mri_coreg error: could not open brainmask.mgz file to register PET image with anatomical - Freesurfer

14 Nov 2024


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Trying to run this command:
mri_coreg --s 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501 --mov 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.nii.gz --reg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.reg.lta
Receiving this output and error:
$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd /blue/babajani.a/SharedFolder_SDT_Fall24/MRI_FreeSurfer_Outputs/ADNI_FreeSurferResults/002_S_0413/MPRAGE_SENSE2/2011-06-16_12_36_58.0/I240808
cmdline mri_coreg --s 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501 --mov 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.nii.gz --reg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.reg.lta
sysname  Linux
hostname login9.ufhpc
machine  x86_64
user     ianlai
dof    6
nsep    2
cras0    1
ftol    0.000000
linmintol    0.001000
bf       1
bflim    30.000000
bfnsamp    30
SmoothRef 0
SatPct    99.990000
MovOOB 0
optschema 1
Seed 53
Reading in mov 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.nii.gz
Reading in ref /apps/freesurfer/7.4.1/subjects/002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/brainmask.mgz
error: mghRead(/apps/freesurfer/7.4.1/subjects/002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/brainmask.mgz, -1): could not open file
I am able to manually download the brainmask.mgz file from that directory and open it in MRIcroGL, wondering what could be the issue here?
Also dealing with a separate issue where when doing mri_gtmpvc \
  --i 002_S_0413_MPRAGE_SENSE2_2011-06 16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/002_S_0413.nii.gz \
  --reg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/pet/template.reg.lta \
  --psf 6 \
  --seg 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/mri/gtmseg.mgz \
  --default-seg-merge \
  --auto-mask 1 .01 \
  --mgx .01 \
  --km-ref 46 47 \
  --km-hb 11 12 50 51 \
  --no-rescale \
  --o 002_S_0413_MPRAGE_SENSE2_2011-06-16_12_36_58.0_I240808_MPRAGE_SENSE2_SENSE_I240808_20110616121849_501/gtmpvc.kmref-46-47.kmhb-11-12-50-51-output,
The output in the gtmstats file seems to be exactly the same when changing km-ref from 7 8 46 47 to 46 47, which I have also attached. Have never done this before so no idea if these values are in a range that seems reasonable or if it means we are providing it a blank file.
Any help would be appreciated,
Ian.
1) FreeSurfer version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
2) recon-all.log: see attached