of the brain extremely bright
(close to
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fischl
> what resolution?
>
> On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
>
> This was a fairly regular MPRAGE, unfortunately not very well optimized
>> for
>> contrast. However, the main issue see
It sounds like two issues:
1. p-values not consistent with your program. What did you use to
compute? Did you do a two-sided (which is what fsfast uses)?
2. Using pcc maps. Why not use -m pcc?
doug
On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> I loaded the pcc.nii file that
Dear FreeSurfers,
While running analyses in QDEC, it only allows me to select one continuous
variable at a time instead of the usual two –so running analyses in QDEC is
extremely limited. I have used QDEC before, and this is a new issue. Has anyone
else encountered this problem?
Thanks,
Prapt
Hi Caspar,
that's probably part of the problem. Is this human data? If you actually
run it at 1mm (conforming it) does it work better?
Bruce
On Thu, 3 Oct 2013,
Caspar M. Schwiedrzik wrote:
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar
2013/10/3 Bruce Fisch
Hi there,
So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn
my ROIs, used mris_anatomical_stats to create a .stats files for each subject
from my hand drawn ROIs and now I want to use aparcstats2table to gather the
thicknesses from all my subjects Is there an o
Hi Jack,
You can specify the .stats file created. Here is an example from the script I
use.
Anyone, correct me if this is wrong!
Tara
mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f
${subject}/stats/lh_frontal_surface.stats ${subject} lh pial
aparcstats2table --hemi lh \
-
Hi Doug,
On Thursday, October 3, 2013, Douglas N Greve wrote:
>
> It sounds like two issues:
> 1. p-values not consistent with your program. What did you use to compute?
> Did you do a two-sided (which is what fsfast uses)?
I used ttest in Matlab, two sided.
2. Using pcc maps. Why not use -m p
Hi Tara,
Brilliant, that's exactly what I need. For some reason I was under the
impression that the --parc flag was restricted to either the Killiany/Desikan
atlas or the Destrieux atlas. Thanks again!
Jack
On 2013-10-03, at 2:03 PM, Tara Ann Miskovich
wrote:
> Hi Jack,
>
> You can specify
preproc-sess -s -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask
-no-subcort-mask
I also tried per-session and mni305-2mm but still did not help.
I even tried doing it in native space (by not mentioning mni305/fsaverage)
but did not work either.
> What was your preproc-sess command?
>
>
> On 10/0
OK, try it like this using the dev env
1. When you run preproc-sess use -no-subcort-mask but do not spec -nomask
2. When ruy run mkanalysis-sess use both -no-subcort-mask and -no-mask
Note that the eyes may get cut off in the mni305 space. You might just
want to keep it in native space.
doug
Hello all,
I'm trying to run Freesurfer recon-all on a series of T1 images with pretty
extreme bias field intensity inhomogeneities. Signal dropoff in the
inferior-most and superior-most slices results in temporal lobe and superior
cortical volume underestimation. It's related to the coil and is
This time, selxavg3-sess finished without any error but everything outside
the brain including eyes are cut (for me i.e. failure). Apparently, no-mask
flag is ignored (!). To help you find the problem I copy/paste my commands
here:
preproc-sess -s Sbj_53/abir/ -fwhm 2 -per-session -fsd bold -no-su
Hello,
read_patch (patch_name) gives x,y and z values. Are these vertex RAS?
Thank you.
Hiroyuki
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The information in this e-
yes, and all the z values should be zero if it has been flattened. Note
that the coordinates in the flat space are pretty arbitrary
cheers
Bruce
On Thu, 3
Oct 2013, Oya, Hiroyuki wrote:
Hello,
read_patch (patch_name) gives x,y and z values. Are these vertex RAS?
Thank you.
Hiroyuki
If I have vertices for making a new patch, is there any command line tool for
this?
Hiroyuki
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 October 2013 16:01
To: Oya, Hiroyuki
Cc: freesur
Sure! Where/how do I upload the subject's folder? I've tried attaching a
zipped copy to my email but it exceeds the size limit.
Thanks!
Krista
On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl wrote:
> Hi Krista
>
> I've never seen that happen before. Can you upload this subject and we
> will take a
you can do it here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Thu, 3 Oct 2013, krista kelly
wrote:
Sure! Where/how do I upload the subject's folder? I've tried attaching a
zipped copy to my email but it exceeds the size limit.
Thanks!
Krista
On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fisch
Hi Bruce,
sorry, I meant to say that data is conformed.
It is primate data. I am having trouble with this particular data set only;
the other ones are at the same resolution and worked fine.
I am attaching another screenshot to show that the control points
unfortunately do not solve the problem. Se
Hi,
I'd like to take some masks that I have in MNI standard space in FSL and map
them to Freesurfer surface space. The goal is to extract measures of average
cortical thickness (or area or etc) for those regions for each subject. Is
there a standard way to do this?
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