Hello,
I am new to freesurfer. I went through the Wiki and FAQ's but couldn't find information on
the format of the input for recon-all. I understand that one of the input files must have a ".dcm" extension.
I have a CD which has MRI scanned images.
The folder structure is E:\DICOM\PA000000\ST000000
under ST000000 there are 8 folders SE000000, SE000001,... SE000008
Each SE00000* folder has files IM000000, IM000001, ...
There are about 180 files all together in the 8 folders.
At first there were no extentions to any of the image files, so, I add an extension ".dcm" to all of the files.
I ran recon-all got an error.
the error.log file has "MRIresample(): source matrix has zero determinant; matrix is:"
Am I on the right path ? or am I missing something ?
So I need to convert the images before running the recon ?
I see that only 8 files in the first folder in the series are being read, Do I need to input the files in a different structure ?
I am trying to do a proof of concept with our data before buying a machine for running Linux CentOS for freesurfer.
recon-all command generates the following
[freesurfer@localhost freesurfer]# recon-all -i Documents/Sub_9884/SE000000/IM000000.dcm -subject test -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/test
mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm /usr/local/freesurfer/subjects/test/mri/orig/001.mgz
mri_convert /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm /usr/local/freesurfer/subjects/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/freesurfer/Documents/Sub_9884/SE000000/IM000000.dcm...
Getting Series No
INFO: Found 8 files in /home/freesurfer/Documents/Sub_9884/SE000000
INFO: Scanning for Series Number 1
Scanning Directory
INFO: found 6 files in series
INFO: loading series header info.
RunNo = 0
INFO: sorting.
INFO: (512 512 6), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName /home/freesurfer/Documents/Sub_9884/SE000000/IM000004.dcm
Identification
NumarisVer syngo MR A35 4VA35A
ScannerModel Symphony
PatientName 9884^9884^^^
Date and time
StudyDate 20131203
StudyTime 082101.937000
SeriesTime 082131.093000
AcqTime 082138.020010
Acquisition parameters
PulseSeq *fl2d1
Protocol LOCALIZER 3 PLANE
PhEncDir ROW
EchoNo 0
FlipAngle 40
EchoTime 5
InversionTime -1
RepetitionTime 20
PhEncFOV 280
ReadoutFOV 280
Image information
RunNo 0
SeriesNo 1
ImageNo 3
NImageRows 512
NImageCols 512
NFrames 1
SliceArraylSize 6
IsMosaic 0
ImgPos 140.0000 6.0000 140.0000
VolRes 0.5469 0.5469 12.0000
VolDim 512 512 6
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -0.0000 -1.0000
Vs -1.0000 -0.0000 0.0000
VolCenter -36.0000 6.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00
warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
warning: output volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
writing to /usr/local/freesurfer/subjects/test/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Mar 6 11:02:35 CST 2014
Found 1 runs
/usr/local/freesurfer/subjects/test/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/test/mri/orig/001.mgz /usr/local/freesurfer/subjects/test/mri/rawavg.mgz
/usr/local/freesurfer/subjects/test
mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz /usr/local/freesurfer/subjects/test/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/test/mri/rawavg.mgz /usr/local/freesurfer/subjects/test/mri/orig.mgz --conform
MRIresample(): source matrix has zero determinant; matrix is:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/test/mri/rawavg.mgz...
TR=20.00, TE=5.00, TI=-1.00, flip angle=40.00
warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000
i_ras = (-1, -0, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
Original Data has (0.546875, 0.546875, 12) mm size and (512, 512, 6) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
-0.547 -0.000 -12.000 140.000;
-0.000 -0.000 -0.000 6.000;
0.000 -0.547 0.000 140.000;
0.000 0.000 0.000 1.000;
Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test exited with ERRORS at Thu Mar 6 11:02:38 CST 2014
For more details, see the log file /usr/local/freesurfer/subjects/test/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting