Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Control points coordinates
by Andrea Gerardo Russo 08 Mar '16

08 Mar '16

Hi Freesurfer users! We are performing such analysis on Matlab using cartesian coordinates of the control points for the study of cortical thickness. We have some problems to exactly localize control points from matlab viewing to freview or tkmedit: if the localization in Matlab is fine, in freeview are there some trasformations that I'm missing? We' d like to know if is there a file that exactly reports the trasformation matrix to change Cartesian coordinates (row, column, slice) into the "Volume RAS coordinates§" ( i.e. the coordinates used in "control.dat" file)? Any suggestions will be appreciate. Thanks in advance Andrea Gerardo Russo Student at University of Naples "Federico II" (Italy)

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Medial crossing surfaces
by maryam koochaki 08 Mar '16

08 Mar '16

Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases. I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process. Does Celine's case apply to mine? Here is your answer to Celine: Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemicheers Bruce Could you help me with the exact command line? Thank you in advance for your help,Maryam

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mean thickness
by Caroline Beelen 08 Mar '16

08 Mar '16

Dear Freesurfer team, Forgive me if this is a foolish question... I wanted to overlook cortical thickness, area and volume measures in Gnumeric file after recon-all (checking edits made). However, for several subjects I noticed that the values of mean thickness (final column) were calculated wrong, whereas this is not the case for their independent cortical thickness values. For instance, this happened to subject A09. I'm including the excel file to show the example. In the gnumeric file the number for this subject was depicted as 2/4964 instead of 2.4 etc.. What could have went wrong? Thank you for your answer in advance. Kind regards, Caroline

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T2pial shrinks pial surface
by Chris Adamson 07 Mar '16

07 Mar '16

The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? [cid:image013.jpg@01D17862.9262C650] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adamson(a)mcri.edu.au www.mcri.edu.au<http://www.mcri.edu.au/> [cid:image014.png@01D17862.9262C650]<https://www.facebook.com/MurdochChildrensResearchInstitute>[cid:image015.png@01D17862.9262C650]<https://twitter.com/MCRI_for_kids>[cid:image016.png@01D17862.9262C650]<http://instagram.com/murdoch_childrens>[cid:image017.png@01D17862.9262C650]<http://www.youtube.com/user/MurdochChildrens/videos>[cid:image018.jpg@01D17862.9262C650]<https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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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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Freesurfer March 2016