Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Hi Knut
you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there.
cheers Bruce
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce
I converted the dicom into 001.mgz. Then I tried to reslice.
mri_convert -rl -i orig/001.mgz -o orig/001.mgz mri_convert -rl -i orig/001.mgz -o orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig/001.mgz... TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) reading template info from volume -i...
mri_read(): couldn't determine type of file /home/knutjb/freesurfer/expo/test/mri/-i error reading from volume -i
Could you please give me an example on how to use mri_convert to reslice please?
Knut J
On 10/15/2012 12:43 AM, Bruce Fischl wrote:
Hi Knut
you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there.
cheers Bruce
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100
is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235
is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
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.
Don't use the -I, just give it an input (the dicoms) and and output
On Oct 15, 2012, at 1:23 AM, Knut J Bjuland knutjbj@hotmail.com wrote:
Hi Bruce
I converted the dicom into 001.mgz. Then I tried to reslice.
mri_convert -rl -i orig/001.mgz -o orig/001.mgz mri_convert -rl -i orig/001.mgz -o orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig/001.mgz... TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) reading template info from volume -i...
mri_read(): couldn't determine type of file /home/knutjb/freesurfer/expo/test/mri/-i error reading from volume -i
Could you please give me an example on how to use mri_convert to reslice please?
Knut J
On 10/15/2012 12:43 AM, Bruce Fischl wrote:
Hi Knut
you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there.
cheers Bruce
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
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.
I am able to convert using mri_convert, but when I try to reslice with mri_convert -rl input output. I get the error message shown below. I according to the documentation I could use mri_convert to reslice, but it does not mention how I should set an vaule for the -rl input. Should I use matlab instead please?
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
mri_convert -rl 001.mgz 001t.mgz mri_convert -rl 001.mgz 001t.mgz
mri_convert: missing output volume name
type mri_convert -u for usage
Knut J
On 10/15/2012 01:23 PM, Bruce Fischl wrote:
Don't use the -I, just give it an input (the dicoms) and and output
On Oct 15, 2012, at 1:23 AM, Knut J Bjuland knutjbj@hotmail.com wrote:
Hi Bruce
I converted the dicom into 001.mgz. Then I tried to reslice.
mri_convert -rl -i orig/001.mgz -o orig/001.mgz mri_convert -rl -i orig/001.mgz -o orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig/001.mgz... TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) reading template info from volume -i...
mri_read(): couldn't determine type of file /home/knutjb/freesurfer/expo/test/mri/-i error reading from volume -i
Could you please give me an example on how to use mri_convert to reslice please?
Knut J
On 10/15/2012 12:43 AM, Bruce Fischl wrote:
Hi Knut
you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there.
cheers Bruce
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
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.
Hi
I think i understood it. Should i use mri_convert -rl template input output
from mri_convert.c printf("reading template info from volume %s...\n", reslice_like_name); template = MRIreadInfo(reslice_like_name); if(template == NULL) { fprintf(stderr, "error reading from volume %s\n", reslice_like_name); exit(1);
Knut J
On 10/15/2012 02:22 PM, Knut J Bjuland wrote:
I am able to convert using mri_convert, but when I try to reslice with mri_convert -rl input output. I get the error message shown below. I according to the documentation I could use mri_convert to reslice, but it does not mention how I should set an vaule for the -rl input. Should I use matlab instead please?
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
mri_convert -rl 001.mgz 001t.mgz mri_convert -rl 001.mgz 001t.mgz
mri_convert: missing output volume name
type mri_convert -u for usage
Knut J
On 10/15/2012 01:23 PM, Bruce Fischl wrote:
Don't use the -I, just give it an input (the dicoms) and and output
On Oct 15, 2012, at 1:23 AM, Knut J Bjuland knutjbj@hotmail.com wrote:
Hi Bruce
I converted the dicom into 001.mgz. Then I tried to reslice.
mri_convert -rl -i orig/001.mgz -o orig/001.mgz mri_convert -rl -i orig/001.mgz -o orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig/001.mgz... TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) reading template info from volume -i...
mri_read(): couldn't determine type of file /home/knutjb/freesurfer/expo/test/mri/-i error reading from volume -i
Could you please give me an example on how to use mri_convert to reslice please?
Knut J
On 10/15/2012 12:43 AM, Bruce Fischl wrote:
Hi Knut
you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there.
cheers Bruce
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
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
yes On Mon, 15 Oct 2012, Knut J Bjuland wrote:
Hi
I think i understood it. Should i use mri_convert -rl template input output
from mri_convert.c printf("reading template info from volume %s...\n", reslice_like_name); template = MRIreadInfo(reslice_like_name); if(template == NULL) { fprintf(stderr, "error reading from volume %s\n", reslice_like_name); exit(1);
Knut J
On 10/15/2012 02:22 PM, Knut J Bjuland wrote:
I am able to convert using mri_convert, but when I try to reslice with mri_convert -rl input output. I get the error message shown below. I according to the documentation I could use mri_convert to reslice, but it does not mention how I should set an vaule for the -rl input. Should I use matlab instead please?
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
mri_convert -rl 001.mgz 001t.mgz mri_convert -rl 001.mgz 001t.mgz
mri_convert: missing output volume name
type mri_convert -u for usage
Knut J
On 10/15/2012 01:23 PM, Bruce Fischl wrote:
Don't use the -I, just give it an input (the dicoms) and and output
On Oct 15, 2012, at 1:23 AM, Knut J Bjuland knutjbj@hotmail.com wrote:
Hi Bruce
I converted the dicom into 001.mgz. Then I tried to reslice.
mri_convert -rl -i orig/001.mgz -o orig/001.mgz mri_convert -rl -i orig/001.mgz -o orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig/001.mgz... TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, 0, 0) reading template info from volume -i...
mri_read(): couldn't determine type of file /home/knutjb/freesurfer/expo/test/mri/-i error reading from volume -i
Could you please give me an example on how to use mri_convert to reslice please?
Knut J
On 10/15/2012 12:43 AM, Bruce Fischl wrote:
Hi Knut
you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there.
cheers Bruce
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series?
Knut J
output
k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Knut J Bjuland