[Freesurfer] Problem with mriconvert
Hello, We are medicine students who are using freesurfer for research. We had been using freesurfer in Ubuntu 12.02 without encountering any trouble; recently we updated to 14.04. Now, when we attempt to convert a mgz file to nii using mriconvert, we have an error regarding failure to write the files .nii The command we are using is as follows: mri_convert ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_ cortical_seg.nii The error message we find is this one: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.74975e-08, 0) j_ras = (0, 0, -1) k_ras = (1.21072e-08, 1, 0) writing to ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii... niiWrite(): error opening file ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii ERROR: failure writing ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii We really could use your help, since we can't find any solution in the Internet. Thanks in advance for your attention. Regards, Óscar and Alba ___ 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.
Re: [Freesurfer] Problem with mriconvert
Do you have write permission to that folder? Is the disk full? On 03/02/2016 11:12 AM, Óscar Soto Angona wrote: > Hello, > > We are medicine students who are using freesurfer for research. We had > been using freesurfer in Ubuntu 12.02 without encountering any > trouble; recently we updated to 14.04. > > Now, when we attempt to convert a mgz file to nii using mriconvert, we > have an error regarding failure to write the files .nii > > The command we are using is as follows: > > mri_convert > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz > > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.nii > > > The error message we find is this one: > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -4.74975e-08, 0) > j_ras = (0, 0, -1) > k_ras = (1.21072e-08, 1, 0) > writing to > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii... > niiWrite(): error opening file > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii > ERROR: failure writing > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii > > > We really could use your help, since we can't find any solution in the > Internet. Thanks in advance for your attention. > > > Regards, > > > Óscar and Alba > > > ___ > 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.
Re: [Freesurfer] Problem with mriconvert
Hi, Yes, we have permission, and the disk have plenty of space :/ On Thu, Mar 3, 2016 at 6:30 PM, Douglas N Greve wrote: > Do you have write permission to that folder? Is the disk full? > > On 03/02/2016 11:12 AM, Óscar Soto Angona wrote: > > Hello, > > > > We are medicine students who are using freesurfer for research. We had > > been using freesurfer in Ubuntu 12.02 without encountering any > > trouble; recently we updated to 14.04. > > > > Now, when we attempt to convert a mgz file to nii using mriconvert, we > > have an error regarding failure to write the files .nii > > > > The command we are using is as follows: > > > > mri_convert > > > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz > > > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.nii > > > > > > The error message we find is this one: > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from > > > /home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, -4.74975e-08, 0) > > j_ras = (0, 0, -1) > > k_ras = (1.21072e-08, 1, 0) > > writing to > > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii... > > niiWrite(): error opening file > > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii > > ERROR: failure writing > > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii > > > > > > We really could use your help, since we can't find any solution in the > > Internet. Thanks in advance for your attention. > > > > > > Regards, > > > > > > Óscar and Alba > > > > > > ___ > > 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. > > ___ 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.
Re: [Freesurfer] Problem with mriconvert
what if you change the destination directory? Does it work? On Fri, 4 Mar 2016, Óscar Soto Angona wrote: Hi, Yes, we have permission, and the disk have plenty of space :/ On Thu, Mar 3, 2016 at 6:30 PM, Douglas N Greve wrote: Do you have write permission to that folder? Is the disk full? On 03/02/2016 11:12 AM, Óscar Soto Angona wrote: > Hello, > > We are medicine students who are using freesurfer for research. We had > been using freesurfer in Ubuntu 12.02 without encountering any > trouble; recently we updated to 14.04. > > Now, when we attempt to convert a mgz file to nii using mriconvert, we > have an error regarding failure to write the files .nii > > The command we are using is as follows: > > mri_convert >../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_se g.mgz >../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_se g.nii > > > The error message we find is this one: > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from >/home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/ C2090_cortical_seg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -4.74975e-08, 0) > j_ras = (0, 0, -1) > k_ras = (1.21072e-08, 1, 0) > writing to > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii... > niiWrite(): error opening file > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii > ERROR: failure writing > ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii > > > We really could use your help, since we can't find any solution in the > Internet. Thanks in advance for your attention. > > > Regards, > > > Óscar and Alba > > > ___ > 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. ___ 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.
