Hi,
I have run into the same problem. I have managed to partially diagnose
it, got some workarounds, but no real solutions. I would greatly
appreciate FreeSurfer team for some feedback.
So it's all about orientations. FreeSurfer internally uses LPI and FSL
(Especially FSLView) uses RAS. Try conver
Hi
You should reinstall FSL 5.0 since it is missing a file.
Knut J
On 10/08/2012 08:05 PM, David Soto wrote:
Hi, just trying to install Fresufer in Ubuntu OneiricOcelot 11.10,
I followed the installation steps in your web and seemed fine
in one of the last steps I did
wmen-dsoto3:/> sourc
thanks, I'll try though I have already reinstalled
FSL now I have FSL 5.0.1- should that fine prevent
FS from starting up anyway?
Cheers
On Tue, Oct 9, 2012 at 9:06 AM, Knut J Bjuland wrote:
> Hi
>
> You should reinstall FSL 5.0 since it is missing a file.
>
> Knut J
>
>
>
> On 10/08/2012 08:05
Hi,
I have two questions about Freesurfer. How can I import dicom files,
which include "#" as part of the files names into freesurfer witouth
renaming the files? Recon-all -i seem to cut the files name after "#" so
that image#1.dcm becomes image.
Would you recommend me to run this command for a
Hi Knut
sorry, I don't think you can. We interpret stuff after the # as a frame
number.
Bruce
On Tue, 9 Oct 2012, Knut J Bjuland wrote:
> Hi,
>
> I have two questions about Freesurfer. How can I import dicom files,
> which include "#" as part of the files names into freesurfer witouth
> renamin
Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2
group analysis (search for "paired" on our wiki).
doug
On 10/09/2012 12:45 AM, hhal5...@uni.sydney.edu.au wrote:
> Hello,
>
> We are currently doing a longitudinal Group Analysis using FreeSurfer,
> and were wondering if
This errer message mean that you are missing
/usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh in your
/usr/share/fsl/5.0/etc/fslconf. You should get a copy of this file and
place in /usr/share/fsl/5.0/etc/fslconf/f
knut J
On 10/09/2012 02:00 PM, David Soto wrote:
hi - so the output to source
Hi Noam, sorry, this one slipped through the cracks (would not have seen
it except for Chris' email today). The problem with your data is not
that the brain is upside down but that the letters (AP, LR, SI) are not
appropriate. I just tried this procedure on my data and could not
replicate this
Hi Chris, I don't really see this as a problem for FreeSurfer or BBR as
much as it is a problem with FSLView not being able to re-orient images
so that they don't show up upside-down. If you have two matrices (one to
convert to T1 space, the other to the reoriented space), you can merge
the mat
You can register the brain.mgz (and so all conformed volumes) to MNI152
with the mni152reg script. This will create
$SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat. If you have a
registration for the CT to freesurfer space, then you can combine them like:
Rfinal = inv(Rct)*R152
with
mr
You should model sex as a categorical factor, not as a continuous
variable, so there is no issue of centering sex. Whether you really need
to center age depends on what you want to test. If you want to test of a
difference in age slopes regressing out the effects of sex, then you
don't need to
Hi Catherine, there is something wrong with that file or else the error
msg would not be generated. Make sure it is world-readable. Make sure
you did not download it to a windows machine first and then copy it (if
so run dos2unix on it). Look inside it and make sure you can see plain
text chara
Try this
cd $SUBJECTS_DIR/subject/scripts
mri_annotation2label --subject vol17 --hemi rh --lobesStrict lh.lobesfile
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject
lh white
doug
On 10/05/2012 09:53 AM, Carol
Dear Freesurfer experts,
I'd like to transform a surface S to a native volume V which is not the
original T1.
I first computed the transform V_to_orig.mat using flirt. Loading the resulting
volume and the lh.pial showed satisfactory results in freeview.
Now I'd like to obtain the surface in th
Dear experts,
About the previous subject I have one more question.
Based on Morey, et al. article we can say that there is better results for
the right hippocampus. Generally, it is known that right hippocampus volume
is often bigger than left hippocampus.
So, is there any possible explanation fo
Dear all,
Does anyone have information on the accuracy of cerebellar segmenation
into GM and WM?
Thank you very much.
ines
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The inf
Hello-
I just downloaded the updated freeview.bin (8/23/2012) file (from:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/).
I am running Linux 64-bit (2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42
CDT 2012 x86_64 x86_64 x86_64 GNU/Linux).
When I tried to exe
not that I know of. Our manual data have hippocampi that are pretty
symmetrical.The automatically generated segmentations are also very
symmetric.
doug
On 10/09/2012 01:28 PM, Ana Arruda wrote:
> Dear experts,
>
> About the previous subject I have one more question.
>
> Based on Morey, et al. a
What command are you using to visualize it?
doug
On 10/09/2012 12:51 PM, Arnaud Guidon wrote:
> Dear Freesurfer experts,
>
> I'd like to transform a surface S to a native volume V which is not the
> original T1.
>
> I first computed the transform V_to_orig.mat using flirt. Loading the
> resultin
Wil,
I've just uploaded the latest-greatest dev build of freeview.bin for
centos6 here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
hopefully that will work. there could be library dependency issues
though.
Nick
On Tue, 2012-10-09 at 18:32 +, Irwin, Wil
Hi,
Is anyone familiar with Redhat Linux workstation commands? I think the
problem here was with the "setenv" command and I looked in root's bin and
there is an "env" command?
Just need help getting freesurfer to work.
Am a total newbe.
Thanks,
Catherine
Can you please take a look to my previous posted hippocampi values? What do
you think about them?
Thank you for your prompt help.
Best regards,
Ana Arruda
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I have one MRI and I run freesurfer on it . It runs through completely . When I
see the output though , the surface does not include a huge part of the
temporal lobe.
I looked at the brain mask, and the deskulling is perfect. But the wm.mgz does
not include temporal regions and hence the surface
Hi Catherine
what shell are you running?
Bruce
On Tue, 9 Oct 2012, Nucleos P wrote:
> Hi,
>
> Is anyone familiar with Redhat Linux workstation commands? I think the
> problem here was with the "setenv" command and I looked in root's bin and
> there is an "env" command?
>
> Just need help getti
Hi Darshan
sounds like something pretty big is wrong. If you upload the dataset we'll
take a look
Bruce
On Tue, 9 Oct 2012, Darshan P wrote:
I have one MRI and I run freesurfer on it . It runs through completely .
When I see the output though , the surface does not include a huge part of
th
Hi Nick-
Yes, library dependency issues which don't appear to easily be solved.
Presumably they would be easier to solve if I moved to the centos6 version of
5.1, but the centos4 version is working just fine.
Thanks for your help.
-Wil
|-Original Message-
|From: Nick Schmansky [mailto
Dear freesurfer crew,
I'm having a few issues with segmentation around the hippocampus, I have
included a few screenshots of main and aux vol where the hippocampus has
been excluded even with the addition of control points. Have you got any
tips for rectifying this? It's happened a fair few times
Dear FreeSurfers,
Due to motion I have to exclude participants from my analysis.
Is there an objective measure which could serve as a cut off value concerning
motion in the scanner? Can I find it in one of the FreeSurfer files generated
through the recon-all process?
Subjectively, one can see
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