Dear Freesurfers,
In an effort to figure out why my field sign data is a bunch of
blue/red speckles, I looked at the polar and eccentricity maps
separately on the surface.
In both maps, I found that the values range from 0 to approximately
65. Does that seem to be OK, and if so, what do
-- Forwarded message --
From: mohan boddu bmohan.bo...@gmail.com
Date: Tue, Aug 9, 2011 at 6:17 AM
Subject: Re: [Freesurfer] Segmentation of hippocampal subfilelds
To: Koen Van Leemput k...@nmr.mgh.harvard.edu
Hello,
I would like to thank you for the information, but the problem
Hi Michelle, I don't think you are looking at the angle. The eccen angle
should go from 0-2pi. The polar angle should go from -pi to +pi. What is
you visualization command-line? You can change the color scale from the
View-Configure-Overlay window.
doug
Michelle Umali wrote:
Dear Freesurfers,
Hi Sandra, it is usually just a matter of setting up a design matrix and
contrast matrices to test what you are interested in then using any glm
software. If you just have two time points, then you can just subtract
them and do a one-sample group mean (design matrix a column of all ones;
Hi Tapsya, it looks like your data are going to require about 12G of memory due
to an inefficient use of memory by selxavg when there are so many time points
across a run (I've never tested it with 6570 total time points!). If you want
to run this on launchpad, then you'll need to request that
What's your command line? Looks like you might be putting a slash (/) as
the first character to your glmdir. You will not have permissions to
create this directory.
doug
Chindhuri Selvadurai wrote:
I am actually getting an error message when I type my mri_glmfit command:
ERROR: fio_pushd:
Dear Freesurfers,
I am ready to run the make_average_subject and I need to specify
-xform for the talairach transform: talairach.lta , talairach.m3z or
talairach.xfm. What is the difference between
this and what should I use for the make_average_subject in order to prepare my
data for the
Hi Antonella
talairach.lta and .xfm are linear transforms to a Talairach coordinate
system. The .m3z is a nonlinear morph and will give you much higher
anatomical resolution.
cheers
Bruce
On Thu, 11 Aug 2011, Antonella Kis wrote:
Dear Freesurfers,
I am ready to run the
Hi Bruce,
Many thanks again for your help. So just to make sure that I understood corect:
is better to use the talairach.m3z win my make_average_subject?
I was reading that the talairach coordinate is based on talairach.xfm (unless
changed with --xform) so your suggestion was to change it to
it depends whether you want things in a coordinate system that is more
anatomically accurate (.m3z) or more of a true Talairach one
(talaraich.xfm)
On
Thu, 11 Aug 2011, Antonella Kis wrote:
Hi Bruce,
Many thanks again for your help. So just to make sure that I understood corect:
is
Hi Mohan,
The short answer is that you can not use the instructions you mention
for the hippocampal subfields.
The long answer is that the instructions only work for segmentations
that are already crisp, such as the ones contained in the aseg.mgz
file: each intensity level in aseg.mgz
I am working to do a volumetric analysis in Freesurfer using Thalamus. I
do not know if this is the correct way to go. Should I first register
thalamus to a surface using tkregister? There was also another post on
this list, which suggested using tkregister2? I am also search to find
a tutorial
Hi Knut
you don't need to register it since the segmentation (aseg) is created
from the same data as the surface. What kind of analysis are you thinking
of doing?
cheers
Bruce
On Thu, 11 Aug 2011, Knut J Bjuland
wrote:
I am working to do a volumetric analysis in Freesurfer using Thalamus.
Hi Doug,
You're right it was the wrong map, and now the angles make sense.
But when I look at the correct images, the eccen and polar maps are
very, very speckled. So, in the relevant visual areas, there are
hardly any 0 values, so I would expect a more contiguous color pattern.
Is there
Hi Doug,
The z-values are consistently near or greater than 4. It just seems that the
visualization of the angles is somehow incorrect...
Is there be anything else that I need to check?
Thanks.
Michelle
___
Freesurfer mailing list
what does the activation look like? Does it look right? Can you send a pic?
doug
Michelle Umali wrote:
Hi Doug,
The z-values are consistently near or greater than 4. It just seems that the
visualization of the angles is somehow incorrect...
Is there be anything else that I need to check?
Hi Bruce
I am now responding to the list as well. I have a group with different
subjects where I wish to correlate thalamus volume with gender
difference. Though I have extract the data using asegstats2table. I wish
to be sure that the group difference is correct. Due to this reason I
wish to use
Hi, I'm trying to create a full flat map. The process of flattening seems
has finished without any errors, but I got this error message when I tried
to show up the full flat patch:
lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list
Thanks a lot
Francesca
Hi Francesca
how are you trying to visualize it? Try:
tksurfer subject lh inflated -patch lh.full.flat.patch.3d
cheers
Bruce
On
Thu, 11 Aug 2011, francesca strappini wrote:
Hi, I'm trying to create a full flat map. The process of flattening seems has
finished without any errors, but I
use --segno 10 --segno 49
These codes are from $FREESURFER_HOME/FreeSurferColorLUT.txt and
correspond to left and right thalamus. Use -m volume to get the volume
of thalamus (this is the default). If you're only looking at one
measure, then no correction for multiple comparisons is necessary.
Dear All,
I acquired the images using Phillips scanner. I converted the images from par
into analyze using MRIcro. I noticed that images were flipped when I view them
in the axial plane, i.e. when I look at the images on the computer screen the
Right hemisphere (where we tapped the fish oil
Hi Ayaz
you are *much* better off avoiding analyze as a format entirely. Can't
you give the dicoms right off the scanner to recon-all?
cheers
Bruce
On Thu, 11 Aug 2011,
Ayaz, Muhammad wrote:
Dear All,
I acquired the images using Phillips scanner. I converted the images from
par into
Dear Bruce
If I use analyze would it effect the results?
Dicoms are preferable because?
I have processed about 30 subjects using analyze. I have noticed some cases
where surfaces were not done correctly in few regions other than that no major
problems.
If it makes big difference to use
Hi Ayaz
the big difference is that once you convert to analyze you will never be
sure which side of the image is anatomically on the left and which is on
the right, as analyze doesn't store this info.
cheers
Bruce
On Thu, 11 Aug 2011, Ayaz, Muhammad wrote:
Dear Bruce
If I use analyze
Hi Catherine
when you say left do you mean the left side of the image or the left side
of the brain? In tkmedit the left side of the image will always represent
the right side of the brain (as indicated by the little green R and
arrow).
As for the goodness of the surface fit to talairach,
Hi Hyojeong,
on the wiki release notes is a fixed mris_calc binary.
Best, Martin
On Aug 11, 2011, at 8:00 AM, Administrator wrote:
Dear Martin,
I've received the same error as below which discussed previously.
Would you tell me if you managed build a fixed file, please?
Hyojeong Lee
p.s. note that the image you show of the surface over the tal volume has
a caption saying surface registration, but in fact what you are showing
is the talairach (volume) registration applied to the surface, *not* the
surface registration. The easiest way to check the surface registration is
We tap tablet on the right side of the head wouldn't that help to identify the
anatomical left?
Or is it preferable to use dicom for many other reasons?
Thanks for the quick reply.
Ayaz
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August
yes, that will help, but life will be easier if you avoid analyze. There's
really no reason to use it instead of nifti these days, and *many* reasons
not to. You can get other flips (e.g. front/back) that will completley mess
things up, and you really don't want to process things with a
what format are you using? Is it analyze?
And yes, Doug can confirm but I think that's as good as you are going to
get for registering a subject's surfaces to a talairach average volume with
a linear xform
On Thu, 11 Aug 2011, Catherine Wan wrote:
Hi Bruce,
Thanks for your prompt
FreeSurfers,
Is there a way to get BA cortical thickness in a table to export from
FS? As there is for aseg and aparc stats.
Thanks!
Andreia
--
Andreia Pereira, MSc student
Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-354 Coimbra Portugal
Phone
The activation looks pretty reasonable. As you point out, the angles are
a mess. How did you set the color scale for the angles? You should leave
it as a heat scale (if you're using tksurfer-sess). How much did you smooth?
doug
Michelle Umali wrote:
Hi Doug,
Attached is a pic of the
I'm not sure what you would visualize. These are just single numbers per
subject.
doug
Knut J Bjuland wrote:
Hi
Is is possible to visualize this data on sub-cortical structure in wya
similar to the aging tutorial?
Knut J
On 08/11/2011 09:03 PM, Douglas N Greve wrote:
use --segno 10
you will have to run mris_anatomical_stats on each label to get a stats
file. Look in recon-all for the command line. You can then run
aparcstats2table on that.
doug
_andre...@sapo.pt wrote:
FreeSurfers,
Is there a way to get BA cortical thickness in a table to export from
FS? As there
Thank you all for your help. Nick, I installed fs 5.1.0, and it is running
correctly now. This brings up another question though. We have about 200
subjects (600 scans) we are doing reconstruction on. We are done with the
cross-sectional, and have completed 20 of the base templates, all in fs
Dear List,
I have a question regarding using .img in Freesurfer.
We only have analyze images, but we can tell the orientation of the images
through the patient's lesion location. Because freesurfer sometimes flips
these image after recon-all, I'm now flipping the problematic ones using
Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also
try using the sphere instead of the occip patch.
doug
Michelle Umali wrote:
Hi Doug,
Thanks again for your advice, the heat maps look much better. However,
they still do not visualize the continuous range of angles or
Dear Catherine
I think freesurfer uses the voxel space not world space (hdr file). some
other programs use hdr file too which means world space like spm.
if you want to have same world space and voxel space you have to have
re-slice your img file in spm if you use spm. then everything would be
Dear Bruce
I think I found the problem. The problem came from the original oriantation
of T1 image and I think mris_register could not find it itself during the
recon-all. I added to have initial alignment to inflated and the problem
solved.( mris_register -curve -inflated ?h.sphere template
Dear Bruce,
I have two questions.
I saw there are a lot of algorithms for mris_register. Which one are more
precise and has less distortion on sulci pattern?
In initial alignment if I want to rotate the surface with -rotate [ alpha is
(ear to ear) beta(Back to nose) ... ]. Am I right?. and if I
Dear Tracula experts
Is it possible to change the number of fibres per voxel in bedpostx (from 2
to 3) within the trac-all command?
I did not see any option for that.
Thanks in advance
Cheers
Jürgen
Jürgen Hänggi,
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