Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Cerebellar edits to correct aseg
by Zeng,Victor (BIDMC - Psychiatry) 10 Oct '19

10 Oct '19

Hi, according to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview , there is a separate protocol to correct cerebellar errors with rois such as the lingual gyrus, fusiform and etc specially the creation of the brain.finalsurfs.manedit file. I have a few questions about this step: I'm assuming that the recon-2, if it detects a brain.finalsurfs.manedit, it makes a mask out of it, and applies it to brain.finalsurfs? The potential conflict I see here if that's not the case is this scenario: I'm doing all the manual edits for the brainmask, re-run recon23, then I create the brain.finalsurfs.manedit and correct the cerebellum, running the recon-all -autorecon-pial. Then I realize that there are still recon errors, and I edit the brainmask again. Would this second instance of editing the brainmask be negated by the fact that the brain.finalsurfs.manedit file doesn't have these edits? Also, generally, is it okay to do other sort of edits (e.g removing the blood vessel between the cerebral cortex and the cerebellum) @ the brain.finalsurfs.manedit, rather than the brainmask.mgz? best Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Error in running make_average_subject
by Himanshu Aggarwal 10 Oct '19

10 Oct '19

External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running into a segmentation fault. I have attached the recon-all.log file. I found a few other posts about the same problem which direct the users to the following patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/) But this patch does not have a readme file which can instruct the users about the steps that need to be followed to get rid of this bug. However, I have replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) with the files given in this patch directory. But the problem still persists. Kindly provide the steps that need to be followed to make use of this patch properly. Regards Himanshu

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Brainhack Global 2019: Call for Local Event Sites and Participation
by brainhack org 10 Oct '19

10 Oct '19

External Email - Use Caution Dear colleagues, *apologise for cross posting* Brainhack Global 2019 is collecting registrations for hosting sites! The event will be run globally, on November 13-17, to share ideas and experiences with colleagues across diverse disciplines and institutes. Don’t forget that you are the designer of your own event! You can run your hackathon around a theme that your institute is working on, hold a train track to share the expertise among your colleagues or broadcast all around the world, propose your own projects to run collaboratively and make them heard across the globe, or work on local proceedings and guidelines that would facilitate open and transparent scientific research for the local and global neuroscience community. Brainhack Global 2019 team is ready to help in hosting local events. Please check our website for more information and FAQs, and our Github repository for guidelines and materials that we provide. If you are interested in running a Brainhack, please fill the form in the Brainhack Global 2019 website! If you are planning to participate in an event, please check out the 2019 event hosts registered with us so far from the Brainhack Global 2019 website. http://brainhack.org/global2019/ Read our FAQs! http://www.brainhack.org/global2019/#faq Follow Brainhack Twitter! https://twitter.com/brainhackorg Join discussions on Brainhack Mattermost! https://mattermost.brainhack.org/brainhack/channels/brainhack-global-2019 Important Dates 13 November 2019 Host confirmation 13-17 November 2019 Brainhack events We look forward to having you all in this very exciting event! The Brainhack Global 2019 Organizing Committee Cameron Craddock, The University of Texas at Austin Dell Medical School, Texas, USA Pierre Bellec, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Canada Daniel Margulies, CNRS, Paris, France Isil Poyraz Bilgin, The University of Reading, Reading, UK Sofie Van Den Bossche, Ghent University, Ghent, Belgium Damion Demeter, The University of Texas, Texas, USA Anibal Sólon Heinsfeld, The University of Texas at Austin Dell Medical School, Texas, USA Peer Herholz, Montréal Neurological Institute & Hospital, McGill University, Montréal, Canada Jon Haitz Legarreta, Université de Sherbrooke, Sherbrooke, Canada

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PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia
by Narly Golestani 10 Oct '19

10 Oct '19

External Email - Use Caution PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia PhD and Postdoc positions are available at the Brain and Language Lab (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org>) at the University of Geneva. The PhD position is for 3-4 years, and the postdoc position is for up to 4 years, and salary will be commensurate with experience. Several projects will be done in collaborations with Maastricht University and with the University of Vienna. Applicants should have a strong interest in human brain imaging, and in language function and dysfunction, and should have one of (or a combination of) the following profiles: 1. Candidates with a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and with solid experience in computational modelling (i.e. encoding / decoding) of fMRI data, machine learning, statistics and programming. Projects will include extensions of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) to higher levels of language processing. 2. Candidates with a degree in Cognitive Neuroscience, Biomedical Engineering and/or Psychology, with solid experience in the acquisition and analysis of brain functional (and structural) imaging data. Projects will include real-time fMRI neurofeedback training studies, focusing on different levels/aspects of language learning. Candidates for either position (depending on experience) will also have the opportunity to become involved in the analysis of data from a 7T myelin mapping (R1) study. The positions are available immediately, and applications will be considered until the position is filled. Applicants should send me their CV, a statement of research interests, and the names and contact information for 2-3 references, at Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Prof. Narly Golestani Brain and Language Lab Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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FS dev install error at mri_surf2vol on mac
by fsbuild 10 Oct '19

10 Oct '19

External Email - Use Caution Hello Jonathan, It could help to add -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON to the cmake command line to see what the compiler is doing when you run make and see the first instance of those errors, but clearly something is not right with the linker options.. You could also try downloading makefile.wiki from, https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=… - and then rename it to makefile.   This should go in the same subdirectory as your ./freesurfer folder as created by git. The makefile has targets to  fetch/update/setup everything from github, fetch the archive of 3rd party libs needed to build freesurfer, show you the cmake command it will run, run that cmake command, run the make command to compile the source, then do the install pass.  You can see what the steps are if you type "make help".   This works for me on Mac OS 10.13.6 (High Sierra) with the native clang compilers.  I also use a homebrew installation already on my Mac installed under /usr/local, though the makefile will try and set that up w/o actually installing it under /usr/local. - R. Jonathan DuBois wrote: ld: warning: could not create compact unwind for _MatSetValuesLocal: stack subq instruction is too different from dwarf stack size

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Re: [Freesurfer] Notice about macOS Catalina Notarization and FreeSurfer
by fsbuild 09 Oct '19

09 Oct '19

External Email - Use Caution Hello Aditya, We are aware of the security changes in Mac OS 10.15 such as notarization whereby Apple has decided to extend security rules for applications (*.app bundles) to command line tool/binaries.   From my reading of developer postings it is not clear that the notarization process in the current release of Catalina can actually detect the linkages in and authorize all the Mac software that has been built on and distributed for older versions of Mac OS.  I suspect this is why in the past weeks I have started to receive at least 1 email a day from commercial vendors of Mac software saying not to upgrade to Catalina if you want to use their existing software releases.   So perhaps the the first (10.15.0) release of Catalina cannot support or be backwards compatible with all previous releases of Mac software.   My understanding is that each binary only needs to be authorized once and subsequently the approved state is saved, and the binary will run.  I can imagine writing something to try and authorize each individual command under ./freesurfer/bin starting with the lowest level commands, but I would not start with using the recon-all command.. - R. Aditya Kulkarni October 8, 2019 at 22:26 External Email - Use Caution Hello FreeSurfer team, With Apple’s recent release of macOS Catalina, I wanted to test its compatibility with FreeSurfer. Indeed the executables in the freesurfer/bin folder are subject to the “notarization” problem in the OS, such that every dependent executable that is used in a recon-all stream requires the user to allow it manually through security (a process which becomes cumbersome and interrupts recon-all runs with the many libraries it requires). I know you are all working very hard on the software’s development and just wanted to update with this information in case other users are updating to Catalina and going to run a FreeSurfer stream soon. Best, Aditya Kulkarni _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 14
by Juan Rivas 09 Oct '19

09 Oct '19

External Email - Use Caution Hi anatasia, thank you so much. I made a correction on the file, and the dwi.nii.gz problem was solved. I tried again with the previous script, but now I have a new error announce: JC. [shiraz:esq-15-hc] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-15-hc INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing INFO: Diffusion root is /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 trac-preproc -c /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/dmrirc.local -log /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.log -cmd /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable6/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Oct 9 12:25:33 EDT 2019 mri_convert --bvec-voxel /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc_dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc_dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.999334, 0.0365012) k_ras = (-0, -0.0365012, 0.999334) writing to /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/processing/31190669_bvecs.dat /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.bvecs cp /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/processing/31190669_bvals.dat /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.bvals mv -f /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvecs.tmp /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.bvecs mv -f /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvals.tmp /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.bvals orientLAS /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -11.2683 mri_convert -oni 130 -onj 130 -onk 44 -oid -1 0 0 -ojd 0 0.999334 0.0365012 -okd 0 -0.0365012 0.999334 -oc 3.38982 26.1253 36.373 -rt nearest /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 130 -onj 130 -onk 44 -oid -1 0 0 -ojd 0 0.999334 0.0365012 -okd 0 -0.0365012 0.999334 -oc 3.38982 26.1253 36.373 -rt nearest /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.nii.gz normalizing out_j_direction: (0, 0.999334, 0.0365012) -> (0, 0.999334, 0.0365012) normalizing out_k_direction: (0, -0.0365012, 0.999334) -> (0, -0.0365012, 0.999334) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.999334, 0.0365012) k_ras = (-0, -0.0365012, 0.999334) Reslicing using nearest writing to /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.nii.gz... INFO: found /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.bvecs /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvecs mv -f /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.bvals /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvals eddy_correct /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig_las.nii.gz /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi.nii.gz 0 File "/usr/pubsw/packages/fsl/current/bin/imglob", line 78 print "Usage: $0 [-extension/extensions] <list of names>" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Usage: $0 [-extension/extensions] <list of names>")? Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value mv -f /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvecs /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi.ecclog /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvecs.norot /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/bvecs grep: /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi.ecclog: No such file or directory head: cannot open ‘/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi.ecclog’ for reading: No such file or directory wc: /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi.ecclog: No such file or directory wc: /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi.ecclog: No such file or directory ERROR: Transform file should be eddy_correct/eddy log file or .mat file Linux shiraz.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 9 12:28:15 EDT 2019 [shiraz:esq-15-hc] (nmr-stable6-env) [shiraz:esq-15-hc] (nmr-stable6-env) # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc # Subject IDs # set subjlist = (esq-15-hc) # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc set dcmlist = (esq-15-hc_dwi.nii.gz) # Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/processing/31190669_bvecs.dat # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/processing/31190669_bvals.dat # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: # set cvstempdir = $FREESURFER_HOME/subjects # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 El mié., 9 oct. 2019 a las 12:01, <freesurfer-request(a)nmr.mgh.harvard.edu> escribió: > 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. Re: Questions re slice thickness, aseg and longitudinal > analysis (Martin Reuter) > 2. Re: Label created in the symmetric space (Jose Graterol) > 3. How to measure the cortical thickness in tumor patients? (???) > 4. Re: ECC or non-ECC Memory? (Sotiris Michos) > 5. Re: Freesurfer Digest, Vol 188, Issue 13 (Juan Rivas) > 6. Re: Brodmann area parcellation (sang ho shin) > 7. Re: [FSL] Hippocampus subregions question > (Iglesias Gonzalez, Juan E.) > 8. Re: Freesurfer Digest, Vol 188, Issue 13 (Yendiki, Anastasia) > 9. Re: How to measure the cortical thickness in tumor patients? > (Bruce Fischl) > 10. mri_convert no scaling (Ezequiel Mikulan) > 11. Re: mri_convert no scaling (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 09 Oct 2019 10:48:48 +0200 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Questions re slice thickness, aseg and > longitudinal analysis > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > 7a4d059cb5cb42f390e03f523677a3362d17cb81.camel(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="UTF-8" > > Hi David, > > I am not very optimistic: > > 5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You > will certainly get something, but it can be very unreliable and > completely wrong. Especially longitudinally these thick slices will > induce large variance due to different head positioning (and different > slice angulations) in the scanner. > > Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will > not work if tumor lesions are present. > > About your questions: > > 1. Surfaces update the aseg, but if you are only interested in the > volumes, you can skip this expensive step (potentially at the cost of > slightly higher noise levels in your measurements). > > 2. I think not (see above). 5mm is too low. > > 3. Theoretically yes, but I have never tested if the scripts will do > it. You could run up to the aseg in the cross, then create base (up to > aseg) and then run the longs up to aseg. Not even sure you really need > the base aseg. You might be able to just run the initial base > registration step, obtain the transformations and median norm.mgz > image, could be sufficient for the long runs. > > 4. No. Gad images won't work. > > Best, Martin > > > On Mon, 2019-10-07 at 18:12 +0000, David Kamson wrote: > > External Email - Use Caution > > Freesurfers, > > > > First of all, I'd like to express my gratitude to the community for > > the support that keeps researchers like myself afloat! > > > > > > I have a unique set of oncology patients that I want to evaluate for > > brain atrophy in a retrospective longitudinal analysis. > > I was thinking about using Aseg.auto results to assess longitudinal > > volume changes, but before I invest all the time I wanted to check > > with the community whether this makes any sense at all: > > > > The dataset that looks like this: > > - 22 patients (no control dataset [yet]) > > - 10-25 MRIs per patient acquired over 2-8 years in relatively > > uniform intervals > > - Patients had most of their scans on the same scanner, but > > scanners differed widely between patients > > - All patients have axial T1 post gadolinium scans of 1x1x5mm > > resolution (3D acquisition available in <10%) > > - About 80% of scans have an axial pre-contrast T1 sequence > > - All scans are skullstripped (third party algorithm) > > > > I'm looking for crude changes, no subtleties; volumes of interest > > are: > > - Whole brain volume > > - White matter volume > > - Ventricular volume (mainly lateral ventricle) > > - Subcortical gray matter volume (whole thalamus most importantly) > > > > I ran a few test analyses and to my surprise I was able to generate > > pretty acceptable surfaces, however, topology fixing took about 24H > > per scan, and I feel aseg.auto contained all the volumetric data I > > was really interested in. > > > > My concrete questions are: > > 1) Does the full autorecon pipeline affect Aseg.auto? If there is no > > benefit, I could reduce the per scan analysis time from 28 hours to > > 1-2 h. > > 2) Would this low-resolution dataset be accepted by reviewers if used > > for Aseg? Should I do any quantitative validation beyond a visual > > quality analysis of Aseg? > > 3) Can I perform a longitudinal analysis only for the Aseg results? > > 4) Is it OK to use T1-gad images for the analysis? > > > > I'd appreciate any input! > > > > Best regards, > > David O. Kamson, MD PhD > > Neuro-oncology fellow > > Johns Hopkins Hospital & > > National Institutes of Health > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 2 > Date: Wed, 9 Oct 2019 11:34:59 +0200 > From: Jose Graterol <gpjosealberto13(a)gmail.com> > Subject: Re: [Freesurfer] Label created in the symmetric space > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAFMm1s5_X3SzSWv=+ > wUKKH0z3HbVRceBQFG1v7SOA6_jWMbNYg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > It worked as intended. Thank you very much. > > On Tue, Oct 8, 2019 at 6:43 PM Greve, Douglas N.,Ph.D. < > DGREVE(a)mgh.harvard.edu> wrote: > > > In that case, run mris_preproc in the same way but don't include the > > paired-diff. Concatenate the two groups together to give you one file. > > Smooth as you did before. Now with that one file run > > mri_segstats --seg csdbase.sig.ocn.mgh --i youronefile.mgh --avgwf > > subject.hemi.cluster.dat --excludeid 0 > > > > The output file subject.hemi.cluster.dat will have a row for each > > subject and hemisphere (the order will be subject.lh, subject.rh, > > nextsubject.lh, nextsubject.rh) and a column for each cluster. The > > values will be the thickness. > > > > > > > > On 10/8/19 12:22 PM, Jose Graterol wrote: > > > > > > External Email - Use Caution > > > > > > Aha, yes. That is what I want. The original thickness values. > > > > > > Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu > > > <mailto:DGREVE@mgh.harvard.edu>> schrieb am Di., 8. Okt. 2019, 17:36: > > > > > > That all looks fine, I'm just not sure what problem you want me to > > > solve. You said that the values in the y.ocn.dat file were all > > > negative, > > > it has to be this way because you specified only negative values > when > > > you ran glmfit-sim (and negative values are possible because you > have > > > computed left-right and negated half of your subjects). Do you > > > want the > > > original thickness values? > > > > > > On 10/8/19 11:14 AM, Jose Graterol wrote: > > > > > > > > External Email - Use Caution > > > > > > > > I will try to go back a bit, just to be sure I did not make a > > > mistake. > > > > I registered both hemispheres of every subject (affected and > > > > non-affected) with xhemi. > > > > > > > > Then for the left-affected subjects I ran: > > > > mris_preproc --target fsaverage_sym --hemi lh --xhemi > --paired-diff > > > > --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out > > > > leftlesionsubjects.lh.lh-rh.thickness.sm00.mgh --s sub-xxx > > > > > > > > For the right-affected: > > > > mris_preproc --target fsaverage_sym --hemi lh --xhemi > --paired-diff > > > > --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out > > > > rightlesionsubjects.lh.lh-rh.thickness.sm00.mgh --s sub-xxx > > > > > > > > Then I changed the sign of the right-affected subjects: > > > > fscalc rightlesionsubjects.lh.lh-rh.thickness.sm00.mgh mul -1 -o > > > > rightlesionsubjects.lh.rh-lh.thickness.sm00.mgh > > > > > > > > Then I concatenated them: > > > > > > > > mri_concat leftlesionsubjects.lh.lh-rh.thickness.sm00.mgh > > > > rightlesionsubjects.lh.rh-lh.thickness.sm00.mgh --o > > > > allsubjects.lh.lesion-healthy.thickness.sm00.mgh > > > > > > > > Then I smoothed the file: > > > > mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only > > > --fwhm 10 > > > > --i allsubjects.lh.lesion-healthy.thickness.sm00.mgh --o > > > > allsubjects.lh.lesion-healthy.thickness.sm10.mgh > > > > > > > > Then glmfit: > > > > mri_glmfit --y allsubjects.lh.lesion-healthy.thickness.sm10.mgh > > > > --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10 > --osgm > > > > --surf fsaverage_sym lh > > > > > > > > and finally the correction for multiple comparisons: > > > > > > > > mri_glmfit-sim --y > allsubjects.lh.lesion-healthy.thickness.sm10.mgh > > > > --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10 > > > > --cwpvalthresh 0.05 --cache 4 neg > > > > > > > > > > > > Hopefully this helps. > > > > > > > > > > > > > > > > > > > > On Tue, Oct 8, 2019 at 4:45 PM Greve, Douglas N.,Ph.D. > > > > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > wrote: > > > > > > > > The input has both positives and negatives, so is is not > > > > surprising that the y.ocn.dat also has positive and > > > negative. Not > > > > sure what is going wrong here ... > > > > > > > > On 10/7/2019 5:48 PM, Jose Graterol wrote: > > > >> > > > >> External Email - Use Caution > > > >> > > > >> Ok, I uploaded it with the name > > > "glmdir.jg.allsubjects.tar.gz". I > > > >> had to log in as anonymous and not with my email, otherwise > it > > > >> would throw an error (503 Login with USER first. Login > > > failed.). > > > >> The mgh file is inside the gz file too. Thanks again for > your > > > >> time and help. > > > >> > > > >> On Mon, Oct 7, 2019 at 7:06 PM Greve, Douglas N.,Ph.D. > > > >> <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > > wrote: > > > >> > > > >> ok, I still don't know what is going on. Can you upload > > the > > > >> glmdir and the input to mri_glmfit (ie, the argument of > > the > > > >> --y flag). You can upload it using these instructions: > > > >> > > > >> From the linux command line, > > > >> Create the file you want to upload, eg, > > > >> cd $SUBJECTS_DIR > > > >> tar cvfz subject.tar.gz ./subject > > > >> Now log into our anonymous FTP site: > > > >> ftp surfer.nmr.mgh.harvard.edu > > > <http://surfer.nmr.mgh.harvard.edu> > > > >> <http://surfer.nmr.mgh.harvard.edu> > > > >> It will ask you for a user name: use your email address > > > >> It will ask you for a password: use "anonymous" (no > > quotes) > > > >> cd transfer/incoming > > > >> put subject.tar.gz > > > >> > > > >> Send an email that the file has been and the name of > > > the file. > > > >> > > > >> On 10/7/2019 11:53 AM, Jose Graterol wrote: > > > >>> > > > >>> External Email - Use Caution > > > >>> > > > >>> Hi Douglas, > > > >>> > > > >>> thanks for you answer. I have attached the file to the > > > email. > > > >>> > > > >>> On Mon, Oct 7, 2019 at 5:24 PM Greve, Douglas N.,Ph.D. > > > >>> <DGREVE(a)mgh.harvard.edu > > > <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu > > > <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > > >>> > > > >>> Let's backup a moment. Can you send the y.ocn.dat > > file > > > >>> that has problematic values? > > > >>> > > > >>> On 10/4/2019 4:58 AM, Jose Graterol wrote: > > > >>>> > > > >>>> External Email - Use Caution > > > >>>> > > > >>>> Dear Freesurfer Experts, > > > >>>> > > > >>>> I would appreciate your help. I will explain > > > first what > > > >>>> I have done and where my problem is. > > > >>>> > > > >>>> I want to measure the cortical thickness in stroke > > > >>>> patients. Therefore I followed Douglas' > instructions > > > >>>> provided in this link > > > >>>> > > > < > > > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… > > >to > > > >>>> join both affected hemispheres (left or right, > > > >>>> depending on the patient) and to analyze them > > > with xhemi. > > > >>>> > > > >>>> After mri_glmfit and mri_glmfit-sim > (--cwpvalthresh > > > >>>> 0,05 --cache 4 abs/neg) have run I obtained 2 > > > >>>> significant clusters. One in the precentral area, > > > which > > > >>>> I am interested in. When I check the > > > *abs/neg.y.ocn.dat > > > >>>> file the values are all -0.XXXX. If I understood > it > > > >>>> correctly, those should be cortical thickness > > > values in > > > >>>> mm, making those values implausible. For that > > > reason I > > > >>>> made a label of that cluster using the autofill > > > option > > > >>>> from tksurfer. The idea was to obtain the mean > > > cortical > > > >>>> thickness using mris_anatomical_stats after > > > mapping the > > > >>>> label to the subjects. > > > >>>> > > > >>>> Now my questions, what would be the best method > > > to map > > > >>>> the label created from the fsaverage_sym space to > > the > > > >>>> subject space? Or just simply, is this the right > > > way to > > > >>>> do this? or should I check why I am obtaining > those > > > >>>> values in the *y.ocn.dat file? > > > >>>> > > > >>>> Thanks in advance. > > > >>>> > > > >>>> Kind Regards > > > >>>> > > > >>>> Jos? Graterol > > > >>>> > > > >>>> _______________________________________________ > > > >>>> Freesurfer mailing list > > > >>>> Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > >>> _______________________________________________ > > > >>> Freesurfer mailing list > > > >>> Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> > > > >>> > > > >>> _______________________________________________ > > > >>> Freesurfer mailing list > > > >>> Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >> > > > >> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: > > 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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[FSL] Hippocampus subregions question
by briend, Frederic 09 Oct '19

09 Oct '19

External Email - Use Caution Dear FSL members, First, thanks for your great work about the hippocampus subfield. Second, I have some question about your subfield/subregions definitions: 1. Can you give me your actual definition of the GC-ML-DG in your last release (FSL6.0) of the hippocampus segmentation? Is-it possible to speak about granular cell layer, like used in the Ho, 2017 (Molecular psychiatry) article? 2. Moreover, is-it possible to say for the the hippocampal tail that it is comprised of portions of CA and dentate gyrus? 3. For molecular layer (ML), is it the ML of the CA subiculum sub volumes or the ML of the DG or both? Thank you in advance, -- Frederic Briend, PhD

2 2

mri_convert no scaling
by Ezequiel Mikulan 09 Oct '19

09 Oct '19

External Email - Use Caution Dear All, I have a similar problem to the one posted here ( Re: [Freesurfer] mri_convert scaling ). In my case I'm trying to convert from ANALYZE (.img, .hdr and .mat) to NIFTI and I need to keep the scale as in the original file. I've tried the -ns 1 flag but it doesn't work (which is not surprising as I've seen on the help page that it is for COR). The file was originally in NIFTI format and was converted to ANALYZE (mri_convert), as I had to use a tool that only accepts this format, and now I'm trying to go back to NIFTI. I would like to know if there is a way of doing it without rescaling the output. These are the contents of the folder:. ├── CC0061_philips_3_55_F_full_normfilter.hdr ├── CC0061_philips_3_55_F_full_normfilter.img ├── CC0061_philips_3_55_F_full_normfilter.mat And this is the output of the command call: $ mri_convert -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii mri_convert.bin -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from CC0061_philips_3_55_F_full_normfilter.img... analyzeRead() roi_scale 0.003921570 analyzeRead() scaling by 0.003921570 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.984889, -0.156173, 0.0748529) j_ras = (0.154421, 0.987589, 0.0286842) k_ras = (-0.0784036, -0.0166919, 0.996782) writing to test.nii... Thanks in advance for your time, Best

2 1

How to measure the cortical thickness in tumor patients?
by 王子谦 09 Oct '19

09 Oct '19

External Email - Use Caution Dear developers, right now I'm trying to measure the cortical thickness of the right hemisphere in the left side tumor patients. Here I met some problem. Since the complex intensities in the tumor, it makes the 'recon-all -all' command to be very time consuming(3 days per subject). Do you have any experience dealing with the tumor patients? I also tried the '-lh' flag, but there is only one file named 'rh.curv.stats' in stats folder. The command is:recon-all -s 130 -i 130.nii -qcache -3T -hemi rh -all Do you have any idea about where the problem is? Best wishes, James

2 1

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