Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

surface based fMRI gorup analysis from spm
by Elisa Castaldi 15 Nov '17

15 Nov '17

Dear Freesurfer users, I would like to perform surface based fMRI gorup analysis in Freesurfer starting from SPM first level output files, but I am not succeding. I have already preprocessed the data in spm and used Freesurfer for boundary based registration, I have succesfully ran the recon -all comand and ovelayed the first level analysis output file (created with spm). Now I would like to perform surface based fMRI group analysis with Freesurfer, but I am worried it is crashing either because the folders are not organized the way they should or because I am missing some files. first I have converted .dat into .lta file tkregister --mov bbrumeanSBref_sess1_mp1.nii --targ bbrumeanSBref_sess1_mp1.nii --reg bbrumeanSBref_sess1_mp1.dat --ltaout mp1reg.lta --noedi then mris_preproc --out lh.con.mgh --target ${SUBJECTS_DIR}/surfaces/fsaverage --hemi lh \ --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii ${SUBJECTS_DIR}/sub02/fmri/ab1reg.lta\ --projfrac 0.5 \ ERROR: cannot find SUBJECTS_DIR/surfaces/fsaverage in SUBJECTS_DIR Trying to move files in the requested directory caused other errors, everytime not finding what it needs. At the moment the project folder contains one folder per each subject (each one containing fmri, stats, t1mri folders, containing spm results) and one folder called 'surfaces' containing 1) the fs average and 2)one folder per subject containing the results of the recon -all command. Is it possible to run the surface based group analysis if I have not used Freesurfer since the beginning? How should I reorganize the directories? I could not find any related issue in the archive. Thanks a lot for your help

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Freeview Crashes!!
by vin rasa 14 Nov '17

14 Nov '17

Dear FS Experts, While using updated Freeview in ubuntu 16.04, I reproducibly get two following errors: 1st Crash (While selecting color for the volume): Volume - Colormap -Lookup Table option: 0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN6QMutex12lockInternalEv 2nd Error/Crash: Loaded lh.pial and rh.pial surfaces + a volume activated as an isosurface. Now while rotating the 3D window Freeview crashes with following error: Did not find any volume info p9\d�Did not find any volume info p9\d�[0]PETSC ERROR: ------------------------------ ------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/p etsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------ ------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------ ------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named WS52 by wiki Thu Nov 9 16:29:50 2017 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/L inux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3- p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------ ------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ######### I don't think RAM/memory is an issue, as the computer has 65GB RAM. Any other options/update I should try? I am planning to load multiple volumes as isosurface in multiple colors, and show them with lh.pial and rh.pial. Thank you very much

3 2

Simultaneously morphing to CVS + Downsampling.
by Mehta, Chintan 14 Nov '17

14 Nov '17

Dear FreeSurfer community, I have applied mri_cvs_register to subjects' T1 scans using FreeSurfer 6.0 and mri_vol2vol to warp fractional anisotropy spatial maps warped to CVS space. A previous post talks about functionality of "morph + downsampling" in a single step coming in the future: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30724.html. Is this functionality now incorporated in mri_vol2vol? For example, are there additional flags where I can specify the voxel size of the output volume as being, say 4mm x 4mm x 4mm? mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$sub/cvs/final_CVSmorph_tocvs_avg35.m3z \ --noDefM3zPath --reg $reg --mov $vol \ --o $vol_cvs \ --interp trilin --no-save-reg As it is, the output volume in CVS space as the same voxel size as cvs_avg35 template (1mm x 1mm x 1mm). Thank you. Best, Chintan

1 0

Freeview display issue in Ubuntu 14/16 VM
by Nicholas Blauch 14 Nov '17

14 Nov '17

Hi Freesurfer folks, I’ve recently started using an Ubuntu virtual machine on PC host, and have noticed a problem in both Ubuntu 14 and 16 (but not 12) with Freeview. When a freeview window is opened, the black screen for displaying volumes/surfaces is necessarily at the front of the screen (i.e., nothing can be viewed in front of it). This makes viewing menu options and selecting volumes difficult and annoying, as well as working with other applications such as the terminal which cannot be placed over the freeview screen. I’m wondering if others have experienced this or know of a solution? Thanks, Nick

2 1

Changing operating system.
by Ramesh Babu 14 Nov '17

14 Nov '17

Dear Experts, Recently I am facing lot of problem with Ubuntu OS 16lts. In one year I have formatted 4 times because of nvidia graphic card driver issue (happens after update) or some unknown reason ( I am not tech tech guy to figure out all the problem). Yesterday onwards problem started again. I couldn't open ubuntu. Initially it was blank screen, after following some suggestion from forum I removed nvidia driver and tried lot other things. Still not functioning. Therefore I am planning to go for cent os. After installing cent os should I redo all analysis again? or I can continue with whatever so far done by using Ubuntu os? Thanks RB

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PostDoctoral Position to Study Multimodal Connectomics of Neuromodulation at MGH (Boston, MA)
by Camprodon, Joan A.,M.D.,M.P.H.,Ph.D. 14 Nov '17

14 Nov '17

POST-DOCTORAL RESEARCH FELLOW LABORATORY FOR NEUROPSYCHIATRY AND NEUROMODULATION MASSACHUSETTS GENERAL HOSPITAL, HARVARD MEDICAL SCHOOL Background: The Laboratory for Neuropsychiatry and Neuromodulation (Camprodon Lab) in the Division of Neuropsychiatry at Massachusetts General Hospital (Harvard Medical School) is seeking a full time Post-Doctoral Research Fellow for an NIMH RO1-funded project studying the mechanisms of action of neuromodulation therapies (TMS and ECT) in neuropsychiatric disorders. This project will use multimodal MRI Human Connectome sequences to study structural and functional circuit dynamics longitudinally with a dimensional neuropsychiatric focus. There will be opportunities to address basic and pathophysiological systems neuroscience questions, in addition to develop translational and clinical research skills (e.g. target discovery, individualized treatment development and biomarker/predictor development). The Laboratory for Neuropsychiatry and Neuromodulation is located in the incredible scientific and translational environment of the MGH/HMS Charlestown Navy Yard campus, affiliated with the Martinos Center for Biomedical Imaging. We are a multidisciplinary team conducting clinical, translational and basic research with healthy and neuropsychiatric human populations, using device-based neuromodulation interventions (TMS, tDCS, ECT, DBS, etc.), neuroimaging, EEG, behavioral and clinical methods. Additionally, the program includes the Transcranial Magnetic Stimulation (TMS) clinical service, tightly integrated with our research mission, where we treat neuropsychiatric patients. The laboratory, clinical service and the Division of Neuropsychiatry are directed by Joan Camprodon, MD MPH PhD; you will work directly with him and an array of collaborators and co-investigators. There will be many opportunities to lead high impact publications starting on day one, working with rich and unique existing datasets. Extensive mentorship will be provided to facilitate the transition to an independent research career. Duties and Responsibilities: The Post-Doctoral Fellow’s responsibilities will include, but are not limited to: 1. Analyze longitudinal multimodal MRI data (functional connectivity, task-based fMRI, diffusion tractography and volumetrics). 2. Model complex datasets including imaging, behavioral and clinical data. 3. Coordinate the acquisition of high quality connectome data working with a team of research assistants. 4. Be inquisitive, curious and publish! Qualifications: 1. Ph.D. in Neuroscience, Psychology, Engineering or a related field. 2. Background in systems/cognitive neuroscience, neuroanatomy and psychological/clinical constructs. 3. A demonstrated capacity to drive first author publications. 4. Strong proficiency in various neuroimaging analysis platforms, multivariate modeling strategies and connectivity toolboxes. 5. Established quantitative and statistical skills, including programming and comfort with diverse computing environments. 6. Great writing skills, motivated and driven to publish. Additional Qualifications: 1. Connectomics network analysis and machine learning modeling confer a significant advantage. 2. Management/coding of neuroimaging databases (XNAT or others) preferred. Additional Information: This is an NIH-funded 2 to 5-year term position with great opportunities for training in human systems neuroscience, translational/clinical applications and diverse integrated methodologies (including neuromodulation). Applications must be sent by email to Dr. Joan Camprodon (jcamprodon(a)mgh.harvard.edu<mailto:jcamprodon@mgh.harvard.edu>) CCing Lauren Johnson (ljohnson49(a)mgh.harvard.edu)<mailto:ljohnson49@mgh.harvard.edu)> and include a CV, cover letter and names of three references. Expected start date: Fall 2017/Winter 2018

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[strip skull for unregistered images]
by Yi Li 13 Nov '17

13 Nov '17

Dear FS experts, I would like to strip skulls from unregistered images which have gone through GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the following two commands in freeSurfer: recon-all -autorecon1 -subjid <subjid> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz My questions are 1) Currently I use 5 as threshold (-T 5). Is there a guidance for the setting of this parameter? 2) In the output file T1.final.mgz, is the skull-stripped image represented in ijk space (image index space) or in XYZ space (via transformation matrix)? 3) If the skull-stripped image is represented in XYZ space, how do I get it in ijk space? Thanks in advance for the help! Best Regards, Yi Li (PhD) Senior Computational Scientist Computational Sciences The Jackson Laboratory Farmington, CT 06032 Tel: 860-837-2156 --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

2 4

dmrirc.tutorial problem
by lanbo Wang 13 Nov '17

13 Nov '17

Dear experts, I try to run trac-all -bedp -c dmrirc.tutorial, but error shows like this, then stop: INFO: SUBJECTS_DIR is /HD4/DTI INFO: Diffusion root is HD4/DTI Actual FREESURFER_HOME /HD2/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.2nd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.3rd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri [mtobia@localhost DTI]$ trac-all -bedp -c dmrirc.tutorial INFO: SUBJECTS_DIR is /HD4/DTI INFO: Diffusion root is HD4/DTI Actual FREESURFER_HOME /HD2/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.2nd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.3rd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri Thanks for your patient and help. All best, Lanbo Wang

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Unrealistic "mri_fdr" Results
by Hossein Rejali 13 Nov '17

13 Nov '17

Hi, Sorry I am very new to this field, forgive me for ignorance. I am trying to do multiple comparison correction on my data set that I ran through mri_glmfit. I am currently using mri_fdr as a means for multiple comparison correction. The problem I am having now is that after running mri_fdr, the output surface overlays are completely zero. This seems very unlikely from the clusters I had, well at least hopefully unlikely. Below I have posted part of the code for my analysis that is calling the mri_fdr function: mri_fdr --fdr $thresh --${sign} --i $SUBJECTS_DIR/Group_Analysis/R1_projdist0.${dist}.fwhm${fwhm}/GLM_Output/${hemi}.Output/Diff-con-scz-R1/sig.mgh nomask $SUBJECTS_DIR/Group_Analysis/R1_projdist0.${dist}.fwhm${fwhm}/GLM_Output/${hemi}.Output/Corrected/FDR-Output-${sign}-thresh${thresh}.mgh Sorry for the mess but essentially, I am running though a couple of for loops that runs through variable values posted below: for thresh in 0.5 0.1 0.05 0.01 for sign in neg pos for hemi in lh rh for fwhm in15 20 for dist in 2 I am hoping there is something wrong with the way I am calling mri_fdr, any help would be greatly appreciated. Kind Regards, Hossein Rejali

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Re: [Freesurfer] functional to anatomical registration
by Douglas N Greve 13 Nov '17

13 Nov '17

Hi David, please post to the list ... answers below On 11/13/2017 01:48 PM, David Beeler wrote: > Hi Doug, really helpful thanks! > So if I want all the motion corrected functional data across runs to be aligned with a downsampled version of my anatomical, is it better to run preproc-sess with -per-session or should I do -per-run and then map each functional to anatomical without resampling using: > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg \ --o > fmcpr.new.vox2ras.nii.gz --no-resample > and then run selxavg3-sess on the fmcpr.new.vox2ras.nii.gz in each run > folder? I've heard motion correction with -per-run is better but I > don't understand why... can you explain? Oh, if you want to do it that way, then you would not use the --no-resample (that just changes the geometry in the header). per-run registers and resamples to the middle time point, meaning that there is generally less interpolation. You should add --fstarg orig.mgz This will have it sample into the 1mm orig space. This will create a very largefile. If you want to downsample the anat, you can run mri_convert --downsample 2 2 2 orig.mgz orig.ds2.mgz and then --fstarg orig.ds2.mgz > Further, I don't get how selxavg3-sess chooses its input. If I first > do preproc-sess with -per-run, do my transformation to downsampled > anatomical space (as described above), and then run selxavg3-sess with > the -no-preproc flag, what volume will selxavg3-sess use by default? I > assume it will search the run folders for fmcpr.nii.gz (because using > f.nii.gz would defeat the purpose of doing motion correction in the > first place), but is there a flag I could use to tell selxavg3-sess to > use my transformed fmcpr.new.vox2ras.nii.gz as input instead? Should I > just rename fmcpr.new.vox2ras.nii.gz to fmcpr.nii.gz and then > selxavg3-sess will take it automatically? When you create your analysis, you should put -funcstem fmcpr.new.vox2ras > Thanks again! > David > PS is this the correct way to respond to threads on this mailing list > so that the thread is maintained? > On 11/8/17 5:57 PM, David Beeler wrote: > > Hi freesurfer people, > > I'm trying to understand preprocessing a little better, especially > registration of functional data to anatomical space. I am > currently running everything in the volume, doing motion > correction per-run and then pooling all the runs in the session > together for the first level analysis.As far as I can tell, > running preproc-sess with -per-run takes the rawfunctional data > (f.nii.gz), pulls out the middle timepoint and calls it > template.nii.gz, bbregisters func to anat and creates a > register.dof6.lta file in each of the functional run folders, > transforms the aparc+aseg from the subject's mri folder and > binarizes it into a brainmask (brain.nii.gz), and runs mc-afni > using f.nii.gz as the input vol and template.nii.gz as the > template vol to create the motion corrected volume (fmcpr.nii.gz). > Is this correct? > > yes > > Then when I run selxavg3-sess it somehow mri_converts an > intermediary motion corrected volume from the mc-afni command > above (eg <run#>/tmp.mc-afni2.20097/outvol.nii.gz) into an > fmc.nii.gz file in each run folder. Are these fmc.nii.gz's > supposed to be coregistered between runs? (i.e. if the subject > moved a bunch between two of the runs, would those two volumes be > aligned at all?). How do these files work? > > Not with -per-run. per-run was designed with the idea that you would > beresampling to some common space (eg, surface or mni305 or cvs), and > then running sexlavg3-sess on that data. If you want all the > fmc.nii.gz to be in the same space, then use -per-session. > > At the end I have an analysis directory with my betas, sigmaps, > etc. What functional volume is everything registered to? Is the > transform between this functional volume and anatomical space the > register.dof6.lta file located in the session directory? > > Thanks for bearing with me! > -David > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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/

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Freesurfer November 2017