Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

displaying a single label from aparc in tksurfer
by Maria Kharitonova 18 Sep '14

18 Sep '14

Hi all, I would like make a figure where only 1 or 2 regions (labels from the aparc.a2009s atlas are displayed). I know how to turn on/off all labels, but how do I only display 1? (e.g. rh_G_and_S_cingul-Mid-Ant). Turning off all but the one I need is tedious and I was wondering if there was a better way. I was able to change the color of the ACC region I needed to make it more apparent (see attached), but was looking for a way that the white region is only label that is shown. I looked through the archives but could not find anything. Thanks in advance for the help! Best, Maria -- Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.kharitonova(a)northwestern.edu<mailto:maria.kharitonova@northwestern.edu>

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problem with mris_preproc
by Lars M. Rimol 18 Sep '14

18 Sep '14

Hi, I get the following error message when running mris_preproc, and I'm wondering what file is it looking for?: Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file This subject, 007, seems to have all the files it should: [rimol @ ~/subjects/long/long_v0v2_amd]$ ls /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf lh.area lh.inflated.H lh.pial_lgi lh.smoothwm.K1.crv lh.thickness rh.avg_curv rh.orig rh.smoothwm.BE.crv rh.smoothwm.S.crv rh.white lh.area.mid lh.inflated.K lh.pial-outer-smoothed lh.smoothwm.K2.crv lh.volume rh.curv rh.orig_pial rh.smoothwm.C.crv rh.sphere lh.area.pial lh.jacobian_white lh.smoothwm lh.smoothwm.K.crv lh.w-g.pct.mgh rh.curv.pial rh.orig_white rh.smoothwm.FI.crv rh.sphere.reg lh.avg_curv lh.orig lh.smoothwm.BE.crv lh.smoothwm.S.crv lh.white rh.inflated rh.pial rh.smoothwm.H.crv rh.sulc lh.curv lh.orig_pial lh.smoothwm.C.crv lh.sphere rh.area rh.inflated.H rh.pial_lgi rh.smoothwm.K1.crv rh.thickness lh.curv.pial lh.orig_white lh.smoothwm.FI.crv lh.sphere.reg rh.area.mid rh.inflated.K rh.pial-outer-smoothed rh.smoothwm.K2.crv rh.volume lh.inflated lh.pial lh.smoothwm.H.crv lh.sulc rh.area.pial rh.jacobian_white rh.smoothwm rh.smoothwm.K.crv rh.w-g.pct.mgh Here's the entire output: ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long ~/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh nsubjects = 172 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.11745 /cluster/home/rimol/subjects/long/long_v0v2_amd Log file is test_pial.mris_preproc.log Thu Sep 18 17:23:19 CEST 2014 setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd cd /cluster/home/rimol/subjects/long/long_v0v2_amd /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh Linux login-0-1.local 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.11745 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 -------------- ----------------------- mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 007v2.long.007_base srcval = (null) srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.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 /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg Loading source data Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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mri_vol2surf
by Nicholas Heugel 18 Sep '14

18 Sep '14

I looked over the documentation but can;t seem to find what I am looking for. How exactly does the function project the mdi data onto the surface? What method is it using to accomplish this, is it just projecting to the nearest neighbor or is there something more complex occurring. I ask because I just want to make sure I completely understand what every step in my analysis is doing and not have it be a blackbox that I put data in and it gives me stuff out. Thanks for your help. Nicholas

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exporting QDEC results
by elisa veronese 18 Sep '14

18 Sep '14

Dear FreeSurfers, can anybody tell me if there is a way to export results in form of table (or text file) from the QDEC GUI after having performed analysis on thickness, area, volume, etc etc... ? I mean, is the infomation regarding the significant clusters saved in table format? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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mincost bb_register
by lorenzo pasquini 18 Sep '14

18 Sep '14

Dear Freesurfer users, I have used the command bb_register to automatically register raw fMRI data on the anatomy. The output looks visually fine, however the mincost file gives me values around 0.5 for my subjects. Is this range acceptable? Does anybody has a hint on how the registration could be optimized? I use init-fsl and --bold as contrast in my bbregister command. Best, Lorenzo

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sMRI using Freesurfer 5.1 followed by DTI using Freesufer 5.3
by prasser 17 Sep '14

17 Sep '14

Hi, Could you please let me know if it's okay to use subjects analyzed using Freesurfer 5.1 (os x 10.6) for DTI analysis using Freesurfer 5.3 (os x 10.8)? Thanks.

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Segmentation failure
by Jan-Patrick Stellmann 17 Sep '14

17 Sep '14

Dear all, we observe some segmentation faults in the temporal lobe in single patients. Gyri are within the brain mask but outside the pail boundaries. Editing brain mask.mgz or wm.mgz does not resolves the problem. Examples are attached. How can we add missing brain? we are using free surfer v5.3.0 on a linux mint workstation. Thanks in advance. Best regards, Patrick -- DANKE FÜR 125 JAHRE ENGAGEMENT UND VERTRAUEN. www.uke.de/125 _____________________________________________________________________ Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vertreter des Vorsitzenden), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Displaying labels in FreeView
by Mohammed Goryawala 16 Sep '14

16 Sep '14

Hello All, I am doing a study and I have determined some regionals volumes in the Aparc and Aseg files which are significant. I would like to show these in Freeview while hiding the other insignificant ones. Please advice if its possible in Freeview. Thank you Mohammed Goryawala, PhD University of Miami Miller School of Medicine

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how to choose the best random effect in LME models
by Bernardoni, Fabio 16 Sep '14

16 Sep '14

Dear Freesurfer Users, I am trying different LME models to describe the time evolution of cortical thickness in anorexia patients. The LME tools provide a function (lme_mass_LR) to test whether a model with q+1 random effects is better (fits the data better) than one with q random effects, eg whether a model with random intercept and slope is better than one with only intercept random. I have two questions: 1- is there a similar function to test whether the model with intercept as a random effect is better than the model with slope as a random effect (ie two models with the same number of random effects)? In another thread I read one should judge which random effect is to be chosen from the percentage of voxels where one has convergence. It sounds reasonable, but an explanation of why this should be so would be welcome. 2- does it make sense to use lme_mass_LR to test whether a model with 1 random effect is better than one with 0 random effects? I have it with something like: LR_pval = lme_mass_LR(lhstats_0RE,lhstats_1RE,0); And I get as a result LR_pval= 0.3 (a constant vector) which I do not know how to interpret: something wrong, this test does not make any sense, choose the 0 random effect model ... Thanks in advance for your help. Cheers, Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] problems with tracula pre-processing (bvecs)
by lshih＠bidmc.harvard.edu 15 Sep '14

15 Sep '14

Hi, I was having similar errors as Michele Cavallari regarding "error reading /path/to/subject/dmri/dwi_frame," but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat command. I am attaching my trac-all.log and config file. Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated after I converted my dicoms to nifti using dcm2niigui (GE scanner). Can anyone tell me how dwi_frame is generated? Ludy 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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