will help me a long way in my
work
Thanks in advance
Take care
Chacko Cherian.
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Freesurfer mailing
Hello all,
I am having some trouble in using the freesurfer
version I had downloaded.The FREESURFER_HOME file is
missing and so I cannot source or setenv anytime I
want to use it.Do I need to tar and unzip again or is
there any other way?
Thanks in advance
Chacko.
Hello,
I am having some trouble in running Analyze format
images on freesurfer.Could someone please guide me on
how to run images on this format..
THanx
Chacko.
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Hi everybody,
I ve got a small question on converting .img
scans(Analyze) TO .mgz...
suppose i have a raw.img(and raw.hdr) file and I want
to
use recon-all for converting this to .mgz do I just
need to do
recon-all -i raw.img -s subject_name
Or is there any other way I can directly use .img
Hello everyone,
I have used an Analyze format data(.img) on Freesurfer
and was running the Morphometry and REconstruction
tutorial on the wiki.THey were running fine till i
reached the automatic topology defect correction step.
I used :recon-all -fix -s subject_name and it
started fxing all the
answer!
Bruce
On Thu, 22 Jun 2006, Chacko Cherian wrote:
Yes when I load the image in tkmedit I odnt have
any
problems.Its perfectly clear and
coronal,horizonatal
and sagittal are all correct.
--- Bruce Fischl [EMAIL PROTECTED]
wrote:
when you load it in tkmedit does
No, the nofix surfaces are also displaying just a
small piece of the surface..similar to the ?h.orig
surfaces.
--- Bruce Fischl [EMAIL PROTECTED] wrote:
hmmm, looks okay. Can you see the ?h.orig.nofix
surfaces okay?
On Thu, 22
Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl [EMAIL
are also displaying just
a
small piece of the surface..similar to the
?h.orig
surfaces.
--- Bruce Fischl [EMAIL PROTECTED]
wrote:
hmmm, looks okay. Can you see the
?h.orig.nofix
surfaces okay?
On Thu, 22
Jun 2006, Chacko Cherian wrote:
--- Bruce Fischl
[EMAIL
Hello everyone,
How can I can I print out the display images from
tksurfer and tkmedit other than manually saving them
into tiff and then printing them.IS there any way to
print them directly?
THAnx
Chacko.
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when i want to print-out the outputs using Save TIFF
as it isn't giving me any results.Is there something
else that I need to do to save the outputs as TIFF
files??
--- Bruce Fischl [EMAIL PROTECTED] wrote:
but you could write a tcl script to do it
automatically
On Fri, 30 Jun 2006,
Kevin
mri_watershed: error while loading shared libraries:
libstdc++.so.6: cannot open shared object file: No
such file or directory
Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005
i686 unknown unknown GNU/Linux
recon-all exited with ERRORS at Fri Jul 14 16:40:38
MST 2006
--- Chacko Cherian [EMAIL
Hello everyone,
I am using a Red Hat Enterprise Linux AS release
3(Taroon update 6) version.While running tkmedit for
the bert data..this is what i get..
tkmedit: error while loading shared libraries:
libglut.so.3: cannot open shared object file: No such
file or directory.
I tried the
Hello all,
I was running recon-all for one of my images and this
happened to be the error that i got.Could someone
please clarify,
Thanks in advance
Chacko.
mri_watershed: error while loading shared libraries:
libstdc++.so.6: cannot
open shared object file: No such file or directory
Linux elmo
Hello all,
Could someone please clarify why this library cannot
provide the correct 'GLIBCXX_3.4'.
Thanks in advance.
Chacko.
mri_watershed -keep brainmask.auto.mgz brainmask.mgz
brainmask.mgz
T1.mgz brainmask.auto.mgz
mri_watershed: /usr/lib/libstdc++.so.6: version
`GLIBCXX_3.4' not found
the file
names(for each slice) for the recon-all procedure or
is there a simpler way.
THanks in advance
Chacko Cherian.
Arizona State University
Graduate Research Assistant
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I got this error while running a single subject in
DICOM format.the 'recon-all -autorecon1 -subjid
subject_name ' stopped at this stage.
INFO: Modifying talairach volume c_(r,a,s) based on
average_305
MRInormalize: could not find any valid peaks
mri_normalize: normalization failed
Linux
Hello all,
Here's an error I got while doing 'recon-all
-autorecon2 -s subject_name.
Could someone please clarify.
Thank you.
Chacko Cherian.
[EMAIL PROTECTED] EM Registration Wed Aug 2 16:35:22 MST 2006
/home/ttest/freesurfer/subjects/case1/case1/case1/mri
mri_em_register -mask
Hello all,
Can we use tkmedit for T2-weighted images or is it restricted to T1 -weighted?
Thanks
Chacko.
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Hello all,
I have a small query.Just wanted to know which stable
Freesurfer version I should install for Linux
Slackware 10.0.0 version.
Has anybody experienced any issues usig this platform.
Thanks in advance.
Chacko Cherian.
Arizona State University
:21:26 MST 2006
Thanks in advance
Chacko Cherian
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this could possibly mean?
THanks in advance.
Chacko Cherian.
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?
Thanks in advance
Chacko Cherian.
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Hello all,
I wanted to know where the mritotal.log file is created.I checked the /scripts
directory but couldnt find it there. I'd like to have a look at the Final
objective function value for the subjects I'm running.
Thanks in advance
Chacko Cherian
Hello users,
Is there any information available regarding the parameters used for N3
correction in the autorecon process?
Thanks,
Chacko.
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[EMAIL PROTECTED]
To: Chacko Cherian [EMAIL PROTECTED]
Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Monday, November 6, 2006 4:25:05 PM
Subject: Re: [Freesurfer] is this ok?
Hi Chako,
I wouldn't worry too much about the inflated - it looks okay. Probably a
result of the large motion
Hello Users,
I wanted to know if there is a command to directly export the aseg-stats table
to a spreadsheet rather than cuttting and pasting.
And wishing all of you a very happy Thanksgiving and a great weekend!!
Regards
Chacko.
Thank you Jenni.
How do i use asegstats2table?What is the command?Is it a tcl script file?If
so,could you also mention where it is located.
Regards
Chacko.
- Original Message
From: Jenni Pacheco [EMAIL PROTECTED]
To: Chacko Cherian [EMAIL PROTECTED]; Freesurfer
freesurfer
Hello users,
I am using the latest stable version of FreeSurfer and there are two files
wm.plt and gm.plt which are created after the recon-all process.What do these
signify and how do I open them?
Thanks in advance
Chacko.
Hello users,
Is there a typo on the longitudinal analysis page on
the wiki..
does the command go like this??
recon-all-long -long -subjid tp1 -subjid tp2
Thanks
Chacko.
Expecting? Get great news
want to use (like
-all).
Nick
On Mon, 2007-01-22 at 10:35 -0800, Chacko Cherian
wrote:
Hello users,
Is there a typo on the longitudinal analysis page
on
the wiki..
does the command go like this??
recon-all-long -long -subjid tp1 -subjid tp2
Thanks
Chacko
Hello all,
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
Is this page on thickness reproducibility intended for
longitudinal analysis or is it just a general group
analysis procedure?
THanks in advance,
Chacko.
Hello all,
Here's an error that i got while running group
analysis on a couple of subjects...i checked the
rh.orig file and the rh.sphere.reg and i could open
both using tksurfer.
Reading
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm
--- Chacko Cherian [EMAIL PROTECTED] wrote:
Hello all,
Here's an error that i got while running group
analysis on a couple of subjects...i checked the
rh.orig file
Hello users,
I was running longitudinal analysis for a couple of
scans and recon-all exited with this error.
CTABread(/usr/local/freesurfer/ASegStatsLUT.txt):
could not open file
No such file or directory
atlas_icv = 1.74537e+06
Loading mri/aseg.mgz
Loading mri/norm.mgz
Loading mri/norm.mgz
Hello users,
I wanted to use mri_surf2surf for surface smoothing
but it gives me an error saying --s is not an option.
mri_surf2surf --hemi lh \
--s average \
--sval lh.gender_age.thickness.mgh \
--fwhm 10 \
--tval lh.gender_age.thickness.10.mgh
it didnt work with srcsubject either.The
order version that
does not support the
--s option. If so, then you'll need to spec the src
and trg subjects
explicitly.
Chacko Cherian wrote:
Hello users,
I wanted to use mri_surf2surf for surface smoothing
but it gives me an error saying --s is not an
option.
mri_surf2surf --hemi
Hello users,
I created an average subject(my_average) with 25
subjects.Now when I compare the fsaverage and
my_average inflated views,the display shows fsaverage
as way bigger than my_average.Is this normal?Is it
something to do with how fsaverage is scaled and
displayed? Area-wise my_average is
Hello all,
Is there some information on the wiki about the
srctoDst voxel-to-voxel transform and the rastoRAas
transform?
THAnks
Chacko.
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Hello all,
To rectify the talairach transform, I am editing
brainmask.mgz using tkregister2 and aligning the
subject and talairach volume.
THank you.
Chacko.
What are you trying to register?
Chacko Cherian wrote:
Hello All,
After making changes using tkregister2 the input
Hello ALL,
Has anybody had trouble with tkregister2..I loaded the
transform and the coronal and horizontal views are
mixed up.Coronal view of the subject is coupled with
the horizontal view of the talairach volume.
Thanks in advance
Regards,
Chacko.
No, It has the same problem in tkmedit too.
--- Doug Greve [EMAIL PROTECTED] wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
Hello ALL,
Has anybody had trouble with tkregister2..I loaded
the
transform and the coronal and horizontal views are
mixed up.Coronal view
. Where did
the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve [EMAIL PROTECTED] wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
Hello ALL,
Has anybody had trouble
orientation
should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the
transform..i checked brainmask.img and T1.img after
loading the transform and they had this
problem..The
header and geometry info look fine..
--- Doug Greve [EMAIL PROTECTED] wrote
Hello all,
This is an error I got while running the longitudinal
analysis on one of our subjects.It didnt create the
filled.mgz volume and so the surfaces weren't created.
[EMAIL PROTECTED] Fill Tue Feb 13 20:59:04 MST 2007
/ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri
mri_fill -a
Hello all,
I got an error while running longitudinal analysis
using recon-all -long and the process exited with
errors.
THis is the error message:
mri_fill -a ../scripts/ponscc.cut.log -xform
transforms/talairach.lta -segmentation aseg.mgz
-topofix norm.mgz wm.mgz filled.mgz
logging cutting
Hello developers,
How can I get access to QDEC?
Regards
Chacko.
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Hello users,
I am doing the group analysis stats results...using
FDR correction 0.01 and checking the pial surface with
curvature and overlay. I see this line come up
whenever i change the FDR..is this some kind of error
which I need to be concerned about?
surfer: Error sending tcl command
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