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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