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
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