The terminal output looks ok. Do you mean that there is something wrong with the output volume? What? doug
On 11/12/2012 11:30 AM, Yangmei LUO wrote: > Hi Douglas, > > It appeared the same error as before. The picture of the results is > the same. I am so sorry. > Thanks again! > > Best, > Yangmei > > $ /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm s105.run1.nii > /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm s105.run1.nii > $Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 fischl Exp $ > reading from I0001.dcm... > Getting Series No > Scanning Directory > INFO: Found 230 files in /home/fsl/data/emotion/s105/run1 > INFO: Scanning for Series Number 3 > INFO: found 228 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 2 > INFO: ( 64 64 32), nframes = 228, ismosaic=1 > Could not parse NUMARIS version string syngo MR B17 > found in dicom tag 18,1020 (len = 3 != 6) > Repetition Time = 2000, TR = 2000 ms > PE Dir COL COL > 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/fsl/data/emotion/s105/run1/I0001.dcm > Identification > NumarisVer syngo MR B17 > ScannerModel TrioTim > PatientName LuoYangmei_s5^caoguoguo > Date and time > StudyDate 20121009 > StudyTime 084434.968000 > SeriesTime 090357.640000 > AcqTime 090309.732500 > Acquisition parameters > PulseSeq *epfid2d1_64 > Protocol run1 > PhEncDir COL > EchoNo 1 > FlipAngle 90 > EchoTime 30 > InversionTime -1 > RepetitionTime 2000 > PhEncFOV 192 > ReadoutFOV 192 > Image information > RunNo 2 > SeriesNo 3 > ImageNo 1 > NImageRows 384 > NImageCols 384 > NFrames 228 > SliceArraylSize 32 > IsMosaic 1 > ImgPos 99.3735 107.4917 -33.8349 > VolRes 3.0000 3.0000 3.9900 > VolDim 64 64 32 > Vc -1.0000 -0.0000 0.0000 > Vr -0.0000 -0.9999 0.0105 > Vs -0.0000 0.0105 0.9999 > VolCenter 3.3735 12.1655 31.0069 > TransferSyntaxUID 1.2.840.10008.1.2 > UseSliceScaleFactor 0 (slice 0: 1) > sagrev = 0, correv =1, trarev = 1 > Vs = -0 0.0104718 0.999945 > INFO: detected a Siemens slice order reversal in mosaic, so > I'm going to reverse them back to their 'original' order. > TR=2000.00, TE=30.00, TI=-1.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.999945, 0.0104718) > k_ras = (-0, 0.0104718, 0.999945) > writing to s105.run1.nii... > > > > > > > > > > On Mon, Nov 12, 2012 at 4:11 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > sorry, remove the slash from the end of the line > > > On 11/12/2012 10:49 AM, Yangmei LUO wrote: > > Hi Douglas, > > Thank you for your kind help. The command still can not work. > > $ /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm > s105.run1.nii/ > > /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm > s105.run1.nii/ > mri_convert.linux: can't determine type of output volume > ind = 86581; % bad > Ct0 = y(:,ind+1); > %Ct0 = load('tcp.dat'); > intCt0 = cumtrapz(t0,Ct0); > > HalfLifeMin = 20.4; %min > TDecayMin = -HalfLifeMin/log(.5); > TDecaySec = TDecayMin*60; > intDecay = t0.*exp(-t0/TDecayMin); > w = sqrt(intDecay/sum(intDecay)); > W = diag(w); > > > X0 = [Cr0 intCr0 -intCt0]; > X = W*X0; > WCt = W*Ct0; > beta = inv(X'*X)*X'*WCt; > R1 = beta(1); > k2 = beta(2); > k2a = beta(3); > BPnd0 = k2/k2a -1; > CtHatSRTM = X0*beta; > > psrtm0 = max([R1 k2 k2a],0) + eps; > if(BPnd0 > 7 | BPnd0 < 0) psrtm0(3) = abs(k2)/(6+1); end > psrtm = fminsearch('srtm_err',psrtm0,[],Ct0,t0,Cr0,w); > [err CtHatsrtm] = srtm_err(psrtm,Ct0,t0,Cr0,w); > BPndNL = psrtm(2)/psrtm(3)-1; > > k3Init = .35; > paramsInit = [beta(1) abs(beta(2)) k3Init k3Init/abs(BPnd0)]; > paramsInit = [beta(1) .066 0.3 0.06]; > params = fminsearch('frtm_err',paramsInit,[],Ct0,t0,Cr0,w); > [err CtHat] = frtm_err(params,Ct0,t0,Cr0,w); > BPndF = params(3)/params(4); > k2aF = params(2)/(1+BPndF); > betaF = [params(1:2) k2aF]'; > yhatF = X0*betaF; > > plot(t0,Ct0,t0,CtHat,t0,CtHatSRTM,t0,CtHatsrtm); > legend('Data','FRTM','SRTM','NL-SRTM') > > > > > when I typed the type of the output volume, there were some > errors. > > /usr/local/freesurfer/bin/mri_convert.linux --out_type nii > I0001.dcm s105.run1.nii/ > /usr/local/freesurfer/bin/mri_convert.linux --out_type nii > I0001.dcm s105.run1.nii/ > $Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 fischl Exp $ > reading from I0001.dcm... > Getting Series No > Scanning Directory > INFO: Found 230 files in /home/fsl/data/emotion/s105/run1 > INFO: Scanning for Series Number 3 > INFO: found 228 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 2 > INFO: ( 64 64 32), nframes = 228, ismosaic=1 > Could not parse NUMARIS version string syngo MR B17 > found in dicom tag 18,1020 (len = 3 != 6) > Repetition Time = 2000, TR = 2000 ms > PE Dir COL COL > 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/fsl/data/emotion/s105/run1/I0001.dcm > Identification > NumarisVer syngo MR B17 > ScannerModel TrioTim > PatientName LuoYangmei_s5^caoguoguo > Date and time > StudyDate 20121009 > StudyTime 084434.968000 > SeriesTime 090357.640000 > AcqTime 090309.732500 > Acquisition parameters > PulseSeq *epfid2d1_64 > Protocol run1 > PhEncDir COL > EchoNo 1 > FlipAngle 90 > EchoTime 30 > InversionTime -1 > RepetitionTime 2000 > PhEncFOV 192 > ReadoutFOV 192 > Image information > RunNo 2 > SeriesNo 3 > ImageNo 1 > NImageRows 384 > NImageCols 384 > NFrames 228 > SliceArraylSize 32 > IsMosaic 1 > ImgPos 99.3735 107.4917 -33.8349 > VolRes 3.0000 3.0000 3.9900 > VolDim 64 64 32 > Vc -1.0000 -0.0000 0.0000 > Vr -0.0000 -0.9999 0.0105 > Vs -0.0000 0.0105 0.9999 > VolCenter 3.3735 12.1655 31.0069 > TransferSyntaxUID 1.2.840.10008.1.2 > UseSliceScaleFactor 0 (slice 0: 1) > sagrev = 0, correv =1, trarev = 1 > Vs = -0 0.0104718 0.999945 > INFO: detected a Siemens slice order reversal in mosaic, so > I'm going to reverse them back to their 'original' order. > TR=2000.00, TE=30.00, TI=-1.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.999945, 0.0104718) > k_ras = (-0, 0.0104718, 0.999945) > writing to s105.run1.nii/... > niiWrite(): error opening file s105.run1.nii/ > ERROR: failure writing s105.run1.nii/ as volume type 24 > > > > > > On Mon, Nov 12, 2012 at 3:29 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > /Run this command line instead > mri_convert.linux I0001.dcm s105.run1.nii/ > doug > > On 11/09/2012 01:57 PM, Yangmei LUO wrote: > > Hi Dr, Douglas, > > > I attached the capture of the result using fslview. > > Thanks very much! > > Yangmei > > On Fri, Nov 9, 2012 at 12:51 PM, Yangmei LUO > <yangmei...@gmail.com <mailto:yangmei...@gmail.com> > <mailto:yangmei...@gmail.com <mailto:yangmei...@gmail.com>> > <mailto:yangmei...@gmail.com <mailto:yangmei...@gmail.com> > <mailto:yangmei...@gmail.com <mailto:yangmei...@gmail.com>>>> > > wrote: > > Hi Dr.Douglas, > > Thanks very much for your patient help. > MRI_convert can > work. It > is great. However, there was another problem about the > convert. > The results of the convert is unknown file and > there is a > warning. > Could you help me again? > > This the command : > //usr/local/freesurfer/bin/mri_convert.linux > --in_type dicom > --out_type nii I0001.dcm s105.run1.nii/ > > The result is: > > //usr/local/freesurfer/bin/mri_convert.linux > --in_type dicom > > --out_type nii I0001.dcm s105.run1.nii > $Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 > fischl Exp $ > reading from I0001.dcm... > Starting DICOMRead2() > dcmfile = /home/fsl/data/emotion/s105/run1/I0001.dcm > dcmdir = /home/fsl/data/emotion/s105/run1 > Ref Series No = 3 > Found 231 files, checking for dicoms > Found 228 dicom files in series. > First Sorting > Computing Slice Direction > > > WARNING: it appears that the image position for all > slices is the > same. > This is a problem with the DICOM file. Using > direction > cosines > from col and row > to compute slice direction, but the output may be > misoriented. > > Vs: 0 -0.0104718 0.999945 > Vs: 0 -0.0104718 0.999945 > Second Sorting > Counting frames > nframes = 228 > nslices = 1 > ndcmfiles = 228 > PE Dir = COL (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2-- > Loading pixel data > TR=2000.00, TE=30.00, TI=0.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.999945, 0.0104718) > k_ras = (-0, 0.0104718, 0.999945) > writing to s105.run1.nii.../ > > > > Thank you so much! > > Best regards, > Yangmei > > > > > > On Fri, Nov 9, 2012 at 12:29 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > run these two lines then try again > chmod a+x mri_convert > reshash. > > > On 11/09/2012 01:04 PM, Yangmei LUO wrote: > > Hi Dr. Douglas, > > Thanks for your kind help. The version of > freesurfer is > stable v5.1.0 on CentOS 4 (32b). When I > download the > updated version you provided and switch > the file > in the > bin( I do not know what I did is correct). > When I > run the > command, the terminal appeared "permission > denied". > > What can I do next? > > Thanks so much! > > Best, > Yangmei > > > > > On Fri, Nov 9, 2012 at 11:29 AM, Douglas N > Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>>> wrote: > > The name is not important. I was able to > convert all > of those > files without a problem. What version > are you > using? > Maybe try an > updated version of mri_convert > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linux > > Also, please remember to include previous > correspondences in your > email to me. I always delete the > emails once I > answer > them. > thanks > doug > > > > On 11/09/2012 12:19 PM, Yangmei LUO wrote: > > > Hi Douglas, > > Thank you for your help. I change > the name > of the > dicom file > in order to process conveniently. > So, I > attached > two files of > with origin name and two files > with the > changed > name. I wish > it could help you figure out the > problem. > > > Thanks a million! > > > Best, > > > Yangmei > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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: 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
