Hi Don,
I believe it is from subject ras to talairach ras, and it is definitely
affine (not just rigid). The .lta format is generic enough that it will
list what type of transform it is (e.g. voxel or ras). Here are most of the
relevant types:
#define LINEAR_VOX_TO_VOX 0
#define LINEAR_
Can someone please explain what transformation matrix is contained in
talairach.lta?
Is this the registration matrix from atlas to subject or subject to atlas?
Also, is this matrix for rigid body registration only, or does it have the
affine registration?
Hi,
I'm trying to run mri_motion_correct.fsl to generate the rawavg.mgz file,
and it's failing somewhere before the process completes. I can't seem to
figure out from reading the log file just what is going wrong. Any insight
would be much appreciated!
Thanks
--
mri_motion_correct.fsl log
Hi Jenni,
Sorry for the confusion. We are more familiar with our own
registration/segmentation system, where we edit before segmentation not
after. Anyway, thank you for the advice. We will edit the aseg.mgz
file instead.
Thanks again,
Jared
Jenni Pacheco wrote:
Hi Jared,
It's stil
Hi Derin,
It's probably that you have done something out of order. The easiest way
for me to check this is to see the latest set of processing as dictated by
the subject's scripts/recon-all-status.log. If you paste that into an
email I can see what happened.
Oh, also, were you running this
I'm getting the following error on several of my subjects during the
aparc2aseg stage:
_
[EMAIL PROTECTED] AParc-to-ASeg Sat Jun 9 12:19:58 EDT 2007
/disk/eli/freesurfer/conte_flash/5111
mri_aparc2aseg --s 5111 --ribbon
SUBJECTS_DIR /disk/eli/freesurfer/conte_flash
subj
Hi Jared,
It's still not completely clear to me what you are trying to do. By
segmentation values do you just mean the volumes that will come out of the
aseg.mgz? If thats what you mean you should make these edits to the
aseg.mgz itself.
I'm not certain what will happen if you make these e
I don't know what's going wrong. It looks like you cannot even run a
tcsh script. Do you have a sys admin that you can show this to?
doug
Furlong, Carolyn wrote:
Freesurfer RedHat 9 version
on SUSE Linux 9.3
Cheers
Carolyn
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECT
Jenni,
Another question for you. What is the consequence of running autorecon2
after editing on the brainmask.mgz file itself. You mentioned something
about it not working if we want to obtain surfaces--what did you mean
exactly? CSF surfaces?
Ideally, we are editing the brainmask.mgz fil
Jenni,
Thanks; that was easier than I thought. I also appreciate the warning
about editing the brainmask.mgz. We will be sure to follow your
suggestion and save it as another file before editing it.
Thanks again,
Jared
Jenni Pacheco wrote:
Hi Jared,
Mechanically, yes - you would use t
Hi Jared,
Mechanically, yes - you would use the edit voxels tool and then use the
right button to remove the voxels you do not want.
I'm not sure I understand exactly what you are trying to do - and if you
eventually want to use Freesurfer to obtain surfaces etc, this will not
work. I'd sug
Hi Jenni,
I am trying to edit the greyscale images of the brainmask.mgz. We are
trying to generate an ICC map with only grey/white matter and we need to
exclude a few structures that are not removed in the skull-stripping
step (i.e. some of the cranial nerves, pituitary, etc.). I assume that
Hi Jared,
What happens when you try and edit? What type of editing are you trying
to do? Do you have the right tools selected? I'm going to need a little
bit more information on what you are doing and what is going wrong.
Thanks,
Jenni
On Mon, 11 Jun 2007, Jared Conley wrote:
FreeSurfe
FreeSurfer community,
I am attempting to manually edit brainmask.mgz in TkMedit and cannot
figured out how to do so based on the info in the Wiki. I load the file
in X11 with the command and see the
images just fine, but I cannot seem to manually edit them like I can in
the segmentation fil
Hi,
You don’t need to input the individual subject’s cortical thickness values.
When you run the command you will specify a measure – specify thickness –
Freesurfer will then gather the thickness information for each subject entered
into the FSGD file. You should be able to construct on FS
Thank you for previous help.Now I want to compare the cortical
thickness of the two groups. Mr Pacheco tells me to use the group analysis to
compare. When I read the manual of the group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis";>https://surfer.nmr.mgh.harvard
Freesurfer RedHat 9 version
on SUSE Linux 9.3
Cheers
Carolyn
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 04/06/2007 16:36
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error reg -feat2anat error
what pla
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