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30134 discussions

upgrading to freesurfer 5.3
by Laura Christine Anderson 05 Feb '14

05 Feb '14

Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature? Thanks for your help! Laura Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112

2 4

Cluster Summary
by Natasha Haris 05 Feb '14

05 Feb '14

Hello Freesurfers, Is there any way to get a list of all the clusters (with information on their location, x/y/z vertices, t statistic etc) from QDEC? Thanks , Natasha

2 1

TRACULA -stat
by stdp82＠virgilio.it 05 Feb '14

05 Feb '14

Normal 0 false false false IT JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Cambria; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin;} Hi list,I don’t understand how I can use the -stat option for TRACULA tool.From the guide, I should use a dmrirc file. What it should contains?Thanks, Stefano

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"trac-all -prior" giving "Segmentation fault (core dumped)
by Yong-Hwan Kim 05 Feb '14

05 Feb '14

Hello, FreeSurfer community, I'm trying to run TRACULA sequentially. After running, "trac-all -prior -s <subject> -i <input_DWI.nii> -c <tracula_conf.txt>" that shows an error "Segmentation fault (core dumped)" in my server. (Other options, "-corr, -qa, -intra, -inter, -masks, -tensor", were have done without error) Server was configured as, 1. Fedora 13 - 64bit 2. FreeSurfer v5.1 3. Tracula v5.3 (updated from v5.1) Can anyone suggest a reason why this would be the case? Thank you, Yong-Hwan Kim *Captured Shell logs* -------------------------------------------------------------------------------------------------- . . . Loading cortex mask from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/cortex+2mm.nii.gz Processing pathway 1 of 18... Matching streamline ends INFO: Have 4657 non-truncated streamlines (min/mean/max length: 60/99/137) . . . Finding center streamline INFO: Step is 5 voxels *Segmentation fault (core dumped)* Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 ... trac-preproc exited with ERRORS at Tue Jan 28 21:30:52 KST 2014 -------------------------------------------------------------------------------------------------- *Error Log from <subject>/scripts/trac-all.error* -------------------------------------------------------------------------------------------------- SUBJECT G001 DATE Tue Jan 28 21:30:52 KST 2014 USER user HOST localhost PROCESSOR x86_64 OS Linux Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.46 2013/12/04 17:02:25 ayendiki Exp $ /usr/local/freesurfer/bin/trac-preproc PWD /usr/local/freesurfer/subjects/G001 CMD /usr/local/freesurfer/bin/dmri_train --outdir /usr/local/freesurfer/subjects/G001/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.G001.14153.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /usr/local/freesurfer/subjects/G001/dlabel/mni/aparc+aseg_mask.nii.gz --fa /usr/local/freesurfer/subjects/G001/dmri/dtifit_FA.nii.gz --cptdir /usr/local/freesurfer/subjects/G001/dlabel/diff --reg /usr/local/freesurfer/subjects/G001/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc --------------------------------------------------------------------------------------------------

2 1

SLFP
by stdp82＠virgilio.it 05 Feb '14

05 Feb '14

Hi list, SLFP is SLF III? Is there a way to obtain by TRACULA also SLF I and II, knowing the the cortical targets of the tracts? Thanks, Stefano

2 1

TRACULA error: pre-processing
by Won Sang Jung 05 Feb '14

05 Feb '14

Hi, I have a problem running TRACULA in the pre-processing stage. The error message is the following; Loading streamline start ROI from /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz niiRead(): error opening file /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz ERROR: Could not read /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Linux localhost.localdomain 2.6.18-371.1.2.el5 #1 SMP Tue Oct 22 12:51:53 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at 2014. 01. 23. (목) 18:32:17 KST I guess this error started to happen after I updated Freesurfer version 5.3.0 (I could successfully run TRACULA with same data with the prior version of Freesurfer) In my setting, $TUTORIAL_DATA --> /usr/local/freesurfer/subjects/tracula/tutorialdata I tried re-download the file, diffusion_tutorial.tar.gz, from freesurfer server and extracted file again, but still I couldn't find the file "lh.cst_AS_roi1.flt.nii.gz" in Diff001/dlabel/mni folder. Thank you in advance for your advice. Wonsang Jung

2 1

Outputting all tracula statistics to table
by Salil Soman 05 Feb '14

05 Feb '14

Hi, What is the proper way to generate a single table containing all tracula generated statistics for all subjects in a study? I tought tractstats2table was the way to do this, I am confused as to how trac-all -stat factors into this process in the latest (12-09-13 version)? Thank you. -Sal

2 1

Tracula: from anatomical to diffusion space and FSL probtracx
by Garikoitz Lerma-Usabiaga 05 Feb '14

05 Feb '14

Hi Anastasia, I want to use a hippocampal subfield as a seed in FSL. I am having problems understanding how to change spaces around... 1.- Is this command ok? mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ mri/hippo_subfield_in_anatomical_space.mgz --inv --interp nearest --o mri/hippo_subfield_in_diffusion_space.nii --reg dmri/xfms/anatorig2diff.bbr.dat --no-save-reg 2.- I would like to visualize it in freeview in anatomical space to check if it is ok, if I load nu.mgz and hippo_subfield_in_anatomical_space.mgz and then load hippo_subfield_in_diffusion_space.nii with the registration file dmri/xfms/anatorig2diff.bbr.dat, should I visualize it ok? If I don't register it, they show to be displaced (more than expected). 3.- Afterwards I want to run probtracx with the following command (my doubt is mainly about the files to use, since FSL files are RAS, freesurfer anatomical are LIA and freesurfer diffusion are LIA, are all the files in the same format and FSL is ok with it?): /usr/local/fsl/bin/probtrackx --mode=seedmask -x mri/hippo_subfield_in_diffusion_space.nii -s dmri.bedpostX/merged -m dmri.bedpostX/nodif_brain_mask -o fdt_paths_hippo_subfields --dir=FSL_ConnResults_Hipp -c 0.2 -S 2000 --steplength=0.5 -P 5000 --opd many thanks! Gari

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WM editing and longitudinal processing v5.3.0
by Ed Gronenschild 05 Feb '14

05 Feb '14

Hi, From what I can read in the wiki about wm editing, I understand that edited wm voxels have values of either 255 (added) or 1 (removed) and no other values. These are stored in the file wm.mgz. Is that correct? Before processing a lot of data I want to be sure that running recon-all with the option autorecon2-wm will recognize these voxels, also during longitudinal processing. Can you confirm this. FreeSurfer v5.3.0 Mac OSX10.6 Kind regards, Ed

4 8

3D thickness scale
by Jonathan Holt 05 Feb '14

05 Feb '14

Hi all, I’ve pulled up a 3D inflated thickness figure by loading the following into freeview lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 I’m wondering how the colors correspond to thickness and whether or not I can generate a scale to help interpret the figure. best, Jon

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