External Email - Use Caution
haha. Thanks, works.
On Wed, Aug 25, 2021 at 7:49 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
That must be a record!
Seriously speaking: try adding -all to the command; I guarantee it won’t take 4 seconds this time :-P
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1Q9HyXagUyT4lCMcetbg6yt7AnWPT9pldyicLP8-uK13t8fk...
On Aug 25, 2021, at 12:04, vin rasa vimrasa@gmail.com wrote:
External Email - Use CautionDear 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 (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jlTJcPH2Z123dCmKJ2XGWu2qwl-BatM3mCIgVhwsiDIyhb... https://secure-web.cisco.com/1M8y2jTKqcaZLr3pWIX9ajloxBQ00by9kyM5AmTJvStE6dr5d7BqISQ4OX0IXN53ZgfgLg7fOkHGB7XNRBVvnJnU9CE4TEtRcWizxFRY_pRv26ETLXNIv5BPad84Buj7d3t9drquuWyy6sJ8OVKyynC7ZrWvntCYV05UdwauRqJ-Oj5s7jHBcdgH0rSemnHFVmzXqmZYZiC_RorP1GIfM75Xqw6gwIQhI5qvEOkv_yqtoRk3YLk-9S13Pwu3HA8eCnsiR73m0AaIeaLDbA5qYqg/https%3A%2F%2Fbrainweb.bic.mni.mcgill.ca%2Fanatomic_normal_20.html) .
After i run recon-all, freesurfer ends without any error in 4 seconds.
######
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!
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