Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40
INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/ dt_recon logfile Tue Mar 15 20:37:35 PDT 2016 VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/ cd /Users/jasminalves/Desktop/data/40 /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 Jasmins-MacBook-Pro.local jasminalves /Applications/Utilities/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Tue Mar 15 20:37:35 PDT 2016 cd /Users/jasminalves/Desktop/data/40 mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz... TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999929, 0.0116015, -0.00282784) j_ras = (0.0115984, 0.999932, 0.00109136) k_ras = (-0.00284031, -0.00105848, 0.999995) writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii... cd /Users/jasminalves/Desktop/data/40 mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz Jasmins-MacBook-Pro:40 jasminalves$ On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Can you send the full terminal output from when you run dt_recon with > the nifti as input? > > On 03/15/2016 03:07 PM, Jasmin Alves wrote: > > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw > > dicom data using dcm2nii. > > > > Response for: "What happens if you run mri_info DTI.nii.gz" > > > > Volume information for DTI.nii.gz > > > > type: nii > > > > dimensions: 128 x 128 x 70 x 65 > > > > voxel sizes: 2.0000, 2.0000, 2.0000 > > > > type: FLOAT (3) > > > > fov: 256.000 > > > > dof: 0 > > > > xstart: -128.0, xend: 128.0 > > > > ystart: -128.0, yend: 128.0 > > > > zstart: -70.0, zend: 70.0 > > > > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip > > angle: 0.00 degrees > > > > nframes: 65 > > > > PhEncDir: UNKNOWN > > > > ras xform present > > > > xform info: x_r = -0.9999, y_r = 0.0116, z_r = -0.0028, c_r = > > -0.4290 > > > > : x_a = 0.0116, y_a = 0.9999, z_a = -0.0011, c_a = > > 4.1548 > > > > : x_s = -0.0028, y_s = 0.0011, z_s = 1.0000, c_s = > > 30.9622 > > > > Orientation : LAS > > > > Primary Slice Direction: axial > > > > voxel to ras transform: > > > > -1.9999 0.0232 -0.0057 126.2761 > > > > 0.0232 1.9999 -0.0021 -125.2474 > > > > -0.0057 0.0022 2.0000 -38.8153 > > > > 0.0000 0.0000 0.0000 1.0000 > > > > voxel-to-ras determinant -8 > > > > ras to voxel transform: > > > > -0.5000 0.0058 -0.0014 63.8052 > > > > 0.0058 0.5000 0.0005 61.9083 > > > > -0.0014 -0.0005 0.5000 19.5206 > > > > 0.0000 0.0000 0.0000 1.0000 > > > > > > On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > How was DTI.nii.gz created? What happens if you run > > mri_info DTI.nii.gz > > > > If the DICOM is a siemens dicom but has been stripped of special > > siemens > > info, then we cannot unpack it > > > > > > On 03/15/2016 02:02 PM, Jasmin Alves wrote: > > > > > > Still get the same error: > > > > > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not > > > contain a Siemens ASCII header > > > > > > has this file been anonymized? > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > > > > The error I get when running in nifti format is actually found > > in the > > > log file. > > > > > > ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a > dicom > > > file or some other problem > > > > > > > > > > > > > > > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > if you run > > > mri_convert 00010001 deleteme.nii > > > what happens? > > > > > > what is the error when running with nifti? > > > > > > > > > On 03/14/2016 05:59 PM, Jasmin Alves wrote: > > > > > > > > Dear Freesurfer experts, > > > > > > > > FREESURFER_HOME: /Applications/freesurfer > > > > > > > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > > > > > > > Kernel info: Darwin 14.5.0 x86_64 > > > > > > > > > > > > I received the following error while running the dt_recon --i > > > 00010001 > > > > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40. > > > > > > > > The participant is 40. > > > > > > > > And I received the following error: > > > > > > > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 > > does not > > > > contain a Siemens ASCII header has this file been anonymized? > > > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > > > > > > > I did notice on previous threads this is a common error > > that occurs, > > > > but the files I have were directly exported from our > > siemens scanner > > > > via Osirix. I also tried running dt_recon using nifti > > format but > > > that > > > > resulted in an error as well. Is there anything else I can > do? > > > > > > > > Thanks, > > > > > > > > Jasmin > > > > > > > > > > > > -- > > > > Jasmin Alves > > > > Predoctoral Student > > > > Medical Biology Graduate Program > > > > University of Southern California > > > > jal...@usc.edu <mailto:jal...@usc.edu> > > <mailto:jal...@usc.edu <mailto:jal...@usc.edu>> > > <mailto:jal...@usc.edu <mailto:jal...@usc.edu> > > > <mailto:jal...@usc.edu <mailto:jal...@usc.edu>>> > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e= > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > < > https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=JEMNVqaCWFyhIBYx595b2hHndKvujFMwSozkDcSGbIU&e= > > > > > > > < > https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=GpEEtkD1BnMJzWOlXkecPjAGlZyRbfpUD2D7FRdXC7o&e= > > > > > > FileDrop: > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=K5-xLMTkmvO4akwQ1yNQhCyFkQ3yeGkg4bIrAd6xArI&e= > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > < > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=0iHNzzA_YcOmdUVFE4ZkioQ3jzIzzE4UGUhUbOdZ2Vo&e= > > > > > > > < > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=hwwSX9tQxQeWZq4mK8Rpb7vYFBqUftnwxx3egrwmBdM&e= > > > > > > Outgoing: > > > > > > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=XP0Fok4OAHAC7DYzCOyUrPu9PLDR_RULGfbnE8c0hNs&e= > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e= > > > > > > > > > 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 > > > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=kr8DioqB8ZA30rJ-OJWi601znNchJg-CCjnpQKvHYhI&e= > > > . 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. > > > > > > > > > > > > > > > -- > > > Jasmin Alves > > > Predoctoral Student > > > Medical Biology Graduate Program > > > University of Southern California > > >jal...@usc.edu <mailto:jal...@usc.edu> <mailto:jal...@usc.edu > > <mailto:jal...@usc.edu>> > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&e= > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > < > https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=JEMNVqaCWFyhIBYx595b2hHndKvujFMwSozkDcSGbIU&e= > > > > FileDrop: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=_JLzMZF53oLGA-oQwL-7Z2q1LachFF3-2TIEkkTGdcc&e= > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > < > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=0iHNzzA_YcOmdUVFE4ZkioQ3jzIzzE4UGUhUbOdZ2Vo&e= > > > > Outgoing: > > > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=JLD-nXWKsjEKCvgUh1sKRBa_OnTn05cFSq8QsAEegp8&e= > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&e= > > > > > > 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 > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=8mDIOhbTFEY_zJuCIowaFDgmQ2VVcBIkkgeCv1DGyfQ&e= > > . 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. > > > > > > > > > > -- > > Jasmin Alves > > Predoctoral Student > > Medical Biology Graduate Program > > University of Southern California > > jal...@usc.edu <mailto:jal...@usc.edu> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=QmXOcbmhxk50ab8-qFqSUJq79Xrd-iAPmWQlf_34OVo&e= > > -- > 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=bELNK7f9QHMufVuMX2ijfEBXSpDDdKM8vNr0Jsb-Y5M&e= > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=-5VhrwXWwPpKox8-jmZl_1_Ucv9MQtpYXaGlDDWtkoo&e= > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=QmXOcbmhxk50ab8-qFqSUJq79Xrd-iAPmWQlf_34OVo&e= > > > 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 > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=OD8AVSmvHiAKa7hyRNMRoHXcW7kar7LqwI4rHhtPjSo&e= > . 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. > > -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu
_______________________________________________ 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.
