Not sure. First, let's make sure that the dicom can be converted with mri_convert 01001/0/2/1.dcm deleteme.mgh
try that and let us know if it succeeds On 07/14/2017 04:13 AM, Lars M. Rimol wrote: > Hi, > > I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting > error messages and some strange behavior: > > > ls 01001/0/2/ > 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm > 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm > 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm 4.dcm 55.dcm 60.dcm > 66.dcm 71.dcm 77.dcm 82.dcm 88.dcm 93.dcm 99.dcm > 101.dcm 107.dcm 112.dcm 118.dcm 123.dcm 129.dcm 134.dcm > 13.dcm 145.dcm 150.dcm 156.dcm 161.dcm 167.dcm 172.dcm 18.dcm > 23.dcm 29.dcm 34.dcm 3.dcm 45.dcm 50.dcm 56.dcm 61.dcm 67.dcm > 72.dcm 78.dcm 83.dcm 89.dcm 94.dcm 9.dcm > 102.dcm 108.dcm 113.dcm 119.dcm 124.dcm 12.dcm 135.dcm > 140.dcm 146.dcm 151.dcm 157.dcm 162.dcm 168.dcm 173.dcm > 19.dcm 24.dcm 2.dcm 35.dcm 40.dcm 46.dcm 51.dcm 57.dcm 62.dcm > 68.dcm 73.dcm 79.dcm 84.dcm 8.dcm 95.dcm > 103.dcm 109.dcm 114.dcm 11.dcm 125.dcm 130.dcm 136.dcm > 141.dcm 147.dcm 152.dcm 158.dcm 163.dcm 169.dcm 174.dcm > 1.dcm 25.dcm 30.dcm 36.dcm 41.dcm 47.dcm 52.dcm 58.dcm 63.dcm > 69.dcm 74.dcm 7.dcm 85.dcm 90.dcm 96.dcm > 104.dcm 10.dcm 115.dcm 120.dcm 126.dcm 131.dcm 137.dcm > 142.dcm 148.dcm 153.dcm 159.dcm 164.dcm 16.dcm 175.dcm > 20.dcm 26.dcm 31.dcm 37.dcm 42.dcm 48.dcm 53.dcm 59.dcm 64.dcm > 6.dcm 75.dcm 80.dcm 86.dcm 91.dcm 97.dcm > 105.dcm 110.dcm 116.dcm 121.dcm 127.dcm 132.dcm 138.dcm > 143.dcm 149.dcm 154.dcm 15.dcm 165.dcm 170.dcm 176.dcm > 21.dcm 27.dcm 32.dcm 38.dcm 43.dcm 49.dcm 54.dcm 5.dcm 65.dcm > 70.dcm 76.dcm 81.dcm 87.dcm 92.dcm 98.dcm > > > recon-all -subject 1001_c1 -i 01001/0/2/1.dcm -all > > > ................................ > writing to > /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor fr. 14. juli 10:04:21 +0200 2017 > ERROR: no run data found in > /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri. Make sure to > have a volume called 001.mgz in > /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig. > If you have a second run of data call it 002.mgz, etc. > See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > Linux compute-16-36.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 > 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s �1001_c1 exited with ERRORS at fr. 14. juli 10:04:21 > +0200 2017 > > > Not sure why it crashes, and why does it add "?" to the subject name? > > > Thank you! > > > > sincerely yours, > > Lars M. Rimol, PhD > Senior researcher, > Norwegian Advisory Unit for functional MRI > Department of Radiology, > St. Olav's University hospital, > 7006 Trondheim, > Norway > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
