Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

Re: [Freesurfer] analysing scans other than brain
by Antonin Skoch 06 Mar '18

06 Mar '18

Dear Matyas, this (not brain-specific) R package will be maybe more suitable for your purpose: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12035/full https://cran.r-project.org/web/packages/geomorph/index.html I generally would recommend to rather look for packages used in community of anthropologists or evolutional biologists. Antonin Hi Matyas we have online tutorials on our wiki and data you can download. Not sure how easy it will be though - a lot of what we do is brain specific Bruce On Mon, 5 Mar 2018, Matyas Varga wrote: Dear Bruce, Thank you for your quick reply. I think that whatever software I am going to use, it will require some coding as most similar software are brain specific. I use Matlab on a regular basis, and am happy to learn c in order to complete this project. My ultimate aim is to create a software or adapt an existing one for use on feet, for podiatrist and researchers. I was wondering if you could give me some suggestions as to where to start this using Free Surfer? Thank you. Best Regards Matyas Varga School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR -----Original Message----- From: freesurfer-boun...(a)nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 05 March 2018 17:05 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] analysing scans other than brain Hi Matyas it is possible, but will be a fair amount of work, probably including some c coding since many of our tools are brain-specific cheers Bruce On Mon, 5 Mar 2018, Matyas Varga wrote: Dear Free Surfer, I was wondering if it was possible to analyse (surface-based morphometry and SPM) NOT brain scans. I am doing my PhD looking at how the shape of children’s feet change as they get older (2-7 years old). I will use a 3D scanner which will provide me with a mesh of triangles of the foot and I am considering to create average age group foot shapes and compare them using surface based morphometry and SPM. I will obviously have to create my own foot ”atlas”. I was wondering if this was possible in Free Surfer? Please let me know if it is possible or if you have any suggestions if it is not. Thank you. Best Regards Matyas Varga PhD student School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR Tel: 01273 644189 ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx _______________________________________________ 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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San Diego NIAAA T32 Postdoc Opening
by Eileen Moore 05 Mar '18

05 Mar '18

San Diego NIAAA T32 Postdoc Position Opening Announcement A postdoctoral position in alcohol research is available now through an NIAAA T32 institutional training grant between SDSU and UCSD in San Diego, CA. Postdoctoral appointees are supported for twelve-month, full-time appointments with the ability to receive up to two years of support based upon acceptable progress during their initial year. Qualified candidates must be U.S. citizens (or permanent resident or noncitizen national of the U.S.) and have completed their doctoral degree requirements in the clinical and behavioral sciences. Specific areas of alcohol research include fetal alcohol spectrum disorders, adolescent and adult alcohol/substance use disorders, risk and protective factors for alcoholism, alcohol and brain disease, neurobiological/behavioral effects of alcoholism, neuropsychological function, structural and functional neuroimaging, interventions, and psychiatric and medical comorbidity. Fellows will conduct research with their mentor, including comprehensive literature reviews and participation in data collection and analysis. Fellows are expected to become involved in manuscript and grant writing, to participate in alcohol research training program seminars, and present at national meetings (e.g., Research Society on Alcoholism). Faculty mentors include Drs. Edward Riley (Director), Susan Tapert (co-Director), Robert Anthenelli, Kara Bagot, Sandra A. Brown, Mariana Cherner, Cindy Ehlers, Jay Giedd, Igor Grant, Joanna Jacobus, Terry Jernigan, Ksenija Marinkovic, Sarah Mattson, David Moore, Mark Myers, Sonya Norman, Marc Schuckit, Andrea Spadoni, Michael Taylor, Jennifer Thomas, Ryan Trim, Tamara Wall, and Matt Worley. To apply please complete the online form (http://niaaa-t32.sdsu.edu/apply/) and submit your CV, personal statement, and the names of three references to Edward Riley's assistant, Jill Vander Velde, at vanderv(a)mail.sdsu.edu.

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Skull stripping error - too much brain lost
by Matthew Grecsek 05 Mar '18

05 Mar '18

Following your advice below, it was clearly apparent that the output from the skull stripping step was missing a lot. I tried adjusting the -wsthresh flag from 50 -> 200 and it still left major parts of the brain out. I have a good quality mri and subject with no known anatomical abnormalities. The log file indicates "surface validation has detected possible Error" Does this suggest a more meaningful defect in the base image or something that can be corrected via other parameters or manual editing? Log file attached. Thanks, -Matt Bruce Fischl Fri, 02 Mar 2018 08:00:11 -0800 Hi Matt check the output of the skull stripping. This error usually means that too much (everything?) has been erased and no plausible cc could be found cheers Bruce On Thu, 1 Mar 2018, Matthew Grecsek wrote: My recon-all ended prematurely with the following message: final transformation (x=136.0, yr=-10.054, zr=-0.114): 0.98464 0.00200 -0.17457 15.51372; -0.00197 1.00000 0.00035 17.22442; 0.17457 0.00000 0.98464 -17.83761; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018 I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c My full log file is attached. Please let me know suggestions for correcting and continuing the process. Thanks, -Matt _______

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Re: [Freesurfer] Extraction of cortical thickness in native space
by Albrecht, Daniel S. 05 Mar '18

05 Mar '18

Thanks, Doug! I think we were probably going about this the wrong way. If I transform the ROI from MNI space back into native space, will the following commands give the proper cortical thickness extraction from native space? mri_vol2surf --mov roi_in_native_space.nii.gz --out rh.roi_in_native_space.mgh --hemi rh --regheader ${subj} #Check surface placement with: tksurfer ${subj} rh inflated -overlay rh.roi_in_native_space.mgh -fthresh 1 cd $FSdir/$subj/surf mri_segstats --seg /path_to rh.roi_in_native_space.mgh --in rh.thickness --sum segstats-rh.roi_ns.txt Thanks, Dan

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Fwd: mri_glmfit-sim --surf question
by Adam Mecca 05 Mar '18

05 Mar '18

Hello FreeSurfer Developers, I have run a glm on the left hemisphere to compare cortical thickness between 2 groups. After, I did a cluster-wise correction with permutation testing using this command mri_glmfit-sim --glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs It completes without error, but I have a question about the log file and --surf argument. My concern if about this part of the log file where it shows "--surf fsaverage lh white" (see section from log file and complete log file attached). White is the default I based on the help file for mri_glmfit. Should I be running with --surf fsaverage lh pial? Does this imply that the glm is performed on the white matter surface. I am then visualizing on the inflated pial surface so does this cause a problem? ------------------------------------------------------------ -------------------------------------------------- 1/1 Fri Mar 2 03:23:25 EST 2018 mri_glmfit --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 FWHM = 0.000000 gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd INFO: gd2mtx_method is dods Reading source surface /home1/am2359/fs6_data/fpeb_ app_fs/fsaverage/surf/lh.white --------------------------------------------------- Thank you, Adam

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QATools for Freesurfer v6.0
by Xiaofu 05 Mar '18

05 Mar '18

Dear Sir/Madam, I found that the QATools is still not updated for the Freesurfer v6.0 yet at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools. Could you please let me know what't the timeline for the update? or Do you know if anyone can share the updated QATools with me? Looking forward to hearing from you. Thank you very much! Best, Xiaofu

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How to define midline plane in freesurfer?
by Benjamin Yeske 05 Mar '18

05 Mar '18

Hello Freesurfer Experts, I am using freesurfer looking to get the cross-sectional area of the corpus callosum using the midline plane. Could you please explain how to define the midline plane in freesurfer so we can compute our cross-sectional area? Thank you, Ben

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Creating ROI on the functional map
by Sarah Cole 05 Mar '18

05 Mar '18

Hi, I was wondering if this method is still applicable in version 6 https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs I cannot seem to find any of the options for creating an ROI. Thank you, S

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Novice have a problem
by shilin18 05 Mar '18

05 Mar '18

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage folder to the SUBJECT_DIR folder and run recon-all … -qcache it will go through. But I think something is missing because in the surf folder, there are no *h.pial.outer_smoothed files created. I really need the files to go forward. Thanks. Reporting on 70 segmentations Using PrintSegStat mri_segstats done /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/label INFO: fsaverage subject does not have uptodate *rhinal labels! \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 27 02:44:34 PST 2018 \n mri_label2label --srcsubject fsaverage --srclabel /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject SHICEP_S15_84_KG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n No such file or directory mri_label2label.bin: could not open label file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srclabel = /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SHICEP_S15_84_KG trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label Darwin Lin.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 recon-all -s SHICEP_S15_84_KG exited with ERRORS at Tue Feb 27 02:44:34 PST 2018 For more details, see the log file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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analysing scans other than brain
by Matyas Varga 05 Mar '18

05 Mar '18

Dear Free Surfer, I was wondering if it was possible to analyse (surface-based morphometry and SPM) NOT brain scans. I am doing my PhD looking at how the shape of children's feet change as they get older (2-7 years old). I will use a 3D scanner which will provide me with a mesh of triangles of the foot and I am considering to create average age group foot shapes and compare them using surface based morphometry and SPM. I will obviously have to create my own foot "atlas". I was wondering if this was possible in Free Surfer? Please let me know if it is possible or if you have any suggestions if it is not. Thank you. Best Regards Matyas Varga PhD student School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR Tel: 01273 644189 ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx

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Freesurfer March 2018