Hi Don,
I am in a similar situation. I am on a IBM BladeCenter cluster (though with
one blade only) with 2 Quad core Intels, and I experience intermittent
crashes of mri_volmask as well. Similarly as you, when I run the mri_volmask
on the crashed subject on a desktop, this passes perfectly fine
Hello Doug
The Siemen's Trio gives us Diffusion weighted images in the form
of MR.10284.746.There are no extensions such as .dcm or .ima
I can convert the dicom to nifti .nii format using SPM or FSL.But neither
program extracts the bval or bvec information.
I am working on Mac OsX 10.5 and am usi
Subject: Temporal lobe segmentation
Date: Tue, 2 Jun 2009 17:40:21 +0100
Hi all,
I am interested in automated segmentation of temporal lobe using freesurfer. I
understand that it is possible to add up the individual regions of a specific
lobe, create one massive label for that lobe,
Hi Seyed,
I don't think there's any easy adding up of labels that gives you the
temporal lobe, but Rahul and/or Christophe can correct me if I'm wrong. The
easiest thing to do would be just draw the boundaries on fsaverage and map
it to your subjects using mri_label2label. We should probably p
Hi,
When I plot the probability maps, the color scale bar takes negative
values too (e.g., setting the threshold min 0 max 0.5, you get a scale
bar between -0.5 and +0.5). How can I change the color scale bar so that
it shows percentages?
Thanks!
Eylem
Hi Eylem,
are you configuring it with the configure overlay window? If so, you
should be able to enter 0 for the thresh and 1 for the max, and click
"linear" to generate the same maps as the ones we published. You need to
copy the label stats to an overlay first though (tools->label->copy labe
Hi Bruce,
That's exactly what I do. The maps do look nice, but the color scale bar
does not. It is not a percentage scale, rather it takes a scale of -/+
max value (of course, a negative value does not exist on the probability
map!!!). I think it is just about the options of the color scale b
did you hit return when you typed in the 0/1 values? This is a tk thing -
it won't take the values until you hit return. Then click apply and it
should redraw with the new values
On Mon, 8 Jun 2009, Eylem Kirlangic wrote:
Hi Bruce,
That's exactly what I do. The maps do look nice, but the colo
Hi Seyed,
As Bruce mentions, currently the best way to get a complete temporal lobe
segmentation might be to add each of the invidual temporal lobe labels
(using either of the two parcellation systems). With regards to your
specific questions, 1) both of the parcellation atlases do a fairly good
j
I can change the values min and max in the configuration window, this
changes the threshold and apllies to the map. I can observe these
changes on the map, the scale bar changes accordingly, too. But, as I
said, it is not a percental (%) scale bar, rather takes -/+ max value
(which is input in
I think for the pub it was 0-1, not 0-100. Can you generate that?
On Mon, 8
Jun 2009, Eylem Kirlangic wrote:
I can change the values min and max in the configuration window, this changes
the threshold and apllies to the map. I can observe these changes on the map,
the scale bar changes accord
Don and Martin,
I dont have a good solution for you to this problem. The error code
indicates an 'out-of-memory' error returned by pthread_create, and I do
know the mris_vol_mask uses a lot of memory (at least 1GB).
I have not been able to find any clues to the source of this problem on
the web
mmoay...@uhnres.utoronto.ca wrote:
Hi,
I am studying two groups and have found that age is a confound (or is a covariate with an interaction between the two groups). Simply, when I correlate age between the two groups, there is an interaction (i.e., the slopes are different).
My questions
Just give it one file from the series you want to convert.
doug
ps Please consult surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for
suggestions on how to make bug reports. Thanks!
raka maitra wrote:
Hello Doug
The Siemen's Trio gives us Diffusion weighted images in the form
of
hello freesurfers
i have a doubt:
i have convert a subject brainmask from freesurfer to nii and then
i've convert a label that i create on freesurfer to *.nii using for
registration the brainmask.mgz, i've made that for working in SPM, but when i
open the ROI just not match with my subjec
Dear Freesurfer team,
I used the lh.inflated file in an average subject to obtain its
vertex’s coordinates. My question is: What anatomical space or
reference system was use in this file? or instead, How I could obtain
the Talairach coordinates of each vertex?
Thank you in advance,
Rafa.
_
The coordinates are in mni305 space. If you load it into tksurfer, you
can see both MNI305 and Talairach coords. The Talairach coords are based
on a transform from MNI305 from Mathew Brett.
doug
Rafa x wrote:
Dear Freesurfer team,
I used the lh.inflated file in an average subject to obtain it
Dear List,
in an attempt to divide grey matter segments into an outer and inner
layer, I am currently using the vertex coordinates for pial surface (in
Matlab>> read_surf('lh.pial') ) and vertex coordinates for white matter
surface (MATLAB>>read_surf('lh.white') ). Perhaps naively, I assume,
Hi Nick,
Thanks for the reply. I will look into the memory limit issue some more (we
recently instituted per job memory limits), but I have done a test run with a
16GB memory limit (running one job per node).
Meanwhile, thanks for the novtk suggestion. Our fallback option is to just
disable
Experts,
I got the following error while running a subject with recon-all autorecon1
ERROR: Talairach QA check failed!
z-score = -8 <= -4 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test.
See http://surfer.nmr.mgh.harvard.edu/fswi
I am running mris_anatomical_stats and keep getting the same error. Here's
the entire log file.looks like the big error happens at 'glibc detected'
computing statistics for each annotation in
/ifs/woods/scott_temp/kevin_work/freeseg/subj/078/label/rh.aparc.annot.
outputting results to
/ifs/tm
Hello Surfers,
I am trying to verify the p-value sig.mgh maps outputted from the mri_glmfit
command as the first part of a more advanced analysis. We have been extracting
the thickness data for a single vertex from each of our 58 subjects in two
control groups and then running a significiance
Jeff,
sig.mgh actually stores the -log10(p), not p, so to get the true p-value
of say, -2 (in the sig.mgh), take 10^-2 (giving you the true p-value of
0.01).
Nick
On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote:
> Hello Surfers,
>
> I am trying to verify the p-value sig.mgh maps outputte
Also, p-values for t-tests are two-sided.
Nick Schmansky wrote:
Jeff,
sig.mgh actually stores the -log10(p), not p, so to get the true p-value
of say, -2 (in the sig.mgh), take 10^-2 (giving you the true p-value of
0.01).
Nick
On Mon, 2009-06-08 at 16:48 -0600, Jeff Sadino wrote:
Hello
My name is Flavio, student at Universidade Federal Fluminense. I research
image segmentation methods applied to brain cortical structures
segmentation.
I've compared against the hippocampal region got from FIRST-FSL to
Freesurfer, using the same magnetic resonance (MR) image.
The FSL is a n
Kevin,
I've tracked down some memory trampling going on in
mris_anatomical_stats, and posted a fixed version for linux x86_64 here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/linux-
centos4_x86_64
Nick
On Mon, 2009-06-08 at 15:10 -0700, Kevin Scheibel wrote:
> I am running mris_
did the you look at the registration?
Barnali Basu wrote:
Experts,
I got the following error while running a subject with recon-all
autorecon1
ERROR: Talairach QA check failed!
z-score = -8 <= -4 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check fla
Hi Flavio,
25% is pretty low. Can you send us an example image of our segmentation?
cheers,
Bruce
On
Mon, 8 Jun 2009, Flavio Seixas wrote:
My name is Flavio, student at Universidade Federal Fluminense. I research
image segmentation methods applied to brain cortical structures
segmentation.
No. Do I need to look at it with tkregister?
On Mon, Jun 8, 2009 at 5:05 PM, Douglas N Greve
wrote:
> did the you look at the registration?
>
> Barnali Basu wrote:
>
>> Experts,
>>
>> I got the following error while running a subject with recon-all
>> autorecon1
>>
>>
>> ERROR: Talairach QA check
Yea, as the error message says, you should check out the web page, it
will give you all the instructions you need.
doug
Barnali Basu wrote:
No. Do I need to look at it with tkregister?
On Mon, Jun 8, 2009 at 5:05 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
did the you
Hello Everyone,
Thank you all for your replies. We converted the values into -log10(p) and
accounted for two-tailed, but the values were still off, and they are not even
off in any consistent pattern. For example:
FS: .1541 .1109 .0749 .0641 .0514 .0281 .0182 .0141 .0132
.
I think FreeSurfer has more reliability. In houndreds of manually
segmented hippocampi we found FreeSurfer measures to be pretty stable.
the manually segmented hippocampi usually has 15% - 20% less volume.
However we still don't know which method is more accurate. There's a
study right now in USP
you also have to be careful of differences in definition (e.g. is the
fimbria part of the hippocampus?)
cheers,
Bruce
On Mon, 8 Jun 2009, Pedro Paulo de
Magalhães Oliveira Junior wrote:
I think FreeSurfer has more reliability. In houndreds of manually
segmented hippocampi we found FreeSurfer
also of note, there are three recent papers comparing manual
hippocampal tracing to freesurfer automated segments...
Shen L, Firpi HA, Saykin AJ, West JD. (2009). Parametric surface
modeling and registration for comparison of manual and automated
segmentation of the hippocampus. Hippocampus. Jun;1
Those differences are much too large to be rounding errors.
Are you sure that you are running identical models in mris_glmfit and SAS,
and that the data that you are testing in SAS is in fact what is being
processed in mris_glmfit (e.g., same degree of smoothing)?
-Mike H.
>
> Hello Everyone,
>
Hi,
We are processing our data for the longitudinal pipeline. I found some
subjects' brainmask with skull/dura remaining, and a portion of the skull
was segmented as cortical gray matter in aseg. I'd like to ask if this kind
of problem will affect the longitudinal registration/template creation?
36 matches
Mail list logo
