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30099 discussions

How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?
by Emad Ahmadi 30 Oct '15

30 Oct '15

Hi Freesurfer experts, I hope you’re all enjoying your day! Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms obtained at Martinos Center. The dicoms have the following format: MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919 MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196 MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464 ... I receive error when I run dcm2niix (to extract the b values and b vectors): Command: dcm2niix -f dti <folder of dicoms> The error I receive: Warning: output folder invalid MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try Error: unable to find any DICOM images in Conversion required 0.000000 seconds. When I do the following steps to generate “treatable” dicoms, dcm2niix recognizes these dicoms: 1. copy Martinos Center dicoms to my local Mac 2. import dicoms into OsiriX 3. Export them as dicoms 4. copy the OsiriX-exported dicoms back to Launchpad 5. Run dcm2niix on the new dicoms Since this copying back and forth takes a lot of time, I need a better way to convert the “crazy” Martinos Center dicoms into the “treatable” ones! I would really appreciate your help. Best, Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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License for a University HPC cluster
by Mike Croucher 29 Oct '15

29 Oct '15

Hi I am one of the sysadmins of a University HPC cluster. We've had a request to install Free Surfer and I note the need for a license. If I request one of these licenses, will we be permitted to install it such that all users of the cluster can access it or does each individual user need their own license? Best Wishes, Mike

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comparison of 4 groups: mri_glmfit or Qdec?
by Sandy Schramm 29 Oct '15

29 Oct '15

Dear Experts, we want to compare data (thickness) of 4 groups (3 morbid groups and 1 controll group). Both, Qdec and mri_glmfit, will do the same analyses. But we are not sure, if the usage of Qdec is statistically correct in our case. Because in Qdec we can only compare 2 of the 4 groups. But Qdec is much more comfortable to handle. Or do you advise the mri_glmfit for our data analyses? Thanks for some advice! Sandy Schramm

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R: Re: R: Re: R: import FS-FAST results in FSL
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

Thank you very much, How can I export a conjunction maps from surf to volume? I need to make it to perform the DCM analysis by SPM. Stefano >----Messaggio originale---- >Da: fischl(a)nmr.mgh.harvard.edu >Data: 27-ott-2015 13.21 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh. harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: import FS-FAST results in FSL > >Hi Stefano > >mri_vol2surf samples the volume onto the surface and saves it as a 1D >list of values, one per surface vertex. You can't view that in fslview >AFAIK - you need to load a surface in freeview/tksurfer and visualize it >as an overlay on the surface. > >cheers >Bruce >On Tue, 27 Oct 2015, stdp82(a)virgilio.it wrote: > >> Yes I would like to open with fslview (FSL) the sig.nii.gz of each >> subject which is computed by seed-based analysis by FS-FAST. >> I have mask the sig.nii.gz by fslmaths -div >> I have run: >> mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg >> subj/rest/001/register.dof6.dat --hemi rh --o prova.nii.gz >> >> but when I open the prova.nii.gz with fslview the windows is empty >> with a line. >> >> Thanks >> >> >> Stefano >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 29-set-2015 22.09 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>> >>> Do you mean surface-based analysis? You'd have to put them back into >> the >>> volume using mri_surf2vol, write them out as nifti and then run >> fslview >>> on them >>> >>> On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >>>> >>>> Hi list, >>>> >>>> I would like to import FS-FAST results (conjunction maps) in >> FSL, >>>> opening them by fslview. >>>> Could you provide me any suggestion? >>>> >>>> Thank you very much >>>> Best regards, >>>> >>>> >>>> Stefano >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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 >>> 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(a)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. >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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How to realign a surface in matlab to a realigned parent volume
by Octavian Lie 29 Oct '15

29 Oct '15

Dear All, I ran recon-all and generated a brain.mgz and say, lh.pial. I converted brain.mgz to brain.nii, imported the latter to matlab/spm and realigned it to rbrain.nii, generating a transform matrix M=rbrain.reorient.mat. if MM is the header for rbrain.nii, the header O for the original brain.nii can be calculated with O=inv(M) *MM. How do I reorient the lh.pial to the rbrain.nii? I suppose I need a reader for the pial header in matlab. Many thanks, Octavian

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z-value from a cluster
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

HI list, how can I extract the z-value from a cluster ?I'm referring to subject-level analysis and to resting-state fMRi data analyzed by using FS-FAST. Stefano

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no voxels in mask vcsf.config
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

Hi list, I'm using FS-FAST. For a subject I have the error reported below after fcseed-sess -s subj -cfg vcsf.config.The segmentation of the structural image is fine. $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects/fMRI cmdline mri_glmfit --y /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz --mask /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/mask.nii.gz --qa --glmdir /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm --pca --no-est-fwhm sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz logyflag 0 usedti 0 mask /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/mask.nii.gz maskinv 0 glmdir /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz Saving design matrix to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm/Xg.dat Normalized matrix condition is 61.5872 Matrix condition is 1e+08 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm/mask.mgh search space = 0.000000 DOF = 297 Starting fit and test Fit completed in 0.00075 minutes Computing temporal AR1 Writing results Computing FSNR mean maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 linear maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 quad maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 Computing PCA (300) ERROR: no voxels in mask

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remove label from aseg
by Jacobs H (NP) 28 Oct '15

28 Oct '15

Hi, I am trying to generate a segmentation file containing the aseg+aparc but replacing the hippocampus with the hippocampal subfields. With mergeseg I was able to merge the segmentations, but unfortunately parts of the “old” hippocampus (labeled as 17 and 53) are still in there (as the area covered by the subfields is not 100% equal to the hippocampus of the aseg). How can I remove the remains of the old hippocampal labels? Many thanks! Best Heidi

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Funcroi-Table-Sess Error
by Morenikeji Adebayo 28 Oct '15

28 Oct '15

Hi there, I ran the following analysis commands: mri_cor2label --c /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi roiconfig_ACC_lh funcroi-table-sess -analysis analysis_induc_block.lh -contrast contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat After running the 'funcroi-table-sess’ command I got the following error: ERROR: There is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres of the surface has been changed since the label was created. It seems that the problem might be that the command is using my participant (in this case, nmasa_001) as the source subject BUT it’s using fsaverage as the target subject. I want the target subject to be my participant as well (not fsaverage). Is there a way that I can specify the target subjects? Or is there a more efficient way do what I’m trying to do (ie: 1. generate labels for each participant based on their aparc+aseg file and 2. calculate the mean contrast signal from each ROI for each participant). Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 keji(a)nmr.mgh.harvard.edu

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Minc-tools - cannot find required library hdf5 - Ubuntu 12.04
by Bruno LAD 28 Oct '15

28 Oct '15

Hi everybody. Could anyone help me please? I've downloaded minc-tools source code to compile and install on Ubuntu 12.04, but I've got an error when try to run the *configure* file. The log is below: root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# ./configure --prefix=/root/freesurfer-inst --enable-static checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking whether gcc and cc understand -c and -o together... yes checking for g77... no checking for xlf... no checking for f77... no checking for frt... no checking for pgf77... no checking for cf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for xlf90... no checking for f90... no checking for pgf90... no checking for pghpf... no checking for epcf90... no checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking for flex... no checking for lex... no checking for bison... no checking for byacc... no checking whether time.h and sys/time.h may both be included... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for sys/stat.h... (cached) yes checking sys/wait.h usability... yes checking sys/wait.h presence... yes checking for sys/wait.h... yes checking for unistd.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking values.h usability... yes checking values.h presence... yes checking for values.h... yes checking for int32_t... yes checking for int16_t... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking whether we are using the GNU Fortran 77 compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for pod2man... /usr/bin/pod2man checking for library m... yes checking for library netcdf... yes checking for library z... yes checking for library hdf5... no configure: error: cannot find required library hdf5 The following libs are installed: root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# dpkg -l | grep hdf5 ii libhdf5-mpi-dev 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - development files - MPICH version rc libhdf5-mpich-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - MPICH version ii libhdf5-openmpi-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version ii libhdf5-openmpi-dev 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - development files - OpenMPI version rc libhdf5-serial-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - serial version I've Googled this issue, but cannot find any useful tip to solve my problem. If someone need more information, please let me know. Thank you for the help. -- Best Regards, Bruno Bragança Mendes Laboratório de Alto Desempenho LAD/PUCRS Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120 +55 51 33538001

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