I used freeview, and I tried both to load it through freeview -f <file_path> and by loading it straight from the ribbon menu.

Il Mer 26 Mar 2025, 14:19 Douglas N. Greve <dgreve@mgh.harvard.edu> ha scritto:

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 <dgreve@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 <dgreve@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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