I'm trying to understand the issues related to mri_convert.
It looks like you did the following:
1. mri_convert aparc.DKTatlas+aseg.deep.mgz aparc.DKTatlas+aseg.deep.nii.gz
2. saved the manually edited as aparc.DKTatlas+aseg.deep.edited.nii.gz
3. mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz
aparc.DKTatlas+aseg.deep.edited.mgz
3. MRIcron complained about the first number is not 1 when you tried to open
aparc.DKTatlas+aseg.deep.edited.mgz (There is no error when you open
aparc.DKTatlas+aseg.deep.mgz)
Which version of Freesurfer are you using? We changed the first number to
encode the mgz_intent_code. In dev version of Freesurfer, the first number is
not always 1 in .mgz. It is '((mgz_intent_code & 0xff ) << 8) | 1' depending on
mgz_intent_code. In your case, it should be mgz_intent_code=0 and first
number=1.
mri_info reports intent if you are using dev version.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Tsigaras, Thanos
Sent: Wednesday, May 15, 2024 4:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue related to converting .nii.gz file to .mgz using
FreeSurfer's mri_convert
External Email - Use Caution
Hello FreeSurfer Developers,
I am using FastSurfer for this processing, but the issue is related to
FreeSurfer's mri_convert function. I wanted to perform some manual segmentation
edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of FastSurfer. Since
ITK-SNAP can't open .mgz files, I used the mri_convert function to convert the
.mgz file to .nii.gz. I performed the edits and tried to rerun FastSurfer using
the manually edited .nii.gz file. I got the error:
"ERROR: Specified segmentation output and conformed image output do not have
same file type.
You passed --asegdkt_segfile directory/to/aparc.DKTatlas+aseg.deep.nii.gz and
--conformed_name directory/to/orig.mgz.
Make sure these have the same file-format and adjust the names passed to the
flags accordingly!"
So I used mri_convert once again to convert the .nii.gz file back to .mgz. When
tried to rerun FastSurfer, I got the error:
"You passed --surf_only or --no_asegdkt, but the whole-brain segmentation
(directory/to/aparc.DKTatlas+aseg.deep.edited.mgz) could not be found."
I also tried opening the .mgz edited file using MRIcron, but I get an error
there as well: "Error: first value in a MGH header should be 1 (got 1) and data
type should be in the range 1..4. (got 10)", which is not the case when I open
the original .mgz file. The way I am using the mri_convert function is simply
"mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz
aparc.DKTatlas+aseg.deep.edited.mgz".
I've searched the list and no similar errors have been reported. Please let me
know if you need more details to help me troubleshoot this issue. For your time
and help I would like to thank you in advance!
Best regards
Thanos Tsigaras
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