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.
- FreeSurfer version:
freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 2) recon-all.log: see attached
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