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