Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant
*recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/FreeSurferSubjects/101
mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz
mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012 *
Hi Hemant
sorry for missing your previous post. I'm not sure what to tell you though, if the direction cosines are nans that's going to be trouble. You could still visualize your data in a slice viewer, but you may never be able to tell left from right. Where did you get the dicoms? Are they right off the scanner, or did they go through some other package first? I don't think we've seen this problem before.
cheers Bruce
On Fri, 10 Feb 2012, Hemant Bokil wrote:
Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant
recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/FreeSurferSubjects/101
mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz
mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012
Hi Bruce, Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't get the direction cosines. Which fields is it looking for in the dicom metadata ? When I load the slices in Matlab, I can see ImagePositionPatient and ImageOrientationPatient and SliceLocation and they all seem reasonable. Oddly this problem occurs on some datasets and not others even though I can't spot obvious differences in the dicom metadata fields.
As for your question regarding data origin, the problematic datasets are straight from the scanners as far as I know (although they were acquired from various hospitals as part of a long-done clinical study, so who knows..). Hemant
On Fri, Feb 10, 2012 at 4:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Hemant
sorry for missing your previous post. I'm not sure what to tell you though, if the direction cosines are nans that's going to be trouble. You could still visualize your data in a slice viewer, but you may never be able to tell left from right. Where did you get the dicoms? Are they right off the scanner, or did they go through some other package first? I don't think we've seen this problem before.
cheers Bruce
On Fri, 10 Feb 2012, Hemant Bokil wrote:
Hello,
I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant
recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_** ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/**FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/**FreeSurferSubjects/101
mri_convert /home/hemant/DICOM_MR_DATA/**101/1000430544_ST3445_SR10_**V10000.DICOM /home/hemant/**FreeSurferSubjects/101/mri/**orig/001.mgz
mri_convert /home/hemant/DICOM_MR_DATA/**101/1000430544_ST3445_SR10_**V10000.DICOM /home/hemant/**FreeSurferSubjects/101/mri/**orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/**101/1000430544_ST3445_SR10_**V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/**101/1000430544_ST3445_SR10_** V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012
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/**compliancelinehttp://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.
hmmm, I'll wait for Doug to comment as he knows far more about the dicom stuff than I do
Bruce On Fri, 10 Feb 2012, Hemant Bokil wrote:
Hi Bruce, Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't get the direction cosines. Which fields is it looking for in the dicom metadata ? When I load the slices in Matlab, I can see ImagePositionPatient and ImageOrientationPatient and SliceLocation and they all seem reasonable. Oddly this problem occurs on some datasets and not others even though I can't spot obvious differences in the dicom metadata fields.
As for your question regarding data origin, the problematic datasets are straight from the scanners as far as I know (although they were acquired from various hospitals as part of a long-done clinical study, so who knows..). Hemant
On Fri, Feb 10, 2012 at 4:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Hemant
sorry for missing your previous post. I'm not sure what to tell you though, if the direction cosines are nans that's going to be trouble. You could still visualize your data in a slice viewer, but you may never be able to tell left from right. Where did you get the dicoms? Are they right off the scanner, or did they go through some other package first? I don't think we've seen this problem before. cheers Bruce On Fri, 10 Feb 2012, Hemant Bokil wrote: Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/FreeSurferSubjects/101 mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012The 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 Hemant, sorry for the delay in getting back to you. I'm not sure what could be causing the problem. FreeSurfer definitely reads the direction cosines from the dicom. If you upload the dicom volume to our file drop, I'll take a look. filedrop url is at the end of this email. doug
Hemant Bokil wrote:
Hi Bruce, Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't get the direction cosines. Which fields is it looking for in the dicom metadata ? When I load the slices in Matlab, I can see ImagePositionPatient and ImageOrientationPatient and SliceLocation and they all seem reasonable. Oddly this problem occurs on some datasets and not others even though I can't spot obvious differences in the dicom metadata fields.
As for your question regarding data origin, the problematic datasets are straight from the scanners as far as I know (although they were acquired from various hospitals as part of a long-done clinical study, so who knows..). Hemant
On Fri, Feb 10, 2012 at 4:12 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Hemant sorry for missing your previous post. I'm not sure what to tell you though, if the direction cosines are nans that's going to be trouble. You could still visualize your data in a slice viewer, but you may never be able to tell left from right. Where did you get the dicoms? Are they right off the scanner, or did they go through some other package first? I don't think we've seen this problem before. cheers Bruce On Fri, 10 Feb 2012, Hemant Bokil wrote: Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_ ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_ 64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_ 64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/ FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/ FreeSurferSubjects/101 mri_convert /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM /home/hemant/ FreeSurferSubjects/101/mri/ orig/001.mgz mri_convert /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM /home/hemant/ FreeSurferSubjects/101/mri/ orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012 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 <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
Thanks, Bruce, Doug, I will check how to do that. Hemant
On Thu, Feb 16, 2012 at 11:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Hemant, sorry for the delay in getting back to you. I'm not sure what could be causing the problem. FreeSurfer definitely reads the direction cosines from the dicom. If you upload the dicom volume to our file drop, I'll take a look. filedrop url is at the end of this email. doug
Hemant Bokil wrote:
Hi Bruce, Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't get the direction cosines. Which fields is it looking for in the dicom metadata ? When I load the slices in Matlab, I can see ImagePositionPatient and ImageOrientationPatient and SliceLocation and they all seem reasonable. Oddly this problem occurs on some datasets and not others even though I can't spot obvious differences in the dicom metadata fields.
As for your question regarding data origin, the problematic datasets are straight from the scanners as far as I know (although they were acquired from various hospitals as part of a long-done clinical study, so who knows..). Hemant
On Fri, Feb 10, 2012 at 4:12 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto: fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>> wrote:
Hi Hemant
sorry for missing your previous post. I'm not sure what to tell you though, if the direction cosines are nans that's going to be trouble. You could still visualize your data in a slice viewer, but you may never be able to tell left from right. Where did you get the dicoms? Are they right off the scanner, or did they go through some other package first? I don't think we've seen this problem before.
cheers Bruce
On Fri, 10 Feb 2012, Hemant Bokil wrote:
Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_ ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_ 64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_ 64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/ FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/ FreeSurferSubjects/101 mri_convert /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM /home/hemant/ FreeSurferSubjects/101/mri/ orig/001.mgz mri_convert /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM /home/hemant/ FreeSurferSubjects/101/mri/ orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/ 101/1000430544_ST3445_SR10_ V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012The 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 <http://www.partners.org/**compliancelinehttp://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/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Hemant Bokil