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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Tuesday, March 13, 2018 1:06:25 AM To: freesurfer@nmr.mgh.harvard.edumailto: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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