Hello @all,
I want to segment anatomical data recorded from an experiemental sequence. This
sequence creates pictures with contrasts in a rather narrow range around two
hundred if projected into an 8bit grayscale. Freesurfer fails to segment those
data. However, if I rescale the brightness in
Julia, could you send a snapshot of the area in question?
On Apr 2, 2012, at 5:33 AM, Richter, Julia
julia.rich...@med.uni-heidelberg.de wrote:
Dear freesurfer experts,
I have several subjects whose cortical grey matter isn't included in the pial
surface. Is there any possibility to
You should not use --regheader with --reg, but that should not have
caused a seg fault. I'm not sure what went wrong, but try removing
--regheader and see if it works.
doug
On 4/2/12 2:38 AM, Kaveh Kohan wrote:
Thank you very much for the replies.
I checked the wiki and tutorial and I
For aparc+aseg, the cortex does not take values 3 and 42. Instead, the
cortex is divided into regions of interest that range from 1000 to 1999
(left hemi) or 2000-2999 (right).
doug
ps. Please post questions to the list and not to us personally. Thanks!
On 4/2/12 5:15 AM, lorenzo pasquini
Dear All,
I used the following command line to extract the volumes from Stats file.
asegstats2table --subjects sub1 sub2... --stats wmparc.stats --tablefile
aseg_wm_volume.txt
?h.CorticalWhiteMatterVol generated using the above command does not match the
volume which I calculated by adding
The ?h.CorticalWhiteMatterVol is computed based upon a high-resolution
surface-based analysis which is capable of subvoxel resolution. The
values in the wmparc, by necessity, are computed by just adding up the
number of voxels (actually, there is some partial volume correction
too), so the
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format
using the command mri_convert -i first ct.dicom -o ct.mgz, but got an
Hi Tanja,
Are these healthy controls or do they have any lesions etc on the WM? It
looks like most of the training streamlines from the atlas are rejected
for straying off the subject's brain mask.
Can you please check out a similar posting on the list and overlay your
training histogram over
I have tried and it did not work (the same seg fault, see below). It seems
that it successfully performs the mapping but it fails in final step
probably saving the results. Is the data format that I used OK?
I am using Ubuntu 10.10, the version of mri_vol2surf is stable5. Please
let me knoe if
Hi Jörg
can you rescale them yourself to distribute the values more widely
between 0-255 then try giving that as input to recon-all?
thanks
Bruce
On Mon, 2 Apr
2012, Jörg Pfannmöller wrote:
Hello @all,
I want to segment anatomical data recorded from an experiemental sequence. This
Dear all,
I need to obtain the white matter volume per lobe for a given numer of subjects.
I started by using the following:
mri_annotation2label --subject subjid --hemi rh --lobesStrict lobe
mri_aparc2aseg --s subjid --labelwm --annot lobe
and now I have a lobe+aseg.mgz file. How can I
Dear all,
I need to obtain the white matter volume per lobe for a given numer of subjects.
I started by using the following:
mri_annotation2label --subject subjid --hemi rh --lobesStrict lobe
mri_aparc2aseg --s subjid --labelwm --annot lobe
and now I have a lobe+aseg.mgz file. How can I
use mri_segstats. You can look in subjid/scripts/recon-all.log for
example command lines (look for the one with wmparc). The command will
require a color table. The ones in the log file will use the default
table, but this will not have the numbers/names of your lobar regions,
so you'll need
There does not appear to be an error at the end.
doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S/SE0003/I -o ct.mgz
mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I
-o ct.mgz
$Id: mri_convert.c,v 1.179.2.2
is PE Dir = UNKNOWN okay?
when i run this command spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg
spm.reg.dat --fsvol orig, i get the following error:
ERROR: Flag spm.reg.dat unrecognized.
--s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig
Hmmm, I don't know why it is doing that. Does it really print using
old after the seg fault was that accidentally pasted in? It should not
be printing that twice, maybe it's a clue.
doug
On 04/02/2012 10:26 AM, Kaveh Kohan wrote:
I have tried and it did not work (the same seg fault, see
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Borzello, Mia wrote:
is PE Dir = UNKNOWN okay?
when i run this command spmregister --s RIH_E1_SurferOutput --mov
ct.mgz--reg spm.reg.dat --fsvol orig, i get the following error:
ERROR: Flag spm.reg.dat
I'm not sure. So the stimulus uses a bow tie instead of a wedge? Maybe
Jon has an idea.
On 04/01/2012 02:22 PM, Kiley Seymour wrote:
Dear freesurfers,
I am wondering whether there is a simple way of analysing retinotopy
data that was collected using a rotating bow-tie stimulus? Or should I
Hi Tina, sorry no one got to your first email. Sometimes emails do fall
through the cracks, so always feel free to repost. It is not clear to me
what command you are running or what you are trying to do. Can you
supply more detail?
doug
On 04/02/2012 11:55 AM, Tina Jeon wrote:
Hi Doug could
K I corrected that. I reran, and this was the error (below)..is there a way to
change the double forward slashes? I'm not sure how that happened.
thanks!
spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig
Log file is ./spmregister.log
Mon Apr 2 13:47:24 EDT 2012
It says that it cannot find a file. Does that file exist?
On 04/02/2012 01:50 PM, Borzello, Mia wrote:
K I corrected that. I reran, and this was the error (below)..is there a way
to change the double forward slashes? I'm not sure how that happened.
thanks!
spmregister --s
Yes it's in RIH_E1_SurferOutput/mri. Would the double forward slashes before
RIH_E1_SurferOutput have effect?
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:51 PM
To: Borzello, Mia
Cc: Freesurfer@nmr.mgh.harvard.edu
It looks like it does not exist
ls /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz
ls:
/autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz: No
such file or directory
make sure your $SUBJECTS_DIR is set correctly
On 04/02/2012 01:53 PM, Borzello, Mia
No worries about that.
I have created some manual cortical labels in freesurfer using tksurfer. The
.labels file containing the vertices of the cortical labels does not correspond
to the labels of the pial surface even though they were drawn on the pial. I
noticed however, that they do
Hi Doug,
Thanks for your reply. However, I was not able to succeed. Can you
give me an extra help?
I created a new color table and I tried the following command:
mri_segstats --seg $SUBJECTS_DIR/Subjid/mri/lobe+aseg.mgz --pv
$SUBJECTS_DIR/Subjid/mri/norm.mgz --excludeid 0 --brain-vol-from-seg
It looks like your registration failed (though it completed without
error). Did you check it with tkregister? I don't think that would
explain the segfault, but it is worth tracking it down.
doug
On 4/2/12 2:54 PM, Kaveh Kohan wrote:
I have also attached the fmri-TO-orig.dat.log maybe that
why don't you use the gray/white contrast map that freesurfer produces?
On 04/02/2012 04:24 PM, John Fredy wrote:
Dear Douglas and David,
I am trying to know the gray-white contrast in images from epileptic
patients. In know that I can use the freesurfer surface to obtain the
coordinates
No it did not work, mri_vol2surf still produces the same error (see below).
In the link below, I have shared the freesurfer results (in the FREESURFER
folder) plus fmri image (in the NITFI folder). I am wondering if there is
anything wrong with my installation of the mri_vol2surf (stable 5). The
Dear Douglas
I was searching for that map, I found the curvature map, the thickness map,
and so on
I don't see information about that map in the freesurfer guides
Any help is welcome
John Ochoa
Bioingeniería
Universidad de Antioquia
On Mon, Apr 2, 2012 at 4:47 PM, Douglas N Greve
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