Thanks Doug I started the #2 and its running. Sorry about the personal e-mail.
Thanks Sravan
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, March 06, 2014 3:02 PM To: Mattevada, Sravan; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DICOM input format and structure
Hi Sravan , please post to the list and not to us personally. Thanks!
This is just a list of what you (or whoever you are working with acquired), so I don't know what is in there. Probably #2 is what you want, less sure about #4
doug
On 03/06/2014 03:34 PM, Mattevada, Sravan wrote:
Hello Doug,
I ran the dcmunpac command and below is what I got. Sorry I am new to freesurfer, Linux and MRI Images as well.
Are no. 2 and no. 4 the T1s ? which one do I need to pass to the recon-all ? Thank you very much for your response. It helps a lot.
[freesurfer@localhost freesurfer]# dcmunpack -src /home/freesurfer/Documents/Sub_9884/DICOM
cd /home/freesurfer /usr/local/freesurfer/bin/dcmunpack -src /home/freesurfer/Documents/Sub_9884/DICOM
-rwxr-xr-x. 1 root root 23416 May 13 2013 /usr/local/freesurfer/bin/dcmunpack
Searching for matching files Thu Mar 6 14:22:14 CST 2014 Thu Mar 6 14:22:14 CST 2014 Found 229 total files. Interrogating each and every one of them. Be patient. If you have collected the data in the Martinos center, this will run faster if you kill this job and re-run with -martinos Found 9 unique series: 1 2 3 4 5 6 7 8 9 Subject 9884^9884^^^ Date 20131203 Time 082101.937000 Institution RADIOLOGY ASSOCIATES-CDI 1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000000/I M000003 2 T1SESAG 8 345 90 0.8984375 ROW 140 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000001/I M000011 3 T2TSEAX 85 4010 180 0.8984375 ROW 110 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000002/I M000011 4 T1SEAX 8 500 90 0.8984375 ROW 140 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000003/I M000011 5 T2FLAIRAX 117 9000 180 0.8984375 ROW 130 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000004/I M000011 6 T2AXHEMO 27 1220 25 0.44921875 ROW 195 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000005/I M000011 7 AXep2d_diff_2scan_trace 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000006/I M000011 8 AXep2d_diff_2scan_trace_ADC 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000007/I M000011 9 T2TSECOROBL 87 4260 180 0.4296875 ROW 110 /home/freesurfer/Documents/Sub_9884/DICOM/PA000000/ST000000/SE000008/I M000011
Thu Mar 6 14:22:43 CST 2014 dcmunpack done
-Sravan
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, March 06, 2014 1:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DICOM input format and structure
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 isE:\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
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-- 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/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- 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/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/