Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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

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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

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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

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hippocampal subfield viewing
by Danielle Miller 27 Oct '15

27 Oct '15

Hello, I used recon-all -hippo subfields on an earlier version of free surfer (recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website on how to view the subfields in freeview with versions earlier than 5.2. I noticed when I load all the subfields into free view and use the color LUT file, the subfields have pixelated colors at each voxel. Is there a way to view earlier versions of this similar to what is presented on the website (i.e., where subfields are represented by solid colors)? I assume this may be an issue with intensity values in the image? Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

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QDEC output after Monte Carlo simulation
by Annemarie Brandhofe 27 Oct '15

27 Oct '15

Dear freesurfer experts, I have analyzed inter-group differences in cortical thickness using freesurfer 5.3.0 and QDEC. I have found one significiant cluster in the medialorbitofrontal region that is corrected for multiple comparisons using Monte Carlo simulation (p<0,05) and listed in the qdec output file "mc-z.abs.th13.abs.sig.cluster.summary". However, the cluster shown in the display window of Qdec is located both in the lateralorbitofrontal and the medialorbitofrontal region. Why is the lateralorbitofrontal region not mentioned in the file "mc-z.abs.th13.abs.sig.cluster.summary"? I have attached the contents of the output file and a screenshot of the display window of QDEC after the Monte Carlo simulation. Thank you in advance for your help. Anne

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Centrum Semiovale Labels in Freesurfer
by Syeda Maryam 27 Oct '15

27 Oct '15

Hello Freesurfer experts, I needed to extract the centrum semiovale from freesurfer labels to use for further analysis. The freesurfer website states that the Centrum semiovale is labeled with 5001 (left) and 5002 (right). I found these labels in the wmparc.mgz volume, however they are labeled as left/right unsegmented white matter. Do these still correspond to the centrum semiovale? Thanks in advance for your help! Maryam

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R: Re: R: import FS-FAST results in FSL
by stdp82＠virgilio.it 27 Oct '15

27 Oct '15

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. > >

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Re: [Freesurfer] : FOLLOW-UP question: remove label from aseg
by Jacobs H (NP) 26 Oct '15

26 Oct '15

On 10/25/15, 3:29 AM, "Jacobs H (NP)" <h.jacobs(a)maastrichtuniversity.nl> wrote: >Hi. > >Just one another related question: now that I was able to combine left and >right hippocampal subfields with the aparc-aseg correctly, I noticed that >the left and right hippocampal subfields have the same color labels and >codes. What would be the best way to make sure that FreeSurfer understand >that the left and right subfields (e.g. Left and right CA1) are different >areas? > >Thanks! >Heidi > >On 10/21/15, 11:01 PM, "Jacobs H (NP)" <h.jacobs(a)maastrichtuniversity.nl> >wrote: > >>Thanks! Works wonderful! >>Heidi >> >>On 10/21/15, 10:50 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>wrote: >> >>>If you want to remove them, you can use mri_binarize with the --replace >>>option, replacing them with whatever you want. >>> >>>On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >>>> 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 ³old² 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 >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >> >

1 0

Head circumference
by John Anderson 26 Oct '15

26 Oct '15

4 4

Error with Group Analysis using Qdec
by haidong wang 26 Oct '15

26 Oct '15

Hi FS Experts, When I use Qdec for Group Analysis,I come with an error.Here it is. -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl setenv TUTORIAL_DATA /media/work/FC_DATA/ckd-T1 setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR Data table /media/work/FC_DATA/ckd-T1/qdec/qdec.table.dat loaded. Verifying subject data.sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'con_chenchen' in SUBJECTS_DIR Input table: /media/work/FC_DATA/ckd-T1/qdec/qdec.table.dat Subj#, SubjID, Data... 1 con_chenchen con ... I load qdec.table.dat successfully.However,QdecProject couldn't find subject 'con_chenchen' in SUBJECTS_DIR. As a result,when I use FDR for correction,there is nothing showing in the terminal. I did not dowload the tutorial data.what's more,I have not put the subjs in my Freesurfer install path. How can I deal with it? Thanks for your patience and I am looking forward for your prompt reply.

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