Hi Bruce,
I'm using freesurfer version 5.1.0. I currently try to process quantitative T1
(R1) maps derived from 4 and 18 deg. FLASH images and FA maps. Interestingly,
transformation appears to fail less often when using single (16 deg.) FLASH
images, only. SPM segmentation routine on the othe
Carolina,
It means its smoothing on the surface with a kernel of 10mm full-width
half-max. Smoothing on the surface can generally be larger than in a
volume. See these slides for a description of the difference:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt
you can u
Chris,
This is an unusual error. I dont know why nu_correct would be found for
some subjects but not others, if its being run on the same platform. I
can only think this is a network issue. Is it replicable? nu_correct can
be run from the command line.
The intensity normalization issues in v5
Hello,
I have got the following problem: if I want to load the qdec.table.dat, I get
the following message:
ERROR: 0xbfd96154 is invalid. Must have at least two levels.
Attached is the table and the levels files. Do you know what is wrong?
Best regards,
Viola
_
Dear expert,
I got an error while clicking the Monte Carlo simulation in qdec.
I am using Mac 10.6 and qdec version 1.4, freesufer 5.1
Have no clue why it always gives this error in the terminal:
mri_surfcluster --in
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thi
Hi Dear FS experts,
Doug sent these links, but I can't download them. Do you have the new links?
Download these
filesftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemiregftp://surfer.nmr.mgh.harvard.edu/transfe
Viola,
The .levels files need an extra carriage return after the last level (so
that the cursor is on an empty line). But even doing that, I get an error
for the gender.levels file that I cant figure out right now. But you can
delete the gender.levels file and the qdec.table.dat file will load
c
Dear Fresurfer experts and Koen Van LeemputI have made the hippocampal subfield segmentation of a group a subject in which is supposed to take the hippocampus from the aseg segmentation and calculate the new subfields segmentations inside this hippocampus of each hemisphere, am I right?If so, The v
Hi,
I would like to register FLAIR to T1.
Specifications FLAIR:
axial acquisition, 24 slices,
pixel size = 0.45 * 0.45 mm^2
slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain
to just below the eyes. This is contrary
to the T1 scan which covers the full head
down to the n
try -init-spm
cheers
Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
> Hi,
>
> I would like to register FLAIR to T1.
> Specifications FLAIR:
> axial acquisition, 24 slices,
> pixel size = 0.45 * 0.45 mm^2
> slice thickness = 5.50 mm (no gap).
>
> The slices run from the top of the brain
> to ju
Hi Bruce,
It is slightly better but still displacements
in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
> try -init-spm
>
> cheers
> Bruce
> On Tue, 10 Jul 2012, Ed Gronenschild wrote:
>
>> Hi,
>>
>> I would like to register FLAIR to T1.
>> Specificat
Hi Ed
you are using -t2, right? You can also try -init-header
cheers
Bruce
On Tue, 10 Jul 2012,
Ed Gronenschild wrote:
> Hi Bruce,
>
> It is slightly better but still displacements
> in all directions and rotations too exist.
>
> Ed
>
> On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
>
>> try -in
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
> Hi Ed
>
> you are using -t2, right? You can also try -init-header
>
> cheers
> Bruce
> On Tue, 10 Jul 2012,
> Ed Gronenschild wrote:
>
>> Hi Bruce,
>>
>> It is slightly better but still displacements
Hi Ed,
sorry, you'll have to wait until Doug is back from vacation. Is this from
the same session? I've always had it work on flair images using one of the
types of initialization.
cheers
Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
> Hi Bruce,
>
> Unfortunately, this has no effect.
>
>
Hi Bruce,
It is indeed from the same scan session.
I'll wait patiently, let Doug enjoy his vacation before
he gets bothered again by all our questions.
Cheers,
Ed
On 10 Jul 2012, at 16:57, Bruce Fischl wrote:
> Hi Ed,
>
> sorry, you'll have to wait until Doug is back from vacation. Is
> this
Hi, FreeSurfer experts
I want to generate an average surface and volume using make_average_subject
command based on some of my non-human primate data, which do not have
aparc.annot data. I wonder if it is possible with FS. From the archive, I found
some emails entitled "no seg", in which a --no
glad to hear it :). You may need to repost (and possibly upload your
data)
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
> Hi Bruce,
>
> It is indeed from the same scan session.
> I'll wait patiently, let Doug enjoy his vacation before
> he gets bothered again by all our questions.
>
> Cheers,
> Ed
Hi all,
I have a simple problem that hopefully has a simple solution. I'm going
through an annotation file, trying to find the names of select labels. In the
tksurfer window at the bottom right it displays the name of the label file that
the curser window is hovering over, BUT it only display
Hi Chuck,
The certain area in your snapshots you are refering to is the medial
temporal lobe (hemisphere on left side of the image)? In the snapshots
you have the pial, wm, and orig surface displayed. Please verify that the
yellow line corresponds to the wm surface and not the orig surface.
Hi Sam,
Try going to View->Windows->Labels. With that Labels window open, when
you click on a certain label displayed on the surface in the main tksurfer
window, the name of that label should become highlighted in the list
displayed in the Labels window. You can adjust the size of the Labels
Hi FreeSurfer,
I have two images. One MPRAGE (1x1x1mm) and a T1-weighted (0.682x0.682x3mm)
image used for CBV mapping. We have run FS, with hippocampal subfields on
the MPRAGE and would now like to transform the posterior probability maps
to the T1-weighted CBV space.
I have been using
1) mri_vol2
Hi Usman,
you need to convert the reg to lta (using tkregister2) and then you can
use mri_concatenate_lta .
Cheers, Martin
On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote:
> Hi FreeSurfer,
> I have two images. One MPRAGE (1x1x1mm) and a T1-weighted
> (0.682x0.682x3mm) image used for CBV ma
Hi,
I'm using mri_label2label to reverse normalize labels from fsaverage
space to the native surface.
I'm ending up with some splotchy-looking labels, for lack of a better
word. See what I mean here:
http://web.mit.edu/mwaskom/www/splotchy.png
I'm doing this normalization in a script with the f
Hi Martin,
Thanks for the quick reply. I tried the following commands, but it looks
like the volumes are still out of line. Is there something I am missing?
to get from hc_subfield --> nu.mgz --> t1_cbv
#register and create transforms
1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final
Hi Usman
you may have to repost this question in a few days when Doug is back.
cheers
Bruce
On
Tue, 10 Jul 2012, Usman Khan wrote:
Hi Martin, Thanks for the quick reply. I tried the following commands, but
it looks like the volumes are still out of line. Is there something I am
missing?
to
Hi Usman ,
Try validating each step by applying each transform. I usually use mri_convert
-at
For it.
Best MartinUsman Khan wrote:Hi Martin,
Thanks for the quick reply. I tried the following commands, but it looks like
the volumes are still out of line. Is there something I am missing?
to
Dear Bruce,
Did you also identified a strong rightward asymmetry (with pars triangular
and BA44) in your data analyzed by freesurfer 5.1? Just, to be sure, that
this is not an issue only with our data. I'd like to use the TRACULA as
well, and because tracula uses the cortical parcellation of our s
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