The command below appears to have run successfully but I get a note that the ‘volumesAmygdla.txt’ file could not be moved. See message below at the end of the
freesurfer run. I am using 6.0 (Jan. 18, 2017 release).
Is this expected? 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%
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
On Behalf Of Iglesias Gonzalez, Eugenio
Sent: Tuesday, March 13, 2018 3:22 AM
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0
Looks good to me!
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: Tuesday, March 13, 2018 1:06:25 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0
I need a clarification with the command to run for generating the hippo subfields on 6.0 using both a T1 mprage and T2 space (both 1mm isotropic).
I'd like to run the entire recon-all -all surface and hippo subfields processing stream.
Would this be the correct command:
recon-all -s subject -i dicom.dcm -hippocampal-subfields-T1T2 T2.nii.gz T1T2 -all
Thanks.
Jim
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