error: mghRead(/[...]/mri/brain.mgz, -1): could not open file

[yqliu9240]

Hello!

I got this error when running the mri_convert command under the "=====Creating orig and rawavg from input=======" section:

mri_convert -rl /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/proc_VBG/sub-LS/sub-LS_Brain_clean.nii.gz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/real_T1.mgz
Started @ 2022-10-11_21-56-11
pid = 98958 basicPID = 1957
mri_convert -rl /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/proc_VBG/sub-LS/sub-LS_Brain_clean.nii.gz /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/real_T1.mgz
error: mghRead(/Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz, -1): could not open file
error reading from volume /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz
reading from /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/proc_VBG/sub-LS/sub-LS_Brain_clean.nii.gz...
niiRead(): detected input as 64 bit double, reading in as 32 bit float
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 0, -1)
k_ras = (-0, 1, 0)
reading template info from volume /Users/chenglu/Documents/Liu/LS_VBG/VBG_out/output_VBG/sub-LS/sub-LSfastsurfer/sub-LS/mri/brain.mgz...
Success
Finished @ 2022-10-11_21-56-17

And this resulted in a bunch of other errors onward. I checked and found that the brain.mgz file is indeed missing in the mri folder, and I am attaching a screenshot of what my mri folder contains. I am not sure what is missing because the script prior to this part seemed to have run fine. And this is the command I input:
KUL_VBG.sh -S LS -a sub-LS_T1w.nii.gz -n 1 -l LesionMask_T1.nii.gz -z T1 -B 1 -P 2 -v

Please let me know if you have any insights! Thank you in advance.

Yuqi

[BrainTseng]

I think it's because you are using Freesufer v7 rather than v6. The '-make all' flag is no longer used in v7 while the scripts are based on v6.