Thank for the confirmation.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
On Behalf Of Iglesias Gonzalez, Eugenio
Sent: Monday, March 19, 2018 11:26 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release
Yes! It's all fine. It was just a placeholder for the segmentation of the nuclei of the amygdala, which is available in there development version.
Cheers
Eugenio
Sent from my phone, please excuse brevity and typos
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edu>
Sent: Monday, March 19, 2018 4:22:06 PM
To: Freesurfer support list
Subject: [Freesurfer] no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release
I ran the following command to generate surfaces and hippo subfields on 6.0 (Jan. 2017 version) using both a T1 mprage and T2 space (both 1mm isotropic).
recon-all –s subject –i dicom.dcm –hippocampal-subfields-T1T2 T2.nii.gz T1T2 –all.
The command appears to have run successfully but I get a note at the end of the processing stream that there is no file ‘volumesAmygdla.txt’ (see screen message below).
Is this expected even though I’m not using the later developmental release? Jim
-----------------------------------------------------------------------
Not resampling, only changing vox2ras matrix
To check registration, run:
tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg
mri_vol2vol done
mv: cannot stat 'volumesAmygdala.txt':
No such file or directory
Everything done!
It took 1921.1425 seconds
Started at Wed Mar 14 17:04:06 CDT 2018
Ended at Thu Mar 15 05:35:24 CDT 2018
#@#%# recon-all-run-time-hours 12.522
recon-all -s neo321e_fs finished without
error at Thu Mar 15 05:35:24 CDT 2018
done
jimalex@linux1%
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