Freesurfer

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Question - how to smooth and transform into a template
by Gwang-Won Kim 24 May '17

24 May '17

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Question regarding errors with TRACULA pre-processing
by Simon, Katrina R 24 May '17

24 May '17

Hi, I keep trying to run TRACULA and getting the following errors: ERROR: run list is longer than subject list and : Command not found. : Command not found. : Command not found. Badly placed (. **My configuration file is below: *** # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR $SUBJECTS_DIR/surfaces/ # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR set dtroot = $SUBJECTS_DIR/surfaces/ # Subject IDs set subjlist = ( BPD0067A ) # Input diffusion DICOMs # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) set dcmroot = $SUBJECTS_DIR/dicoms/ set dcmlist = ( $SUBJECTS_DIR/dicoms/BPD0067A/001_000011_000001.dcm ) # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bvec ) # Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = ( $SUBJECTS_DIR/niftis/BPD0067A/dti.bval ) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Then, I am running this command in a script : trac-all -prep -c /data/picsl/mackey_group/BPD/scripts/config_test.txt And to run the command I perform on my group’s cluster is the following: qsub -V trac.sh trac.sh is the name of the script. I just ran this exact same script on another subject a few days ago and it worked fine- which is why I am confused as to why I am getting strange errors now. I checked to make sure reconstruction finished without errors and it did. Thank you! Katrina

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Maximum level of verbosity
by Jens Offenbach 24 May '17

24 May '17

Hallo, I must run FreeSurfer 6.0.0 with a maximum level of verbosity. I require as much log output as possible for monitoring purposes. Someone gave me the hint to run recon-all with DIAG=0x04040. Is this the highest possible log level for running FreeSurfer. Thank you very much. Regards, Jens

2 2

mri_watershed help
by Kanoff, Kristen Elise 24 May '17

24 May '17

Dear Freesurfer community, I am using the mri_watershed command to create BEM surfaces and have run into an issue with a large posterior chunk of skull being treated as brain. [cid:image002.jpg@01D2D47E.75797E70] I have attempted the following to correct the issue: 1. Removed the -atlas flag 2. Used -less to decrease the transition threshold used during the fine surface deformation 3. Used -man to set more/less stringent parameters for the intensity values 4. Adjusted the preflooding height 5. Used the -first_temp flag in combination with -man Removing the -atlas flag and using -less to shrink the surface seemed to provide the best result (image shown above) but the issue is not entirely resolved. Does anyone have any suggestions for a better approach? I can manually adjust the brain mask created during the recon-all process but there doesn't seem to be a way to do something similar when using mri_watershed alone. I also attempted to use the -wat+temp flag (command: mri_watershed -wat+temp -useSRAS -surf ./surfout ./T1.mgz ./brainvol) but I am getting the following error: mri_watershed Error: Problem in find normal The full command window output is attached. Any help/suggestions would be very much appreciated! Best, Kristen

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Question - multiple comparisons in FS versus SPSS
by Noordermeer, S.D.S. 24 May '17

24 May '17

Hi there! I was hoping you could help me with the following 'problem' I am experiencing. Short background: I compared volumetric brain characteristics as output from FreeSurfer parcellations and segmentations between 3 groups, by extracting the volumes per anatomical label from FreeSurfer and analyzing these in SPSS. In SPSS I did a mixed-model analysis, and performed subsequent Benjamini-Hochberg FDR correction for multiple comparisons. At the moment, I want to make brain maps (because this is a nice way to visualize the data and a reviewer suggested it). However... I believe I end up with only being able to use the uncorrected maps? When I perform an FDR-correction (or MonteCarlo, or clusterwise) in FreeSurfer all the group differences disappear. Unfortunately there is nobody that I can consult on this matter in my lab, thus I really hope someone here can help me? Personally, I think that the difference in the presence (SPSS) versus absence (FS) of groups effects is due to the correction method. I believe that in FreeSurfer I apply a whole brain multiple comparison correction, while in SPSS I merely apply a ROI-based FDR-correction I in SPSS (because I look at volume per label). However, I am not sure if this is indeed (theoretically) sound? Could anyone advise me? Is there a way I could visualise my own (SPSS) results? If more info is needed please do say so, and I will provide it! Thank you very much for your time and reply! Best, Siri

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Entorhinal cortex extraction
by Stephanos Leandrou 24 May '17

24 May '17

Dear Freesurfer Developers, I want to extract the entorhinal cortex from the original T1 image of my subect's MRI scans. Is there a way to do it; I used the the commands below to extract the CA1 subfield of the hippocampus. Is there a similar way to do the same for the entorhinal cortex? mri_extract_label lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 leftCA1.mgz mri_extract_label rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 rightCA1.mgz mri_mask orig.mgz leftCA1.mgz orig_left_CA1.mgz mri_mask orig.mgz rightCA1.mgz orig_right_CA1.mgz Many thanks, Stephanos

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mac mghread and freeview error
by Fekonja 23 May '17

23 May '17

Hi FreeSurfer Developers, I’ve just installed FreeSurfer on my MacBook Pro and experience several Problems. 1. If I generate a .profile file with the command to source FS as soon as I open the Terminal, nothing happens. If I source FS manually it works (e.g. the extract below). 2. If I open Freeview, it crashes as soon as I try to load anything. 3. The command to target the subject sample „sample-001.mgz“ works, but the command to convert it doesn’t – e.g. extracted Terminal-Log below. I’ve searched the list and found some similar errors, but unfortunately I couldn’t find working solutions. My Security & Privacy settings allow to open apps downloaded from anywhere. 1)FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c / freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2)Platform: MacOS Sierra 10.12.5 3)uname -a:Darwin Luciuss-MacBook-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 4)recon-all.log: see below Last login: Sun May 21 14:04:09 on ttys001 Luciuss-MacBook-Pro:~ luciusfekonja$ export FREESURFER_HOME=/Applications/freesurfer Luciuss-MacBook-Pro:~ luciusfekonja$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications/fsl Luciuss-MacBook-Pro:~ luciusfekonja$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory Luciuss-MacBook-Pro:~ luciusfekonja$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/luciusfekonja/sample-001.mgz, -1): could not open file Luciuss-MacBook-Pro:~ luciusfekonja$ Luciuss-MacBook-Pro:~ luciusfekonja$ recon-all USAGE: recon-all Required Arguments: -subjid <subjid> -<process directive> Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) Autorecon Processing Stages (see -autorecon# flags above): 1. Motion Correction and Conform 2. NU (Non-Uniform intensity normalization) 3. Talairach transform computation 4. Intensity Normalization 1 5. Skull Strip 6. EM Register (linear volumetric registration) 7. CA Intensity Normalization 8. CA Non-linear Volumetric Registration 9. Remove neck 10. EM Register, with skull 11. CA Label (Aseg: Volumetric Labeling) and Statistics 12. Intensity Normalization 2 (start here for control points) 13. White matter segmentation 14. Edit WM With ASeg 15. Fill (start here for wm edits) 16. Tessellation (begins per-hemisphere operations) 17. Smooth1 18. Inflate1 19. QSphere 20. Automatic Topology Fixer 21. White Surfs (start here for brain edits for pial surf) 22. Smooth2 23. Inflate2 24. Spherical Mapping 25. Spherical Registration 26. Spherical Registration, Contralater hemisphere 27. Map average curvature to subject 28. Cortical Parcellation (Labeling) 29. Cortical Parcellation Statistics 30. Pial Surfs 31. WM/GM Contrast 32. Cortical Ribbon Mask 33. Cortical Parcellation mapped to ASeg 34 Brodmann and exvio EC labels Step-wise Directives See -help Expert Preferences -pons-crs C R S : col, row, slice of seed point for pons, used in fill -cc-crs C R S : col, row, slice of seed point for corpus callosum, used in fill -lh-crs C R S : col, row, slice of seed point for left hemisphere, used in fill -rh-crs C R S : col, row, slice of seed point for right hemisphere, used in fill -nofill : do not use the automatic subcort seg to fill -watershed cmd : control skull stripping/watershed program -wsless : decrease watershed threshold (leaves less skull, but can strip more brain) -wsmore : increase watershed threshold (leaves more skull, but can strip less brain) -wsatlas : use atlas when skull stripping -no-wsatlas : do not use atlas when skull stripping -no-wsgcaatlas : do not use GCA atlas when skull stripping -wsthresh pct : explicity set watershed threshold -wsseed C R S : identify an index (C, R, S) point in the skull -norm3diters niters : number of 3d iterations for mri_normalize -normmaxgrad maxgrad : max grad (-g) for mri_normalize. Default is 1. -norm1-b N : in the _first_ usage of mri_normalize, use control point with intensity N below target (default=10.0) -norm2-b N : in the _second_ usage of mri_normalize, use control point with intensity N below target (default=10.0) -norm1-n N : in the _first_ usage of mri_normalize, do N number of iterations -norm2-n N : in the _second_ usage of mri_normalize, do N number of iterations -cm : conform volumes to the min voxel size -no-fix-with-ga : do not use genetic algorithm when fixing topology -fix-diag-only : topology fixer runs until ?h.defect_labels files are created, then stops -seg-wlo wlo : set wlo value for mri_segment and mris_make_surfaces -seg-ghi ghi : set ghi value for mri_segment and mris_make_surfaces -nothicken : pass '-thicken 0' to mri_segment -no-ca-align-after : turn off -align-after with mri_ca_register -no-ca-align : turn off -align with mri_ca_label -deface : deface subject, written to orig_defaced.mgz -expert file : read-in expert options file -xopts-use : use pre-existing expert options file -xopts-clean : delete pre-existing expert options file -xopts-overwrite : overwrite pre-existing expert options file -termscript script : run script before exiting (multiple -termscript flags possible) This can be good for running custom post-processing after recon-all The script must be in your path. The subjid is passed as the only argument The current directory is changed to SUBJECTS_DIR before the script is run The script should exit with 0 unless there is an error -mprage : assume scan parameters are MGH MP-RAGE protocol -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. both mprage flags affect mri_normalize and mri_segment, and assumes a darker gm. -schwartzya3t-atlas : for tal reg, use special young adult 3T atlas -use-gpu : use GPU versions of mri_em_register, mri_ca_register, mris_inflate and mris_sphere Notification Files (Optional) -waitfor file : wait for file to appear before beginning -notify file : create this file after finishing Status and Log files (Optional) -log file : default is scripts/recon-all.log -status file : default is scripts/recon-all-status.log -noappend : start new log and status files instead of appending -no-isrunning : do not check whether this subject is currently being processed Segmentation of substructures of hippocampus and brainstem -hippocampal-subfields-T1 : segmentation of hippocampal subfields using input T1 scan -hippocampal-subfields-T2 file ID : segmentation using an additional scan (given by file); ID is a user-defined identifier for the analysis -hippocampal-subfields-T1T2 file ID : segmentation using additional scan (given by file) and input T1 simultaneously; ID is a user-defined identifier for the analysis -brainstem-structures : segmentation of brainstem structures Other Arguments (Optional) -sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR) -mail username : mail user when done -umask umask : set unix file permission mask (default 002) -grp groupid : check that current group is alpha groupid -onlyversions : print version of each binary and exit -debug : print out lots of info -allowcoredump : set coredump limit to unlimited -dontrun : do everything but execute each command -version : print version of this script and exit -help : voluminous bits of wisdom

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Problems changing automatic SUBJECTS_DIR file path
by Becker, Valerie 23 May '17

23 May '17

Hi FreeSurfer Developers, I'm new to Linux as well as freesurfer and picking up with the program where an old lab assistant left off. He already installed the program and fsfast, but set the subjects directory using a file path unique to his user and I'm having trouble changing it. Calling up the terminal gives me this output automatically: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/jdunlop/freesurfer/subjects does not exist FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jdunlop/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl I've been unable, thus far, to find a way to change file path the SUBJECTS_DIR is using and trying the setenv command from the website setenv SUBJECTS_DIR <full path to subject dir> with the correct file path input, the terminal output gives me: [vbecker@bhfilbey ~]$ setenv SUBJECTS_DIR /home/vbecker/freesurfer/subjects bash: setenv: command not found I also wasn't able to find a direct reference to this issue searching the archives. Any help would be much appreciated. FreeSurfer Version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Platform: CentOS Release 6.9 (Final), Kernel Linux 2.6.32-573.7.1.el6.x86_64, GNOME 2.28.2 Thanks, Valerie

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Postdoctoral Position at Boston/Children’s Hospital & Harvard Medical School ///pediatric neuroimaging {Disarmed}
by Gaab, Nadine 23 May '17

23 May '17

Postdoctoral Position at Boston/Children’s Hospital & Harvard Medical School The GaabLab (gaablab.com)<gaablab.com> at the Laboratories of Cognitive Neuroscience at Boston Children’s Hospital/Harvard Medical School invites applications for a post-doctoral associate position in the area of developmental cognitive neuroscience/pediatric (f)MRI. The candidate will be expected to oversee the analysis of pediatric and infant (f)MRI experiments, analyze behavioral and (f)MRI data, develop new analysis tools, prepare manuscripts for publication, and participate in conferences. The current projects in the lab aim to characterize trajectories of early structural, functional and metabolic brain development in infants and young children. Participant populations include infants/young children who grow up in adverse environments, young children exposed to alcohol in uterus or children with a genetic or behavioral risk to develop language-based learning disabilities. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, psychology, developmental psychology, medicine) or a background in electrical engineering, biomedical engineering or computer science. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and analysis of functional brain-imaging experiments. Experience with (f)MRI analyses programs (e.g., SPM, FSL, Freesurfer, AFNI) a must. Programming skills (MATLAB, C++; Python) are desirable and experience with MVPA or connectivity analyses a plus. Experience with the analysis of pediatric neuroimaging data sets and language and reading research are useful. Approximate start date is summer/ fall 2017. Successful applicants will be appointed at Children’s Hospital Boston and Harvard Medical School. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Nadine Gaab, PhD (nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>). The search will continue until the position is filled. "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.gaablab.com<http://www.gaablab.com/> Twitter: Nadine Gaab (@GaabLab)

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FS-FAST (preproc-sess)
by Alshikho, Mohamad J. 23 May '17

23 May '17

Hi Doug, I want to analyze rsfMRI data using FS-FAST. Kindly, I have question regarding the command “ preproc-sess / Freesurfer v6” In order to begin the analysis, I followed the steps as in FS-FAST wiki. First, I organized the tree folders for the project as “study_folder/session_ID/bold/run”. Next, I ran the command "preproc-sess" as described in wiki. Unfortunately, the this command output the following error: “ERORR: no run directories found” I tried to investigate the error by running the command "getrunlist "study_folder/session_ID/bold" and this failed to see the runs folders. I had to visit the command "getrunlist " to see how it works, and I found that it depends on the command "find . -maxdepth 1 -name "[0-9][0-9][0-9]" to build the runs list. I tried to run this command in the path study_folder/session_ID/bold/ and this command failed to show any runs folders. I tried "find . -maxdepth 1 " and the output was ok. I saw the runs folders. Similarly I tried “find . -maxdepth 1 -type d” and I saw the runs folders as well. I am not sure if this is a bug in the command “find”. It seems to me that the flags “-name” and “-maxdepth” in command “find” doesn’t work together, but the flags “-name” and “ -type d” are ok. I am not sure how to handle this or what am doing wrong, so I highly appreciate any suggestions. Best, Mohamad

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