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 <p...@corticometrics.com>
escreveu:
> External Email - Use Caution
>
> Hmm, 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 <
> fernandahmor...@gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Dear 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
>>
>> fernandahmor...@gmail.com
>> Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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--
Fernanda Hansen P. de Moraes
fernandahmor...@gmail.com
Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
brainvol.stats
Description: Binary data
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