What is the command you are using when you see the offset? I assume it
is freeview, but what is the full command? Can you send pics of the offset?
On 3/25/2025 11:08 AM, Tommaso Mariani wrote:
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Sorry for the confusion, but as you may have realized I am dealing
with quite an intricated mess.
My main objective is to realize a 3D model of this brain, so that I
need to extract the white matter and pial surfaces, as well as the
other subcortical surfaces. As I am dealing with a bad white matter
segmentation, I would like to check if the new wm surfaces are rebuilt
correctly, though I have a serious problem with that due to this
apparently unfixable offset error. Also, I was wondering if after
fixing the wm.mgz file I should correct somehow the aseg.mgz file with
my new segmentation.
The warning message I reported previously was, I think, the reason
behind this issue.
Thanks in advance,
Tommaso Mariani
Il Mar 25 Mar 2025, 14:39 Douglas N. Greve <dgr...@mgh.harvard.edu> ha
scritto:
Sorry, I'm a little lost as to what problem we are trying to
solve. In your first post, you included some warnings, but I'm not
sure if those warnings are actual errors. Can you restate your
problem?
On 3/17/2025 11:24 AM, Tommaso Mariani wrote:
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The error occurred just immediately after having loaded the
surfaces in freeview. There have been no modifications as the
output is the one that is given straight out of recon-all
command. The issue is encountered both in freesurfer 7.2.0 and
7.4.1 versions.
For what concern the wm edits, I performed some volume edits
hoping to fix the hypo- and hyper-intensity problems, but it is
more of a side question with respect to the main problem, that is
the misregistration of the surfaces.
As for the offset, I mean that the surfaces are not overlapping
the volume images, not the orig.mgz nor the wm.mgz ones, giving
me the feeling that there is a misregistration problem.
I tried to treat it as a tailarach.xfm error, so after following
the tutorial I performed the command
tkregisterfv --s ./subj01 --fstal
Though the recon-all launched after this did not produce anything
different from the beginning.
I tried the command
mri_convert --conform ./subj01/mri/orig.mgz orig_fixed.mgz
And it gives me as output the message:
input_transform(): error reading transform elem [1,1]
input_transform: error reading transform
error: error loading transform from <path_to_file>/talairach.xfm
The xform info prints out this matrix:
x_r = -1.0000 y_r = 0.0000 z_r = 0.0000 c_r = 0.9241
x_a = 0.0000 y_a = 0.0000 z_a = 1.0000 c_a = -5.7364
x_s = 0.0000 y_s = -1.0000 z_s = -0.0000 c_s = -19.9210
If you need anything else please reach me out.
I am available also to schedule a brief call to find out what's
going on, as this issue is what keeps me apart from being able to
use the brain model for an important project.
Thank you in advance,
Tommaso Mariani
Il Lun 17 Mar 2025, 14:56 Douglas N. Greve
<dgr...@mgh.harvard.edu> ha scritto:
Did that error happen before you did anything to the volume?
Can you give a list of commands you used to get to that
point? What do you mean by offset?
On 3/10/2025 4:23 AM, Tommaso Mariani wrote:
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Hi everyone,
I am experiencing a tricky situation in freesurfer. Due to
hypo- and hyper-intensity problems I obtained a bad
reconstruction and I've been working on it since. My first
question is then: do I need to refresh the aseg file after
the wm.mgz intensities modifications?
However I also noticed that when I loaded the surface to
verify the corrections they were all with a significant
offset and this message was printed on the console:
Warning: MatrixInverse failed.
Did not find any volume info
Warning: MatrixInverse failed.
Did not find any volume info
Warning: MatrixInverse failed.
Did not find any volume info
Warning: MatrixInverse failed.
Did not find any volume info
Together with that, I was also unable to obtain the final
parcellization, possibly due to the absence of correlation
between the volumes and surfaces.
I already tried to manually adjust the offset and relaunch
the reconstruction, as suggested in the Freesurfer
documentation for tailarach errors, but it looks like it did
nothing to it.
If you need any file or info to examine the situation
further, feel free to contact me, I would really appreciate
your help.
Thanks in advance,
Tommaso Mariani
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