Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] pre-processing functional data error
by Douglas N Greve 12 Nov '12

12 Nov '12

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(a)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(a)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(a)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(a)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.l… > > 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(a)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. Greve, Ph.D. > MGH-NMR Center > greve(a)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>> > 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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 greve(a)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

1 0

Re: [Freesurfer] pre-processing functional data error
by Douglas N Greve 12 Nov '12

12 Nov '12

/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(a)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(a)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(a)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.l… > > 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(a)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>> > 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> > > > > > 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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 greve(a)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

1 0

Fwd: bad acquisition and noise problem.
by youngmin huh 11 Nov '12

11 Nov '12

Dear all, I'm working with some images, and they have so much noises on temporal areas. I just ran recon2, but not sure if they'll be segmented properly. Does anyone have a recommendation for dealing with it? I wonder if there is any flag or option for this occasion. I would appreciate any comments or help. I attached an example. Thanks, Youngmin Huh

1 0

mri_normalize info
by Martin Kavec 11 Nov '12

11 Nov '12

Hi, I would like to know what method mri_normalize uses to normalize image intensities of wm around 110. I do not mean to correct the bias field. Thanks a lot. Martin

2 1

Feature request (adding origin info to surface files)
by Luke Bloy 11 Nov '12

11 Nov '12

Hi all, I'm not sure where the best place to make this request is. so I thought I'll put this here. I often use freesurfer generated surfaces and images in other software packages (Slicer, Matlab etc) for various things. The MGZ files include the origin in the file headers, meaning that software can correctly interpret the world spaces of these images, allowing correct overlays with other results computed from the same scans. The problem is that the surface files treat the 128,128,128 voxel ( of the T1.mgz and other images) as the origin. But the world coordinates of this origin are, to my knowledge not in the surface files. This creates the situation that to correctly interpret these surfaces in relation to other coordinates systems, basically I either need to ignore the world coordinates and do some registration, or I need to load both an mgz file (to get the origin) and surface files to learn correct world coordinates of the surfaces. Ideally it seems like this information should be included in the surface files themselves. Hopefully my description of the problem makes some sense. Thanks. Luke

2 3

ASCII .curv format viewing problem
by Sourena Soheili-Nezhad 10 Nov '12

10 Nov '12

Hello Freesurfer expert community I have been analyzing the jacobian values outside freesurfer by exporting it to ascii format. Now, I have come up to vertex-wise statistical values which I wish to project on the study surface. Reading the list, I have created an ascii with each row representing <#vertex> <X> <Y> <Z> <scalar value>. This file is only viewable in tksurfer (not freeview) and the problem is that after using the curv_to_val script in tcl, the values outside [-2,2] (the blue and red colors) don't get updated when I load another file (they "freeze" on the previously loaded values). Any suggestion on a better way to view the ascii .curv format is highly appreciated. Also, does there exist any publicly-available I/O for writing binary .curv format so I can import it to freeview as well? Thanks, Sourena Soheili-Nezhad

2 3

nii -> mgz conversion inaccuracy; slice shifted.
by Uri Hasson 10 Nov '12

10 Nov '12

Dear Freesurfer experts, I'm converting a batch of nifti files to start a FS pipeline. There is 1 structural image per participant. The initial 'reconall -i' step does not give any errors. But, looking at the 'mri/orig/001.mgz' I notice for 1 participant what appears to be an imperfect conversion. Here is the link to the image showing this small bug.. http://goo.gl/jJKgM It shows the same coronal slice in AFNI and FS. The one on the right is how the original brain looks in AFNI, the one on the left is the FS's 001.gmz where there appears to be a 'pixel shift both saggitally and axially.. Any assistance, much appreciated. Thanks, Uri

2 1

Re: [Freesurfer] checking talairach.lta
by Douglas Greve 09 Nov '12

09 Nov '12

OK, I see the problem. I should have told you to put tkregsiter2.bin into /apps/fs510/tktools/ (after making a copy of the one there). doug On 11/5/12 5:00 PM, Eric Cunningham wrote: > [e4fs@cluster bin]$ ls -l `which tkregister2.bin` > -rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs510/tktools/ > tkregister2.bin > > [e4fs@cluster bin]$ tkregister2 --all-info > ProgramName: tkregister2.in <http://tkregister2.in/> ProgramArguments: > --all-info ProgramVersion: $Name: stable5 $ TimeStamp: > 2012/11/05-21:43:36-GMT BuildtimeStamp: May 22 2011 08:23:31 CVS: > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $User: > e4fs Machine: cluster.mrilab.net <http://cluster.mrilab.net/> > Playform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC > CompilerVersion: 30400 > > > > fyi: /apps/fs510/ = $FREESURFER_HOME > i tried replacing this file in tktools with the new tkregister2.bin, > and i get a new error: > /lib64/tls/libc.so.6: version GLIBC_2.4 not found > > > > On Mon, Nov 5, 2012 at 11:34 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Can you send me the result of > > ls -l `which tkregister2.bin` > > and > > tkregister2 --all-info > > > doug > > > > > On 11/05/2012 03:54 PM, Eric Cunningham wrote: > > retried it, same error > > new file is .bin, old file is tkregister2, no old > tkregister2.bin file appeared to be in the folder > $FREESURFER_HOME/bin > > On Mon, Nov 5, 2012 at 10:49 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I'm not sure that was the right thing to do. There should > be two > files: > tkregister2 and tkregister2.bin. tkregister2 is just a > script that > calls > tkregister2.bin after setting up some environment > variables. Try > keeping > the original file name. > doug > > On 11/05/2012 03:43 PM, Eric Cunningham wrote: > > i am sure > > there is one irregularity, namely that the '.bin' > extension is > absent > > from our old file, so i renamed the new file without it (as > > tkregister2) and moved the other one to tkregister2_backup > > > > the command i listed from previous threads was given to > someone else > > from our lab (and probably worked), so it is likely that > the problem > > is somewhere on our side, i was just hoping that it was > known and > > recognizable from the error > > > > > > > > On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve > > <greve(a)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: > > > > are you sure you are using the new version? > > > > > > On 11/05/2012 02:38 PM, Eric Cunningham wrote: > > > > tried the new version, and it errored out at the > same step > > > > ERROR: Option --lta-inv unknown > > > > thanks again for your help! > > > > On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve > > <greve(a)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>>> > > <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 > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > Try using this version > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.b… > > copy it into $FREESURFER_HOME/bin (but make > a back up of > > the existing > > tkregister2.bin first!) > > doug > > > > On 11/02/2012 03:58 PM, Eric Cunningham wrote: > > > Hi folks, > > > In previous threads, the command provided to check the > > talairach.lta is... > > > tkregister2 --mov > $FREESURFER_HOME/average/RB_all_2008-03-26.gca > > \ --targ ../brainmask.mgz --lta-inv > talairach.lta --reg > > talairach.lta.reg.dat \ --surfs --s $subject > > > > > > When I try to run this command, I run into trouble > with the > > --lta-inv > > > portion. (it is an unknown option). I am running > version 5.1. > > > Can anyone help? > > > Thanks, > > > -Eric > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)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>>> > > <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 > <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>>> > > <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> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > > greve(a)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> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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> > Fax: 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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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> > >

4 7

source of recon-all errors?
by Angie Morales 09 Nov '12

09 Nov '12

I'm using Freesurfer version 5.1.0 and recon-all keeps exiting with errors during the intensity correction step. The error reads: Writing to ./tmp.mri_nu_correct.mni.24988/output.mean.dat (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.24988/nu2.mnc ./tmp.mri_nu_correct.mni.24988/nu2.mnc mul Linux funcgrid3 3.1.10-1.16-desktop #1 SMP PREEMPT Wed Jun 27 05:21:40 UTC 2012 (d016078) x86_64 x86_64 x86_64 GNU/Linux recon-all -s 402_1 exited with ERRORS at Thu Nov 1 13:19:28 PDT 2012 Any ideas about what might be going wrong? Thanks, Angie

2 5

Re: [Freesurfer] Error in recon-all after updating mri_segstats.
by Douglas N Greve 09 Nov '12

09 Nov '12

Use this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… doug On 11/08/2012 10:01 PM, Zheng Hui wrote: > Hi Doug, > > After updating the mri_segstats, all our recon-all encounter errors as > follow log suggest. Please advice a work around. > > Thank you, > Zheng Hui > > > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4020/ones.mgz --i > orig.mgz --sum ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/input.mean.dat > > $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ > cwd > cmdline mri_segstats --id 1 --seg > ./tmp.mri_nu_correct.mni.4020/ones.mgz --i orig.mgz --sum > ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/input.mean.dat > sysname Linux > hostname compute-08-00.cbdc.rhhpc.cluster > machine x86_64 > user gmszh > UseRobust 0 > Loading ./tmp.mri_nu_correct.mni.4020/ones.mgz > Loading orig.mgz > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0 > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to ./tmp.mri_nu_correct.mni.4020/input.mean.dat > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4020/ones.mgz --i > ./tmp.mri_nu_correct.mni.4020/nu2.mnc --sum > ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/output.mean.dat > > $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ > cwd > cmdline mri_segstats --id 1 --seg > ./tmp.mri_nu_correct.mni.4020/ones.mgz --i > ./tmp.mri_nu_correct.mni.4020/nu2.mnc --sum > ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/output.mean.dat > sysname Linux > hostname compute-08-00.cbdc.rhhpc.cluster > machine x86_64 > user gmszh > UseRobust 0 > Loading ./tmp.mri_nu_correct.mni.4020/ones.mgz > Loading ./tmp.mri_nu_correct.mni.4020/nu2.mnc > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0 > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to ./tmp.mri_nu_correct.mni.4020/output.mean.dat > (standard_in) 1: parse error > mris_calc -o ./tmp.mri_nu_correct.mni.4020/nu2.mnc > ./tmp.mri_nu_correct.mni.4020/nu2.mnc mul > Linux compute-08-00.cbdc.rhhpc.cluster 2.6.18-164.el5 #1 SMP Tue Aug > 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s SS193D_fs exited with ERRORS at Thu Nov 8 16:50:04 SGT 2012 > > For more details, see the log file > /data/research1/cnl/Experiments/SLABS/FS/mempr/SS193D_fs/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer