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:
External Email - Use Caution
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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