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
They do not have to have a dcm extension. The 180 files represent many slices from a single volume (or multiple volumes). You need to find out which ones are which. One way to do this is to run
dcmunpack -src path-to-dicom folder
this will look through all the folders and files under path-to-dicom and sort them into acqusitions. It will print out a list of each volume and a single dicom file that belongs to that volume. When you find the T1 that you want to run thru FS, pass that single dicom file to recon-all with the -i flag
duog
On 03/06/2014 12:57 PM, Mattevada, Sravan wrote:
Hello,
I am new to freesurfer. I went through the Wiki andFAQ'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 8folders.
At first there were no extentions to any of theimage 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(): sourcematrix has zero determinant; matrix is:"
Am I on the right path ? or am I missing something ? So I need to convert the images before runningthe 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Mattevada, Sravan