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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <yangmeiluo@gmail.com <mailto:yangmeiluo@gmail.com> <mailto:yangmeiluo@gmail.com <mailto:yangmeiluo@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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> 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. 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