There are several "RAS" coordinates in tkmedit. One is scanner coords
(vol2ras), the other is "volume RAS" coordinates (tkrvox2ras).
doug
On 12/18/12 11:31 PM, octavian lie wrote:
Dear Douglas,
yes, it matches the T1. I am interested though in matching the volume
RAS as it appears in tkmed
I would not just reverse the images. If something is going wrong with
bbregister/mri_vol2vol then it should be fixed. If you don't keep
careful track of these things and know exactly what is happening, then
it will certainly come back to bite you (or me!).
doug
On 12/18/12 11:26 PM, MCLARE
Thanks, that's what I thought might be happening. I'll check a few
different programs to see if I can recover the correct orientation. If
we need to reverse the images, would you recommend doing it before or
after the bbregister step? Would it be sufficient just to change the
header of the image or
That code looks correct. It should match the scanner coordinates. Does
the volume geometry (ie, vox2ras) in the labelMRI.mgz file match that of
the orig.mgz/T1.mgz?
doug
On 12/18/12 6:10 PM, octavian lie wrote:
Dear Douglas,
I adapted the following script to get the RAS coordinate
Hi Donald, it might be the case. If the fmri has an ordering such that
the columns increase as you go from left to right, then they will have
to be reversed when you map them to the orig.mgz. This is generally not
a problem because we always keep track of which side is left and right.
If you ar
Is $SUBJECTS_DIR/$subject exist?
On 12/18/2012 05:13 PM, priyank wrote:
> I have these files in the folder 18135.
> 18135.RS.mgz 18135_RS_register.dat.log
> 18135_RS_register.dat.sum
> 18135.RS+orig.BRIK 18135_RS_register.dat.log.old
> 18135.RS.template.mgz
> 18135.RS+orig.HEAD
PPJ,
Hi, if you want, you can send me the input files (the two aseg's and the
lta) and i can try to replicate the segfault in a debugger.
also, if you want, there is a beta of the upcoming v5.2 which is posted
here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
which you could
Hi,
tried to use control points to improve the segmentation of the putamen in the
difficult area between putamen,claustrum & insula. adding some white matter
control points does not seem to insluence the aseg segmentation. control points
are set to 110 after reprocessing
with recon-all -autore
Actually I received the reconned data. I did bbregistration: bbregister
--s ${sub}_FS --mov $main_path/$sub/${sub}.RS.mgz --reg
${sub}_RS_register.dat --init-fsl --bold --frame $framenum --nearest --o
${sub}.RS.template.mgz
where $sub is subject id, which is 18135.
And now all the files are in
you don't need to move them. Where is the subject data that you ran
recon-all on? You need to setenv SUBJECTS_DIR to point to that directory
(the one that contains the subject you reconned)
cheers
Bruce
On Tue, 18 Dec 2012,
priyank wrote:
I have these files in the folder 18135.
18135.RS.m
I have these files in the folder 18135.
18135.RS.mgz 18135_RS_register.dat.log 18135_RS_register.dat.sum
18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz
18135.RS+orig.HEAD 18135_RS_register.dat.mincost
18135_RS_register.dat 18135_RS_register.dat.param
and
what is your SUBJECTS_DIR env variable?
On Tue, 18 Dec 2012, priyank wrote:
> Hi,
> I am using the command to check my registration and getting this
> error message: could not find orig as either mgz or COR. This is the
> command I am using.
> tkregister2 --mov 18135.RS.mgz --reg 18135
Hi,
I am using the command to check my registration and getting this
error message: could not find orig as either mgz or COR. This is the
command I am using.
tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf
OUTPUT-
I don't know that function. vox2ras0 is used when you have 0-based
indices (as in C) and vox2ras1 is used when you have 1-based indices
(as in matlab).
doug
On 12/18/2012 02:26 PM, octavian lie wrote:
> Can I use your function xyzlab for this? If yes, I see that uses
> vox2ras0 instead of v
No, they are not in any atlas space. The space is "native" in that 1mm
in the image represents 1mm in the subject's brain. Therefore, you can
directly compare the hippo volume across subjects.
doug
On 12/18/2012 12:59 PM, Mojdeh Zamyadi wrote:
> Hi Doug,
>
> Thanks for the quick reply. I actual
Hi Mojdeh
they are not in atlas space and the volumes are for that subject, so you
shouldn't have to do anything if I understand you correctly
cheers
Bruce
On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote:
> Hi Doug,
>
> Thanks for the quick reply. I actually saw this link before first
> posting my q
Hi Doug,
Thanks for the quick reply. I actually saw this link before first
posting my question but it doesn't quite answer my question. What I want
to know is whether the T1.mgz & aseg.mgz files are in an atlas space? if
that's the case, it means the segmentation for all my subjects are in
the
Use the matlab ind2sub command
doug
On 12/18/2012 12:38 PM, octavian lie wrote:
> Dear Douglas,
>
>
> How do I convert the index to its CRS correspondent?
> I could think of using in matlab something like
> ind=c+r*255+s* 255^2
> then using floor () to obtain c,r,s, but seems convoluted, is there
Can you send the recon-all.log file (located in the subject/scripts folder).
doug
On 12/18/2012 11:41 AM, Tudor Popescu wrote:
> Hello,
>
> First of all, apologies for asking for help three times today! THings
> will hopefully become clearer once I get used to FS a bit; I really do
> appreciat
Hi Linda, check your color table to make sure that the entry indices are
in numerical order without a gap (i,e 1 2 3 4 5 is ok, but 1 3 4 5 would
not be).
doug
On 12/18/2012 11:49 AM, Linda Douw wrote:
> Hi experts,
>
> I have a bunch of custom-made labels (from the ConnectomeMapper software)
>
Hi Andrea, sorry, I don't quite follow what your question is. If I
understand correctly, you have an image that is 70,30,70 that you want
to analyze in FreeSurfer? If that covers the whole head, then the voxel
size is probably going to be to large to get good surfaces.
doug
On 12/18/2012 10:34
Hi Mojdeh, try looking at this doc
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
> Hi all,
>
> I want to segment the hippocampus into head/body/tail in itk SNAP using
> the hippocampus mask that I create from the result of recon-al
Hi Tudor,
Can you run mri_concat from the command line with the --debug option
first. Send us the FULL command line and the full terminal output.
doug
On 12/18/2012 09:35 AM, Tudor Popescu wrote:
> Hello everyone,
>
> I tried doing the QDEC group analysis tutorial, however after doing
> everyt
On 12/18/2012 06:48 AM, Tudor Popescu wrote:
> Dear all,
>
> I have some questions I could not find an answer to myself, I'd really
> appreciate it if anyone could help out.
>
> 1) How should recon-all be used to process all subjects' data (i.e.
> obtain the surface for each subject) before taki
If you load the volume in with MRIread
a = MRIread('yourvolume.mgz');
a.vox2ras1 is the one-based vox2ras matrix which takes a 1-based column,
row, slice and converts it to RAS. So you just need to convert your
indices to col, row, slice and apply this matrix.
doug
On 12/17/2012 06:53 PM, oct
Hi experts,
I have a bunch of custom-made labels (from the ConnectomeMapper software)
that I want to put into a single annotation file. Therefore, I create a
color-lookup table and use mris_label2annot as follows:
mris_label2annot --s fsaveragec --h lh --ctab lh_laus500_clut_new.txt --a
laus500_f
Hello,
First of all, apologies for asking for help three times today! THings will
hopefully become clearer once I get used to FS a bit; I really do
appreciate the amazing support provided by the team behind FreeSurfer!
I ran the following command on one of my structurals:
*recon-all -subject M01
Hi all,
I want to segment the hippocampus into head/body/tail in itk SNAP using
the hippocampus mask that I create from the result of recon-all
segmentation. My question is, are the T1.mgz and aseg.mgz files in the
native space of the image or in the atlas space? I know the voxel size
is diffe
Hello FS experts,
I have a problem to solve.
I have a binary image.nii to estimate the segmentation of freesurfer.
His size is 70,30,70 but format nii includes other information: resolution,
origin, ...
so, when I convert image.nii to image.mgz, I see an image of size256, 256, 256,
(256 slides
I'm having a segfault with mri_cc it's happening sometimes using FreeSurfer
5.1
Searching the mailing list I saw a similar problem in 2008 but with no
answers.
The relevant portion of recon-all.log:
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/usr/local/freesurfer/subjects/c70eb728
Hello everyone,
I tried doing the QDEC group analysis tutorial, however after doing
everything as instructed in the tutorial, when pressing Analyze I get the
error message:
*Error in Analyze: command failed: mri_concat
/media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.m
Dear all,
I have some questions I could not find an answer to myself, I'd really
appreciate it if anyone could help out.
1) How should recon-all be used to process all subjects' data (i.e. obtain
the surface for each subject) before taking it to QDEC (or command prompt)
for a group thickness anal
Dear experts,
In the recommended reconstructions (
http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) it is
stated that one should do CPs first and than do skullstripping.
Why is that?
However the recon-all after CPs (recon-all -autorecon2-cp -autorecon3
-subjid) includes less (o
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