Hi Doug,
The condition numbers were:
- 1e+08 for problematic fsgd file
- 371.233 for previous fsgd file
I tried also v5.1, however with no succes. The matirx was still
ill-conditioned with condition number 2.80809e+07.
Cheers,
Ed
On 1 Feb 2013, at 9:53, freesurfer-requ...@nmr.mgh.harvard.edu w
Hi freesurfer experts,
The output of the segmentation, aseg.mgz only display right hemisphere. I used
option -all in the segmentation. How can I make the both hemispheres visible or
is there any specific option to choose for segmentation to make both
hemispheres visible?
Thank you/
Azeez Ad
Hi Bruce,
Thanks for your answer and sorry about the delay in mine.
Registration seems fine, but I came up with some questions regarding it -
1) When testing the registration, using the "compare" button, I can see
both the diffusion and what is suppose to be the anatomical slices - but
why do the
Hi
I am getting an error while using qdec. It says error while
loading shared libraries ,libjpeg.so.62 cannot open shared object
file No such file or directory
I ran reconall with out any problem.
Any idea,
tx
chikku
___
Freesurfer mailing list
Fre
Do you have libjpeg62 installed?
It is required for visualisation but not for the analysis, hence there was no
error during reconall.
Cheers,
Auer, Tibor M.D. Ph.D.
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge
CB2 7EF
United Kingdom
Phone/Work: +44-(0)1223-355294 (ext. 869)
M
what normalization do you mean, and what do you mean by contrast
results?
On Mon, 25 Feb 2013, Schumman Resonance wrote:
> I would like to play with both normalization and registration steps, and
> contrast results.
> Thanks,
>
> Kev
>
>
> On Mon, Feb 25, 2013 at 6:03 PM, Bruce Fischl
> wro
Hi Azeez
no, both hemispheres should be labeled by default. Are you sure it's not
just the colors that are confusing you? The left hemi WM is shown in white
by default, but if you mouse over it in freeview or tkmedit it should show
the label Left-Cerebral-White-Matter.
cheers
Bruce
On Tue,
Hi Rotem
that's always a problem with FA estimation (the partial volume stuff I
mean). It's hard to diagnose this without seeing some images. Can you send
some of the registration?
cheers
Bruce
On Tue, 26 Feb 2013, Rotem Saar
wrote:
Hi Bruce,
Thanks for your answer and sorry about the
I verified lh.orig.nofix, and it looks fine. But, there has been no new
files created since Saturday (2/23/2013).
I am considering stopping the process.
I was thinking, I had created a skull stripped image, and was giving that
as input to recon-all in the command below:
recon-all -subjid . -nosku
is it still on defect 32? What does the tail of the recon-all.log say? And
can you send us an image of the lh.inflated.nofix (if it is the lh that is
running)?
On
Tue, 26 Feb 2013, Blessy M wrote:
I verified lh.orig.nofix, and it looks fine. But, there has been no new files
created since S
Chikku,
I am guessing that you are using Ubuntu. To fix this problem:
cd /usr/lib
sudo ln -s libjpeg.so.8 libjpeg.so.62
in other words, link whatever libjpeg is already installed to the name
libjpeg.so.62.
Nick
> Hi
> I am getting an error while using qdec. It says error while
> loadi
Paula,
That seems plenty adequate to run recon-all, so four days to process bert
seems odd. Are your energy settings set to goto sleep? The adapter
setting should be set to 'never' sleep.
Nick
> Hi Nick,
>
> These are my system's specifications:
> Processor 2 x 2,4 GHz 6-Core Intel Xeon
> Me
Yes it is still at defect 32.
The tail of the recon-all.log is as follows:
CORRECTING DEFECT 30 (vertices=18, convex hull=22)
After retessellation of defect 30, euler #=-7 (59491,172395,112897) :
difference with theory (-28) = -21
CORRECTING DEFECT 31 (vertices=244, convex hull=142)
After retess
you can save a tif of it and post it to the list
On Tue, 26 Feb 2013, Blessy
M wrote:
Yes it is still at defect 32.
The tail of the recon-all.log is as follows:
CORRECTING DEFECT 30 (vertices=18, convex hull=22)
After retessellation of defect 30, euler #=-7 (59491,172395,112897) :
differenc
I was holing out on an analysis before rebooting but that seemed to do the
trick! Thanks all!
Daniel
On Mon, Feb 25, 2013 at 5:58 PM, Nick Schmansky
wrote:
> have you rebooted since installing XQuartz? i've found a reboot is
> necessary to get Terminal to open up again.
>
> N.
>
>
> On Mon, 2
Daniel,
Are you using your Mac to run recon-all? I'm curious about the
run-times you are seeing. Others have had very long run times, which I
cannot explain. I'd expect about 24 hour runtime, possible half that or
less, on a current Macbook Pro.
Nick
On Tue, 2013-02-26 at 12:51 -0500, Daniel
Yes I am running recon-all on a Mac. It is an office computer (so not a
Macbook pro) and my runtimes are around 15-20 hours for each subject.
Daniel
On Tue, Feb 26, 2013 at 12:54 PM, Nick Schmansky
wrote:
> Daniel,
>
> Are you using your Mac to run recon-all? I'm curious about the
> run-times
The micro instance won't work. You'll need at least one m1.medium instance.
I don't want to advertise it again but have you considered using
http://cerebralvol.com that runs EC2 instances
-
Pedro Paulo de Magalhães Oliveira Jun
hello
i ran a trac-all -prep -c ./dmrirc_single_subject and got the following error:
flirt -in
/BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat.nii.gz
-ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/BrainLabDocs/Studies/Alcohol_Study/Alc
Hi Jon - Are you trying to use CVS for inter-subject registration?
a.y
On Tue, 26 Feb 2013, Jon Wieser wrote:
> hello
>
> i ran a trac-all -prep -c ./dmrirc_single_subject and got the following
> error:
>
>
> flirt -in
> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dm
Hi Bruce,
Ouch, I have quite some subjects. Luckily, with some help I found out
you can reverse it, by using:
annot2label with pial
rm *Medial_wall*
Label2surf (fsl) using a textfile containing all the other labels
This pretty much solves it.
Thank you again,
Andries
Sent from my iPhone
On F
glad to hear it
Bruce
On Tue, 26 Feb 2013, Andries R. Van Der Leij wrote:
> Hi Bruce,
>
> Ouch, I have quite some subjects. Luckily, with some help I found out
> you can reverse it, by using:
> annot2label with pial
> rm *Medial_wall*
> Label2surf (fsl) using a textfile containing all the other la
I ran this command, and got the attached image
tkmedit ./ brainmask.mgz lh.inflated.nofix
For some reason tksurfer is not looking good/complete
tksurfer ./ lh inflated
On Tue, Feb 26, 2013 at 11:53 AM, Bruce Fischl
wrote:
> you can save a tif of it and post it to the list
>
> On Tue, 26 Feb 201
Make sure doregcvs is not set to 1 in your config file. This option is not
meant to be used in 5.1 but will be in 5.2.
On Tue, 26 Feb 2013, Jon Wieser wrote:
> hi anastasia,
> i don't know what "CVS for inter-subject registration " is.
> Jon
>
> - Original Message -
> From: "Anastasia Y
Hi Blessy
what format is this? If you don't send it with an extension there is no
way to know
Bruce
On Tue, 26 Feb 2013, Blessy M wrote:
Forgot the image. please find attached.
On Tue, Feb 26, 2013 at 2:45 PM, Blessy M wrote:
I ran this command, and got the attached image
t
I should have send it with an extension. But it is tiff, just as you asked.
On Tue, Feb 26, 2013 at 3:03 PM, Bruce Fischl wrote:
> Hi Blessy
>
> what format is this? If you don't send it with an extension there is no
> way to know
> Bruce
>
> On Tue, 26 Feb 2013, Blessy M wrote:
>
> Forgot t
thanks. I actually meant a tksurfer image, but this might do. Two
questions:
1. Is this a contrast-enhanced acquisition? That will make things more
difficult, although we have processed them in the past.
2. I think the skull stripping removed some brain tissue, which may be the
source of you
I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus), perhaps this is not included in the
hipposubfields volumes?
Wondering, if I were to take a hand traced hippocampus rename it to
aseg.mgz, and made sure that the label matched what Freesurfer expects
alveus (and fimbria) are defined to be part of the hippocampus in the
aseg. Did you include them in your calculation of subfield hippocampal
volume?
On Tue, 26 Feb 2013, Joshua Lee wrote:
I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus), perha
I think you can analyze the data in SPM as long as you don't do anything
that makes assumptions about the spatial organization of the data (eg,
spatial smoothing or clustering).
doug
On 02/26/2013 11:18 AM, Glen Lee wrote:
> Hi Doug
> Many thanks for clarification.
> Yes, I was hoping to run GL
Hi Daniel, I'm reposting this to the FS list because I don't really use
mri_ca_train.
doug
On 02/26/2013 02:45 PM, Barron, Daniel S wrote:
> Hello Dr. Greve,
>
> I am trying to create a .gca for thalamic nuclei. Based on the Morel
> 2007 atlas, I have created 6 nuclear grouping masks per hemisp
Hi Paul, I'm not sure I understand. What does 3dcalc have to do with the
LUT?
doug
On 02/25/2013 05:13 PM, Paul Beach wrote:
> Hi Doug. Thank you for the e-mail.
>
> I do, actually, have a 'next step' problem.
>
> I've been able to get ROIs drawn in tksurfer into an augmented
> aparc+aseg file
Hi Ed, I think it is just the way you have the matrix set up. You'll
need to alter the matrix in some way.
doug
On 02/26/2013 04:08 AM, Ed Gronenschild wrote:
> Hi Doug,
>
> The condition numbers were:
> - 1e+08 for problematic fsgd file
> - 371.233 for previous fsgd file
>
> I tried also v5.1, h
Hello,
I recently ran freesurfer on a group of patients and controls, and have found a
statistically significant difference between groups in the mean intensities of
certain grey-matter regions (the grey matter volumes of these regions are not
statistically different.) Mean intensity values we
Hi Sarah
typically we assume that myelin content is the dominant source of contrast,
but of course there are other things in there as well for sure
cheers
Bruce
On Tue, 26 Feb 2013, Hunt, Sarah C wrote:
> Hello,
>
> I recently ran freesurfer on a group of patients and controls, and have found
Hello FreeSurfer experts,
I want to export the white matter volumes from the wmparc stats file to a
table. I cannot find the information on the wiki page.
Thanks for your help.
Dr. Mohammed Goryawala
Center for Advanced Technology and Education
Miami, Florida
Hi,
In FreeSurferColorLUT.txt (Freesurfer 5.1), there is a label for the inferior
colliculus (7100), but this structure seems only to be labeled collectively
with other brainstem structures (16) in aparc.a2009s+aseg. It appears from
posts in the mail list that only a subset of the labels in
Fr
Hi Susan
Sorry, it's in the lut because it's n our todo list, but we haven't done it yet
Bruce
On Feb 26, 2013, at 9:27 PM, Susan Alice McLaughlin
wrote:
> Hi,
>
> In FreeSurferColorLUT.txt (Freesurfer 5.1), there is a label for the inferior
> colliculus (7100), but this structure seems onl
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