Thanks Doug I started the #2 and its running. Sorry about the personal e-mail.
Thanks Sravan -----Original Message----- From: Douglas N Greve [mailto:gr...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@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 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 >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the > Partners Compliance HelpLine at http://www.partners.org/complianceline > . If the e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the e-mail. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
