External Email - Use Caution
Thank you very much. It was the version of mri_binarize, and it is processing now. After that, I've got the following error:
*error: could not find stat for lhCortex, lhCortexVol in /your/sub-CC00152AN04/work/sub-CC00152AN04/stats/brainvol.statsroot@computador:/home/fernanda/Documentos/dHCP/freesurfer1# infant_recon_all --s sub-CC00152AN04 --age 4 --segfile sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem87_space-T2w_dseg.nii.gz --masked sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem_space-T2w_brainmask.nii.gz --forceInfantReconAll scripts DIR /usr/local/freesurfer/binPWD /home/fernanda/Documentos/dHCP/freesurfer1*
*Log file is /your/sub-CC00152AN04/work/sub-CC00152AN04_infant_recon_all.2107051123.logseg jul 5 11:23:44 -03 2021--s sub-CC00152AN04 --age 4 --segfile sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem87_space-T2w_dseg.nii.gz --masked sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem_space-T2w_brainmask.nii.gz --forceinfant_recon_all infant-dev-4a14499computadorLinux computador 4.15.0-144-generic #148-Ubuntu SMP Sat May 8 02:33:43 UTC 2021 x86_64 x86_64 x86_64 GNU/LinuxProcessing the following subject: sub-CC00152AN04mri_convert --conform-dc sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem_space-T2w_brainmask.nii.gz /your/sub-CC00152AN04/work/mprage.nu.conf.masked.nii.gz reading from sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem_space-T2w_brainmask.nii.gz...error: niiRead(): error opening file sub-CC00152AN04/sub-CC00152AN04_ses-49200_desc-drawem_space-T2w_brainmask.nii.gz*
Except there is lhCortex in brainvol.stats (attached), but it is negative. We decided to include the segmentation files to improve the surfaces, but it seems to worsen since now we get negative volume values. Do you have any tips on how to improve these surfaces? We've tough about including T1 and T2w images, but I couldn't find a way to do so.
Thank you very much again for the support, Fernanda
Em qui., 1 de jul. de 2021 às 15:48, Paul Wighton paul@corticometrics.com escreveu:
External Email - Use CautionHmm, it looks like the command `mri_binarize` isn't recognizing the `--noverbose` flag. I tested this in my env, and I'm not getting that ("ERROR: Option --noverbose unknown") error.
Could it be that $FREESURFER_HOME is pointing to an older version of FreeSurfer? What does `mri_binarize --version` return?
You can also try running the failed command in isolation:
mri_binarize --match 2 41 --count /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.count.txt --i /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.nii.gz --noverbose-Paul
On Thu, Jul 1, 2021 at 11:41 AM Fernanda Hansen P. de Moraes < fernandahmoraes@gmail.com> wrote:
External Email - Use CautionDear FreeSurfer experts,
I am trying to process some newborn subjects including the segfile. In both situations, including the mask file and using the --forceskullstrip flag I get the following error (log file attached):
*lta_convert successful./home/fernanda/Documentos/dHCP/freesurfer1ERROR: Option --noverbose unknown*
This is the exact command I am running: *infant_recon_all --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz --forceskulltrip --force*
How can I overcome this? Thank you very much. Fernanda Hansen P. de Moraes
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