Hi Angel,
the image doesn't have an extension - what type is it? In general it
isn't a problem if the surfaces don't match the aseg. We usually trust
the surfaces more than the aseg for cortical morphometry - check to see
whether they match the norm.mgz or the brain.mgz.
cheers
Bruce
On Wed, 7
In regard to group differences, roughly 1/3 of the scans in one group match
the voxel size and orientation parameters in the other. The remaining scans
are uniformly different from each other. Not knowing the specific effects
that comparing unequal parameters will have in a Freesurfer analysis, i
why don't you try doing a within-group (ideally control) across-sequence
study and see what the effect is.
On Wed, 7 Oct 2009, James Root wrote:
> In regard to group differences, roughly 1/3 of the scans in one group match
> the voxel size and orientation parameters in the other. The remaining s
I will. Thanks Bruce.
On Oct 7, 2009 9:07am, Bruce Fischl wrote:
why don't you try doing a within-group (ideally control) across-sequence
study and see what the effect is.
On Wed, 7 Oct 2009, James Root wrote:
In regard to group differences, roughly 1/3 of the scans in one group
matc
This error message came up when running the base run with the notal check...any
ideas how to fix this problem?
imgrege: no voxels in register
ERROR: 'imgreg_4dfp /Applications/freesurfer/average/711-2C_as_mni_average_305
/Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g
Hi:
In lh.aparc.a2005s.stats and lh.aparc.stats files, the volume of the
cuneus is different... Why ?..
Sincerely,
--
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
___
because they are different anatomical definitions for the boundaries of
the cuneus
On Wed, 7 Oct 2009, Gonzalo Rojas wrote:
> Hi:
>
> In lh.aparc.a2005s.stats and lh.aparc.stats files, the volume of the
> cuneus is different... Why ?..
>
> Sincerely,
>
>
>
___
Hi group,
i am using for visualisation this commend:
tkmedit bert norm.mgz -segmentation aseg.mgz
$FREESURFER_HOME/FreeSurferColorLUT.txt
However, i would like to view *only* the thalamus.
how can i do that?
thank you,
Asaf
___
Freesurfer mailing lis
Hi Folks,
I was trying to compute the total gray matter volume and I wanted to
check if I was using the correct procedure.
I looked at the "Morphometry Stats" page for this issue
(http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats?highlight=%28gray%29%7C%28volume%29%7C%28matter%29)
The in
Hi Folks,
I was trying to compute the total gray matter volume and I wanted to
check if I was using the correct procedure.
I looked at the "Morphometry Stats" page for this issue
(http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats?highlight=%28gray%29%7C%28volume%29%7C%28matter%29)
The in
Hi all,
I have a question regarding cortical thickness estimation in freesurfer. I
was wondering whether it is possible to input in freesurfer the gray matter
segmentation as an a priori.
Specifically, I run freesurfer on a set of cases on which I previously run
spm and obtained a good discriminat
Hi:
I do all the steps of the "Manual Editing" process that appears in
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, but
the "save main volume as.." option appears in gray (off)... Why ?... I
thought it might be a access permission related issue, but it was not...
Since
Hello,
I recently installed FreeSurfer on one of my laptops running Ubuntu and get
the following error when I attempt to run tkmedit:
Exec format error. Binary file not executable.
I thought I remembered something about setting a soft link for one of the
libraries in Ubuntu. Am I on the right
what does the file transforms/talairach_avi.log say?
On Wed, 2009-10-07 at 10:05 -0400, Weisinger, Brian (NIH/OD) [E] wrote:
> This error message came up when running the base run with the notal
> check...any ideas how to fix this problem?
>
> imgrege: no voxels in register
> ERROR: 'imgreg_4df
are you editing brainmask.mgz? i'm unable to replicate the problem.
On Wed, 2009-10-07 at 13:45 -0400, Gonzalo Rojas wrote:
> Hi:
>
>I do all the steps of the "Manual Editing" process that appears in
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, but
> the "save main vo
Hi:
Yes... I am editing brainmask.mgz...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
Nick Schmansky escribió:
> are you editing brainmask.mgz? i'm unable to repl
you do need to symlink libtiff.so.4 to libtiff.so.3, but that doesnt
look like the problem here. are you sure you're not trying to run the
64b binaries on a 32b system?
n.
On Wed, 2009-10-07 at 13:46 -0400, Andrew Jahn wrote:
> Hello,
>
> I recently installed FreeSurfer on one of my laptops run
Hi Elisa,
Rudolph Pienaar (ccd) put together something for this I think.
cheers
Bruce
On Wed, 7 Oct 2009, Elisa Dell'Oglio wrote:
> Hi all,
>
> I have a question regarding cortical thickness estimation in freesurfer. I
> was wondering whether it is possible to input in freesurfer the gray matt
You can binarize the aseg.mgz with mri_binarize and spec the "binval"
and "match" values to be that of the segmentation you are interested in.
Then load as you would the aseg.mgz
doug
asaf achiron wrote:
>
> Hi group,
> i am using for visualisation this commend:
> tkmedit bert norm.mgz -segmen
eek, that looks pretty bad. Can you tell us what the acquisition
parameters are?
On Thu, 8 Oct 2009, Angel Wong wrote:
> Dear all
>
>
>
> Actually I would like to perform automated reconstruction for my T1 image
> and then obtain anatomical labels after cortical parcellation. I have done
> fully
Hi Rudolph,
I was wondering if you could give me any hint regarding how to use an
apriori GM segmentation in freesurfer. I basically already have a good
segmentation of GM vs WM and CSF from spm and would like to use this towards
the computing cortical thickness.
Thanks,
Elisa
2009/10/7 Bruce Fi
Hi:
I got the following error... How can I solve it ?...
recon-all.log
-
mri_watershed -T1 -brain_atlas
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mg
I see. Your TR is quite short and your TE relatively long, so this is
probably pretty poor CNR between gray and white. If you send me the
orig.mgz I'll take a look and see if it's fixable
On Thu, 8 Oct 2009, Angel
Wong wrote:
> Hi Bruce
>
> Attached please find the parameters for acquiring the
Hi Elisa (and Joost)
It is definitely (*) possible to feed custom segmentations through the
FreeSurfer stream and have surfaces be constructed.
I can sketch the general idea here, but will need to check the system we
actually used for all the detail.
Basically, given a GM segmentation you need
check if the whitematter in the file T1.mgz is around value 110. if
not, then put some control points in the white matter in nu.mgz and
re-run recon-all.
n.
On Wed, 2009-10-07 at 15:34 -0400, Gonzalo Rojas wrote:
> Hi:
>
>I got the following error... How can I solve it ?...
>
> recon-all.l
Hi:
Yes... the occipital white matter has value 110 in general... The
frontal white matter has voxels with values 94 to 117 aprox...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-977717
Hi:
How can I put the control points in the nu.mgz image ?...
Sincerely
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
Nick Schmansky escribió:
> check if the whitematter in th
another thing to try is include the flag -no-wsgcaatlas flag, like this:
recon-all -s subjid -skull-strip -no-wsgcaatlas
this bypasses usage of the atlas.
if that fails, you can send me the 001.mgz input file to the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
n.
On
Hi:
Ok... I test it with the command that you told me, and I added the
option "wsthresh 35"... Then I got a good skull stripped image...
Sincerely,
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97
If you want the pial volume, then you should not use mris_wm_volume as
this excludes subcortical gray. Use mris_volume for both the white and
pial, then do your subtraction.
doug
Mehul Sampat wrote:
> Hi Folks,
>
> I was trying to compute the total gray matter volume and I wanted to
> check if
check to see if the intensity normalization worked (does the T1.mgz white
matter have intensities of 110 most places)
On Wed, 7 Oct 2009, Gonzalo
Rojas wrote:
> Hi:
>
> I got the following error... How can I solve it ?...
>
> recon-all.log
>
Hi Brian,
coming back to your talairach.xfm question. Actually it is not really
used for anything except the eTIV computation (estimated total
intracranial volume). Therefore it is not really necessary to correct
this unless you need that value. The talairach.lta however is used for
the segmentati
sorry, it doesn't sound like this is the problem. You could try putting
some seed points in the white matter for the watershed. Not sure what the
interface is for that. You should also check to make sure that the atlas
transform it is using is reasonable.
On Wed, 7 Oct
2009, Gonzalo Rojas wro
Hello,
I asked this question a couple days ago, but never got an answer.
Please excuse the double posting.
I am running FS 3 and am having problems with auto-recon1, in particular the
mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my
nu.mgz image has intensities all b
Hello Surfers,
I have a number of subjects that are displaying a large number of small
holes in the superior region of their white matter. I believe the medical
term for them is virchow-robin spaces. We would like to try to quantify the
volume that these holes occupy. Is there any way to break d
Hi Jeff,
sorry, I don't know what causes the nu_correct to do this, but you'll
probably have to skip that step as otherwise you've lost too much dynamic
range. I would try copying orig.mgz to nu.mgz and running all the steps
afterwards.
cheers
Bruce
On Wed, 7 Oct 2009, Jeff Sadino wrote:
> He
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