Hello,
I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance.
Best, Lisa Akiyama
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii
mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii
-o 393-2-4.nii
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
rows = 256
cols = 256
TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to 393-2-4.nii...
niiWrite(): error opening file 393-2-4.nii
ERROR: failure writing 393-2-4.nii as volume type 24
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4
mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot
nifti1 -o 393-2-4
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
rows = 256
cols = 256
TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to 393-2-4...
nifti1Write(): error opening file 393-2-4.hdr
ERROR: failure writing 393-2-4 as volume type 20
Are you running out of disk space? What version of FS are you using?
doug
Lisa F. Akiyama wrote:
Hello,
I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance.
Best, Lisa Akiyama
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii -o 393-2-4.nii $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4.nii... niiWrite(): error opening file 393-2-4.nii ERROR: failure writing 393-2-4.nii as volume type 24 % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4 mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nifti1 -o 393-2-4 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4... nifti1Write(): error opening file 393-2-4.hdr ERROR: failure writing 393-2-4 as volume type 20
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I have plenty of disk space available. I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0.
Best, Lisa
On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Are you running out of disk space? What version of FS are you using?
doug
Lisa F. Akiyama wrote:
Hello,
I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance.
Best, Lisa Akiyama
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii
mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii -o 393-2-4.nii $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
rows = 256
cols = 256
TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to 393-2-4.nii...
niiWrite(): error opening file 393-2-4.nii
ERROR: failure writing 393-2-4.nii as volume type 24
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4
mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nifti1 -o 393-2-4 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
rows = 256
cols = 256
TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to 393-2-4...
nifti1Write(): error opening file 393-2-4.hdr
ERROR: failure writing 393-2-4 as volume type 20
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Any suggestions?
Best, Lisa ______________________________
On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama lrisa87@uw.edu wrote:
Hi Doug,
I have plenty of disk space available. I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0.
Best, Lisa
On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Are you running out of disk space? What version of FS are you using?
doug
Lisa F. Akiyama wrote:
Hello,
I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance.
Best, Lisa Akiyama
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii
mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii -o 393-2-4.nii $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
rows = 256
cols = 256
TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to 393-2-4.nii...
niiWrite(): error opening file 393-2-4.nii
ERROR: failure writing 393-2-4.nii as volume type 24
% mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4
mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nifti1 -o 393-2-4 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima...
rows = 256
cols = 256
TR=11.40, TE=4.40, TI=300.00, flip angle=15.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to 393-2-4...
nifti1Write(): error opening file 393-2-4.hdr
ERROR: failure writing 393-2-4 as volume type 20
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Lisa, does the output directory exist and do you have write permissions? Can you convert it to some other format (eg, mgz)?
doug
Lisa F. Akiyama wrote:
Any suggestions?
Best, Lisa ______________________________
On Fri, Oct 8, 2010 at 11:14 AM, Lisa F. Akiyama <lrisa87@uw.edu mailto:lrisa87@uw.edu> wrote:
Hi Doug, I have plenty of disk space available. I am currently running freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.0. Best, Lisa On Fri, Oct 8, 2010 at 11:10 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Are you running out of disk space? What version of FS are you using? doug Lisa F. Akiyama wrote: Hello, I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance. Best, Lisa Akiyama % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii -o 393-2-4.nii $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4.nii... niiWrite(): error opening file 393-2-4.nii ERROR: failure writing 393-2-4.nii as volume type 24 % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4 mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nifti1 -o 393-2-4 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4... nifti1Write(): error opening file 393-2-4.hdr ERROR: failure writing 393-2-4 as volume type 20 ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Lisa F. Akiyama