Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

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

2 5

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

2 1

error finding Matlab
by Jason Haberman 28 Oct '15

28 Oct '15

Dear Freesurfer Community, I am very new to Freesurfer and am trying to work my way through the tutorial. I am currently stuck at the mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 section, having received the error: ERROR: cannot find matlab. Is it in your path? I have searched the forums and found one instance of this being reported, but the suggested solutions did not resolve the problem. Is there anyway further recommendations you might make? I have attached a screenshot of my .bash_profile and of my attempts to run mkcontrast. I would be most grateful for any assistance you might offer. Warm Regards, Jason [image: Inline image 1] -- Jason Haberman Assistant Professor of Psychology Rhodes College Clough Hall 119 901-843-3231 http://jasonmarchaberman.wordpress.com/

2 3

Re: [Freesurfer] Talairach_afd error (Bruce Fischl)
by Anna I. Garcia Diaz 28 Oct '15

28 Oct '15

Hi Bruce, Thanks for the reply. The talairach.xfm file generated by the palarellizing machine is empty; it looks as follows: Talairach.xfm file: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = However, the talaraich.xfm file generated by the non-paralellizing machine is the following: MNI Transform File % avi2talxfm Transform_Type = Linear; Linear_Transform = 1.088816 -0.036409 -0.059575 1.880753 0.047590 1.030018 0.245325 -4.493217 0.029937 -0.211744 1.231518 94.663368; Anna On Thu, Oct 22, 2015 at 6:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. normalization of hippocampal volume (geschwind2013) > 2. Postdoctoral Opportunity: Multimodal MRI registration and > analysis (Frederic Andersson) > 3. Re: A mixed effect model approach in within subject dataset > {Disarmed} {Disarmed} (jorge luis) > 4. Re: Sulcal depth units (Bruce Fischl) > 5. Re: mris_expand - problem reading thickness file? (Bruce Fischl) > 6. Re: How to compute the measures on the average brain? > (Bruce Fischl) > 7. Re: Talairach_afd error (Bruce Fischl) > 8. Re: How to compute the measures on the average brain? > (Douglas N Greve) > 9. Re: normalization of hippocampal volume (Douglas N Greve) > 10. Re: per analysis with covariates (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Oct 2015 17:18:21 +0900 > From: geschwind2013 <neurofree(a)gmail.com> > Subject: [Freesurfer] normalization of hippocampal volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <27AF7ECA-E1B4-4337-BB2C-4CBE4109F342(a)gmail.com> > Content-Type: text/plain; charset=euc-kr > > Hi, FS Experts, > > I?m using version 5.3 and have performed hippo-subfields analysis. > > To perform the statistics, shall I get the normalized volumes of each > hippo-subfields? > or just to do correction for ICV is enough ? > > thanks.. > > Hyon > > > ------------------------------ > > Message: 2 > Date: Thu, 22 Oct 2015 15:30:14 +0200 > From: Frederic Andersson <andersson(a)univ-tours.fr> > Subject: [Freesurfer] Postdoctoral Opportunity: Multimodal MRI > registration and analysis > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <6E3A85F5-C942-49D0-BBE0-4C51C4E8EC27(a)univ-tours.fr> > Content-Type: text/plain; charset="utf-8" > > Postdoctoral Opportunity: Multimodal MRI registration and analysis > > Context and methodology > This postdoctoral position will focus on the registration of ex-vivo onto > in-vivo MR data. Based on some recent advances extending the combined > volume and surface registration, efficient approaches can be provided for > dealing with this issue. However, these methods need to be validated and > several open theoretical questions are related to this problem and will be > investigated during this postdoctoral work. The theoretical results > obtained will be tested and used on real human data in a larger framework > aiming at tractography validation (French National Research Agency Grant > ANR 2014, collaborative study Inserm U930, Universit? de Tours, Neurospin > and Martinos Center). > > Applicant profile > Candidates should have a strong background in image registration and MR > imaging, a good publication record, and strong experience in c++ and matlab > coding. Proficiency in English is required, as well as scientific writing > skills. > Applicants should send a CV, including list of publications and a > description of previous research experience, as well as the names and > emails of two academic referees to: Clovis Tauber ( > clovis.tauber(a)univ-tours.fr <mailto:clovis.tauber@univ-tours.fr>) and > Christophe Destrieux (christophe.destrieux(a)univtours.fr <mailto: > christophe.destrieux(a)univtours.fr> ) > > Conditions > Starting date: January 2016 (adjustable) > Contract: 2 years > Location: Imaging and Brain unit, INSERM U930, Tours. > Salary: related to experience > > References > G.M. Postelnicu, L. Z?llei, B. Fischl: Combined Volumetric and Surface > Registration, IEEE Transactions on Medical Imaging 28 (4), April 2009, p. > 508--522 > Zemmoura I, Serres B, Andersson F, Barrantin L, Tauber C, Filipiak I, > Cottier JP, Venturini G and Destrieux C 2014 FIBRASCAN: a novel method for > 3D white matter tract reconstruction in MR space from cadaveric dissection > Neuroimage 103 106?118 > Serres B, Zemmoura I, Andersson F, Tauber C, Destrieux C and Venturini G > 2013 Brain Virtual Dissection and White Matter 3D Visualization Stud. > Health Technol. Inform. 184 392--396 >

2 1

Understanding the brainstem AtlasMesh file structure format
by Jonathan Plasencia 28 Oct '15

28 Oct '15

Hello, Is the AtlasMesh under the following pathway a standard mesh structure? If so, what is it? Better yet, is there a way for those meshes in the AtlasMesh to be converted to a standard stl file or some other standard mesh file format? To be clear, I know the .gz is a compressed file; I'm referring to the data within the text. freesurfer -> average -> BrainstemSS -> atlas -> AtlasMesh.gz I ask because I would like to use this this template as a target mesh for vertex analysis with the brainstem data I processed using freesurfer. Best, Jon

1 0

FreeSurfer pve correction tool
by m.bahri＠ulg.ac.be 27 Oct '15

27 Oct '15

Dear FreeSurfer Experts, Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6? Many thanks in advance, Best, Mohamed

4 7

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study
by Don Hagler 27 Oct '15

27 Oct '15

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study University of California, San Diego Several funded postdoctoral positions are available in image analysis method development, including automated cortical- and subcortical segmentation, advanced diffusion tractography, and fMRI mapping and time series analysis. We are looking to build a team to help build the next generation of analysis pipelines and visualization tools for a newly funded study to follow 10,000 children with longitudinal structural and functional imaging across 19 sites across the US. The study will use a cross-platform Harmonized Human Connectome Protocol, optimized for quantitative accuracy and consistency of imaging biomarkers across scanners and time. To learn more about the ABCD study, please see http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… <http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan…>. Requirements: Applicants should have research experience in any of the above fields, with a Ph.D. or equivalent degree. They should be comfortable working in a distributed team environment, and should have a track record of quality scientific publications. Candidates are expected to be experienced in programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, FSL, and the Human Connectome analysis pipelines is strongly preferred. To formally apply, submit a current CV, a personal statement describing your research experience and interests, and contact information for 2-3 references to abcd(a)ucsd.edu <mailto:abcd@ucsd.edu>. Or feel free to email Dr. Donald Hagler (dhagler(a)ucsd.edu <mailto:dhagler@ucsd.edu>) or Anders M. Dale (amdale(a)ucsd.edu <mailto:amdale@ucsd.edu>) for more information. The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.

1 0

mri_parse_sdcmdir splitting a single series into two?
by Oliver Hinds 27 Oct '15

27 Oct '15

Hi, I'm running into an issue where the slices from one DICOM series are being parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate series. A few example lines from a scan.out: 6 AR_t.s40.c0 ok 64 64 41 1 <long file name> 7 AR_t.s40.c0 ok 64 64 23 1 <different long file name> The scan AR_t.s40.c0 was run as a single series on the scanner, with 64 slices. Inspection of the dicom header shows that the series UID is the same for the DICOM files in each, except there is an extra string '.0.0.0' at the end of series UID in the DICOMS that are parsed into the second series. Has anyone else experienced this behavior? If so, is there a workaround? Thanks, Oliver

1 0

Freesurfer - minc lib not found - Ubuntu 12.04
by Bruno LAD 27 Oct '15

27 Oct '15

Hi everybody. Could anyone help me please? I've downloaded FreeSurfer 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/freesurfer# ./configure --prefix=/root/freesurfer-inst --enable-static configure: Setting System... checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking AMD Open64 compiler directories... Open64 directory is not supplied 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 how to create a ustar tar archive... gnutar checking for g++... g++ 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 g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gawk... (cached) gawk checking for gcc... gcc 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 how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib ) 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 dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking how to run the C++ preprocessor... g++ -E 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 the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking for file... /usr/bin/file checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking dynamic linker characteristics... GNU/Linux ld.so checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... no checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking dynamic linker characteristics... GNU/Linux ld.so appending configuration tag "F77" to libtool 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 supports -c -o file.o... yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking dynamic linker characteristics... GNU/Linux ld.so checking whether we are using the GNU Fortran 77 compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for memory.h... (cached) yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking sys/file.h usability... yes checking sys/file.h presence... yes checking for sys/file.h... yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/timeb.h usability... yes checking sys/timeb.h presence... yes checking for sys/timeb.h... yes checking for unistd.h... (cached) yes checking values.h usability... yes checking values.h presence... yes checking for values.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking for sys/types.h... (cached) yes checking for stdint.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for mode_t... yes checking for off_t... yes checking for size_t... yes checking whether time.h and sys/time.h may both be included... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for ptrdiff_t... yes checking whether closedir returns void... no checking for error_at_line... yes checking whether lstat correctly handles trailing slash... yes checking whether lstat accepts an empty string... no checking whether lstat correctly handles trailing slash... (cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getpagesize... yes checking for working mmap... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking for sys/socket.h... (cached) yes checking types of arguments for select... int,fd_set *,struct timeval * checking return type of signal handlers... void checking whether stat accepts an empty string... no checking for working strtod... yes checking for vprintf... yes checking for _doprnt... no checking for working volatile... yes checking for pid_t... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for working memcmp... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for pid_t... (cached) yes checking for bzero... yes checking for calloc... yes checking for dup2... yes checking for floor... no checking for ftime... yes checking for getdelim... yes checking for getenv... yes checking for getcwd... yes checking for getpagesize... (cached) yes checking for gettimeofday... yes checking for isascii... yes checking for memmove... yes checking for memset... yes checking for mkdir... yes checking for munmap... yes checking for pow... no checking for putenv... yes checking for rint... no checking for select... yes checking for setenv... yes checking for sqrt... no checking for strcasecmp... yes checking for strchr... yes checking for strcspn... yes checking for strdup... yes checking for strerror... yes checking for strncasecmp... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for strtol... yes checking for uname... yes checking for /bin/tcsh... yes checking for zcat... 1 checking for gzip... 1 checking for latex... no checking for xxd... xxd checking for xmllint... no checking whether byte ordering is bigendian... no byte order is 1234 configure: Setting OS from target... configure: OS is Linux checking for _gfortran_compare_string in -lgfortran... yes checking for /cl.h... no checking for cuInit in -lcuda -L/lib... no checking for nvcc... /bin/nvcc configure: Setting CPU optimization... configure: CPUTYPE is x86_64 checking CPU optimization...... -m64 checking whether gcc accepts -m64... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... no checking whether pthreads work with -pthreads... no checking whether pthreads work with -mthreads... no checking for the pthreads library -lpthread... no checking whether pthreads work with --thread-safe... no checking whether pthreads work with -mt... no checking for pthread-config... no checking for X... libraries , headers configure: x_includes set to /usr/X11R6/include If not correct specify using --x-includes= configure: x_libraries set to If not correct specify using --x-libraries= configure: Checking for directory specification of 3rd-party libraries... checking MNI directory... MNI directory is not supplied checking NIfTI directory... NIfTI directory is not supplied checking VXL directory... VXL directory is not supplied checking FLTK directory... FLTK directory is not supplied checking PETSc directory... PETSc directory is not supplied checking MPI directory... MPI directory is not supplied checking BOOST directory... BOOST directory is not supplied checking ANN Approximate Nearest Neighbors directory... ANN directory is not supplied checking Tcl/Tk config... Not building Tcl/Tk apps. checking for tixwish... no checking for tixwish8.1.8.3... no checking for tixwish8.1.8.4... no checking BLT directory... BLT directory is not supplied checking XawPlus directory... XawPlus directory is not supplied checking Tiff directory... Tiff directory is not supplied checking Jpeg directory... Jpeg directory is not supplied checking Expat directory... Expat directory is not supplied checking for qmake... no checking for qmake-qt4... no checking for qmake-qt3... no configure: WARNING: Cannot find qmake in your PATH. Try using --with-qt. Disabling Qt apps checking CppUnit directory... CppUnit directory is not supplied checking VTK config... checking Cocoa VTK config... checking KWWidgets config... Not building KWWidgets apps. checking wxWidgets config... Not building wxWidgets apps. checking GTS config... Not building GTS apps. checking ITK directory... Not building ITK apps. configure: Getting OpenGL info... checking GL directory... OpenGL directory is not supplied checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for OpenGL library... no GL not found checking for OpenGL Utility library... no GLu found: Setting GLU_CFLAGS='' and GLU_LIBS='' Performing an off-site installation. configure: Making sure that all libraries can be compiled... checking for floor in -lm... no checking for gzopen in -lz... yes checking for crypt in -lcrypt... yes checking for nccreate in -lnetcdf... yes checking for miopen in -lminc... no configure: error: FATAL: minc lib not found. Set LDFLAGS or --with-mni-dir. The following libs are installed: root@ubuntu:~/freesurfer-source/freesurfer# dpkg -l | grep minc ii libminc-dev 2.1.00-2 MNI medical image format development environment ii libminc2-1 2.1.00-2 MNI medical image format library ii minc-tools 2.1.00-2 MNI medical image format tools 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

1 0

T1-coregistered fmri - output to .nii
by Parker, Richard 27 Oct '15

27 Oct '15

Hi Freesurfers, I am interested in running a functional connectivity analysis outside of the Freesurfer environment, using freesurfer-derived ROIs I've run recon-all, and I have run preproc-sess to carry out initial fmri preprocessing steps (motion correction, warping to the anatomical, etc) Next, I need to produce a .nii version of the T1-coregistered (and slice time corrected) fMRI timecourse, which I don't believe is created by preproc-sess. I've tried applying the register.dof6.dat to the motion corrected functional timeseries with mri_vol2vol, but the output is upsampled to the space of the T1 (and also is rotated 90 degrees, a phenomenon already discussed in several previous posts, I believe). I'm trying to produce a co-registered (but not upsampled) timeseries. Final point: another forum post details a process whereby T1-ROIs can be warped to the space of the native, non-coregistered fMRI data. This isn't appropriate for my analysis unfortunately, as I am running a multi-modal analysis, whereby everything needs to be in alignment with the T1. Any help would be greatly appreciated! Best wishes, Richard Richard Parker Postgraduate Research Student Maurice Wohl Clinical Neuroscience Institute King's College London Telephone: 07943515208 Email: Richard.r.parker(a)kcl.ac.uk

1 0

← Newer
1
2
3
4
5
6
7
8
9
...
22
Older →

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 October 2015