Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Position at UW (fwd)
by Bruce Fischl 07 Mar '16

07 Mar '16

FYI ---------- Forwarded message ---------- Date: Tue, 8 Mar 2016 02:00:35 +0000 From: THOMAS J. GRABOWSKI <tgrabow(a)uw.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Position at UW Hi Bruce, I am looking for a research scientist with expertise in fMRI experimental design and neuroscience to fill an unexpected vacancy at our Integrated Brain Imaging Center at the University of Washington (http://www.ibic.washington.edu) This is a key position in our group, and I am reaching out to peer labs to find someone with the necessary expertise and professionalism. It’s a nice opportunity to join a friendly, diverse and smart group in an outstanding university setting. The successful applicant would essentially function as our technical lab manager, and serve as a research navigator for collaborators who want an imaging partner. If anyone who comes to mind as being a good match, here is the link to our ad: https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCategory= jobprofile&szOrderID=128007 I would appreciate any interest! All the best, Tom ------- Thomas J. Grabowski, Jr, MD Professor of Radiology and Joint Professor of Neurology Director, UW Integrated Brain Imaging Center Director, UW Medicine Memory and Brain Wellness Center University of Washington School of Medicine Seattle WA 98195 (206) 616-0021 (voice) (206) 685-0457 (asst) tgrabow(a)uw.edu

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How to find the difference between to different fMRI datasets?
by Silas 07 Mar '16

07 Mar '16

Dear FreeSurfer team, Thank you for all your help so far! I would like to visualize the difference between two fMRI data sets. Data set1: Cortical activation during movement of a finger. Data set2: Cortical activation during movement of a finger different from the first finger. How can i perform this operation? Best, Silas

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Cortical thickness using freesurfer
by Sahil Bajaj 07 Mar '16

07 Mar '16

Dear all, I am working on calculation of cortical thickness from a set of subjects. I am following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I am able to run up-to step-2 successfully i.e. I can display the ROIs on fsaverage subject volume. But when I run step-3 using: *mri_vol2surf --mov /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii --reg TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out ROI5.mgh --reshape* It runs as follow: (here lh_cuneus.nii is one of the ROIs,FTD_Data is my subject directory for FreeSurfer and S01_LP is the output folder for one of the subjects after running recon -all) srcvol = /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii srcreg = TT.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 reshape = 1 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /media/Storage/FTD_Data/fsaverage/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 75054 Reshaping 7 (nvertices = 163842) Writing to ROI5.mgh Dim: 23406 1 7 Although I don't see any error here but when I display using: *tksurfer fsaverage lh inflated -overlay ROI5.mgh -fthresh 0.5* it runs as follow: setting fthresh to 0.5000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /media/Storage/FTD_Data surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /media/Storage/FTD_Data/fsaverage/surf checking for nofix files in 'inflated' Reading image info (/media/Storage/FTD_Data/fsaverage) Reading /media/Storage/FTD_Data/fsaverage/mri/orig.mgz surfer: Reading header info from /media/Storage/FTD_Data/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 tkmedit: Trying to open ROI5.dat surfer: Interpreting overlay volume ROI5.mgh as encoded scalar volume. surfer: curvature read: min=-0.673989 max=0.540227 surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /home/sahil/Softwares/freesurfer/tktools/tksurfer.tcl Reading /home/sahil/Softwares/freesurfer/tktools/tkm_common.tcl Reading /home/sahil/Softwares/freesurfer/tktools/tkm_wrappers.tcl Reading /home/sahil/Softwares/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/sahil/Softwares/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... Again, I don't see any error here. But ROI ROI5.mgh is not displayed on the fsaverage surface. I tried to overlay ROI5.mgh on lh inflated using freeview as well but ROI5.mgh is nowhere. I would really appreciate any help. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. Office: 713-363-9003 E-mail:sahil.neuro@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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Cortical thickness last step
by Sahil Bajaj 07 Mar '16

07 Mar '16

Hello again, To calculate cortical thickness, I am running step-4 & 5 following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness So running step 4: *mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape* where S01_LP is my subject ID, it runs as follow: srcsubject = S01_LP srcval = lh.thickness srctype = trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /media/Storage/FTD_Data/S01_LP/surf/lh.sphere.reg Loading source data Reading target surface reg /media/Storage/FTD_Data/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (98973) Reverse Loop had 7939 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 157350, nTrgMulti = 6492, MnTrgMultiHits = 2.22289 nSrc121 = 49582, nSrcLost = 0, nSrcMulti = 49391, MnSrcMultiHits = 2.47411 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh Next when I run step 5 as follow: *mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt* It runs as follows: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt sysname Linux hostname degas machine x86_64 user sahil UseRobust 0 Loading /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 As mentioned in the instructions I also tried using --reshape-factor 7 in step 4 also but still I get exactly same error after running step 5. Could you please help me in figuring out this problem? Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. Office: 713-363-9003 E-mail:sahil.neuro@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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Embed vol geom in surf file
by marmaduke woodman 07 Mar '16

07 Mar '16

hi Is it possible to embed a volume geometry in a surface file explicitly? I'm unable to find a mri_ or mris_ command which seems to do this. Is there any workaround via the GUI tools? Thanks, Marmaduke

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recon-all issues
by Julian Jäckle 07 Mar '16

07 Mar '16

Dear FS-team For purposes of measuring cortical thickness I’ve been running recon-all as described on your RecommendedReconstruction site. However I am missing some files including e.g the skullstripped file. Could you check my log file for the root cause? Greetings Julian

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Tracula bedpostx error
by Bharadwaj, Pradyumna - (prad) 07 Mar '16

07 Mar '16

Hello Anastasia, I have been trying to run through the tutorial with one of the subjects from the tutorial(elmo.2008) to familiarize myself with Tracula. The preprocessing step seems to have been completed without any errors (Log file attached).However, when I proceed with the ball and stick model fit step, I get the following error bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu 12.04 with FSL 5.0.9. In an earlier post where the same error was encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg… you recommended running bedpostx directly. Would this impact the results or run time in any way? and is there something I can do to fix this error if it is likely to take much longer? Thanks! -Prad

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path.pd.trk format
by Peled, Noam 07 Mar '16

07 Mar '16

Hello, I've noticed that in tracula 5.2 there's also a path.pd.trk file in the output directory. How can I read this file? I would like to read the actual splines and not the probabilistic distribution in path.pd.nii.gz. Thanks, Noam Peled

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Hiring: Houston, TX - Data Processing/Analysis
by Rockers, Elijah D. 07 Mar '16

07 Mar '16

Hello, The Nantz National Alzheimer Center, in Houston, TX is looking to fill two positions pertaining to neuroimaging and analysis. Be aware that we cannot accept remote employment, the candidate would have to work day-to-day in the city of Houston. Any interested person is encouraged to review the job postings, which are attached. If you don't see the attachments but you are interested, e-mail me directly and I'll make sure you get them. Thanks, -- Elijah Rockers Research Data Analyst Houston Methodist Neurological Institute O: 713 363 7729 Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties and designated as a Magnet hospital for excellence in nursing. Houston Methodist has also been named to FORTUNE® Magazine's "100 Best Companies to Work For®" list for 10 years in a row. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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mri_convert Ubuntu 14.04 LTS not working (neither is freeview)
by Veronica.Popescu 07 Mar '16

07 Mar '16

Dear all, I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). The mri_convert doesn't work with no error message. which mri_convert gives /usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which exits with errors with no error message in the log). I made sure all the paths are 777. I did the recommended "sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in x86_64-linux-gnu. The same problem with freeview, nothing happens. Thank you in advance! Veronica -- Revalidatie & MS Centrum VZW | Overpelt Boemerangstraat 2 B-3900 Overpelt Tel.: 011 / 809 100 Fax: 011 / 66 28 86 http://www.msreva.be info(a)msreva.be Disclaimer: http://www.msreva.be/default.aspx?main=2

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