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Dear Freesurfer Experts, Greetings!
I am trying to run freesurfer on Synthetic T1 data (see in snapshot: *''Simulated T1 image', last sentence in the snapshot*') from Brainweb ( https://secure-web.cisco.com/1M8y2jTKqcaZLr3pWIX9ajloxBQ00by9kyM5AmTJvStE6dr...) .
After i run recon-all, freesurfer ends without any error in 4 seconds.
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recon-all -i $data_dir/$i/mT1t.nii.gz -sd $rdir/results/freesurfer -s $i
Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /results/freesurfer Actual FREESURFER_HOME /FreeSurfer/freesurfer-linux-centos8_x86_64-7.1.1
mri_convert /data/subject54_t1w_p4/mT1t.nii.gz /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz mri_convert /data/subject54_t1w_p4/mT1t.nii.gz /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz reading from /data/subject54_t1w_p4/mT1t.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /results/freesurfer/subject54_t1w_p4/mri/orig/001.mgz... @#@FSTIME 2021:08:25:16:50:08 mri_convert N 2 e 3.56 S 0.08 U 2.84 P 82% M 53580 F 0 R 12154 W 0 c 1228 w 1454 I 83632 O 83736 L 3.30 2.59 1.96 @#@FSLOADPOST 2021:08:25:16:50:12 mri_convert N 2 3.27 2.59 1.97 /results/freesurfer/subject54_t1w_p4/mri/transforms /results/freesurfer/subject54_t1w_p4 /results/freesurfer/subject54_t1w_p4
Started at Mi 25. Aug 16:50:07 CEST 2021 Ended at Mi 25. Aug 16:50:13 CEST 2021 #@#%# recon-all-run-time-hours 0.002 recon-all -s subject54_t1w_p4 finished without error at Mi 25. Aug 16:50:13 CEST 2021 done ######
Please help!
Thanks!
[image: image.png]
