Hi Cassie,
It seems to be a problem with mri_robust_register, when trying to allíen the t1 and t2 scans.
Martin, any ideas?

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 Cassandra Wannan <cwannan@student.unimelb.edu.au>
Sent: Thursday, January 18, 2018 10:59:45 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfield segmentation with T1 and T2
 
Hi all,

I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when I try to run the subfield segmentation, I am getting errors. My command line is:

recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz CRC040T1T2 -no-isrunning

but I have also tried:

recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz CRC040T1T2 -no-isrunning

and:

recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2 -no-isrunning

The error I am getting is:

/Applications/freesurfer_v6/bin//mri_robust_register --mov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz --maskmov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz --dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz --lta /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta --noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta
gunzip: can't stat: /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz (/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz): No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192)

MATLAB:badSwitchExpression



Any idea what could be causing the issue? The hippocampal pipeline runs fine without the T2 scan, however I am planning to use the subfield segmentation as a mask for some white matter tractography analysis in FSL, and the dimensions of the output are not close to my nifti files. I was hoping that using the T2 registration would help with this, but can't get it to work! Any help would be greatly appreciated.

Kind regards,

Cassie