Does /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, exist?
Usually people are not putting their subjects in the FS subjects folder, so I'm wondering if your SUBJECTS_DIR is set correctly.

On 11/14/2024 3:38 PM, Lai, Ian M. wrote:

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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
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