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30099 discussions

Rotation involved in recon-all
by Ed Gronenschild 06 Feb '14

06 Feb '14

Hi, Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation of the T1 data early in the pipeline, i.e., converting rawavg.mgz to orig.mgz., see excerpt of output of mri_info below rawavg.mgz: xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813 : x_a = -0.9999, y_a = -0.0066, z_a = 0.0076, c_a = 14.8386 : x_s = 0.0059, y_s = -0.9958, z_s = -0.0913, c_s = 13.1335 orig.mgz: xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 0.0813 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 14.8386 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 13.1335 Is that the default way of processing the data? Cheers, Ed

3 5

dmri_motion Error bvals
by Liliana Maia 06 Feb '14

06 Feb '14

Hi, Within the new Tracula update and with outputs resulted from *trac-all -prep -noqa* I ran *: * *dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog'* And an error message appears: *machine x86_64Output motion measure file: /home/lapsi/test/motion.txtInput transform file: /home/lapsi/test/dwi.ecclogInput DWI file: /home/lapsi/test/dwi_orig.nii.gzInput b-value table: /home/lapsi/test/bvalsLow-b image intensity threshold: 100Nominal diffusivity: 0.001Loading volume-to-baseline affine transformationsComputing between-volume head motion measuresINFO: Processed transforms for 33 volumesLoading DWI volume series from /home/lapsi/test/dwi_orig.nii.gzLoading b-value table from /home/lapsi/test/bvalsERROR: Could not open /home/lapsi/test/bvals for reading* I tried with the b-values one value for each line in file bvalsT (see attachments): *dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' --mat 'dwi.ecclog'*,but the same error occurred. What can I do to verify this head motion? Thank you Best, -- Liliana Maia MEng Biomedical Engineering

2 2

Tracula only outputs merged flt file (and missing bbr)
by Salil Soman 06 Feb '14

06 Feb '14

Hi, Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt file and not the merged ... bbr file in paths? All of my dmrirc files have both bbr and flt =1, and most of my outputs have both, but occasionally I only get 1. Thanks! -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

2 2

Tracula shows some tracks with bbr and others with flt
by Salil Soman 06 Feb '14

06 Feb '14

Hi, I have a couple of dti cases where bbr will include forceps major and missing forceps minor and flt will be the opposite. Similar things have occurred for anterior thalamic tracts and cingulum bundles. Any suggestions on what I may be doing incorrectly? Best wishes, Sal

1 0

thickness visualization in SPM
by Muhammad Naveed Iqbal Qureshi 05 Feb '14

05 Feb '14

Hi, How can I convert freesurfer .thickness files into .nii volume data to analyze in SPM I have already converted the .thickness files into .nii format by using mri_convert command but the converted files can not be visualize in spm probably I need to project the thickness on anatomical volume to visualize it correctly in spm can anyone help me waiting for your replies Thank you Best Regards, Muhammad Naveed Iqbal Qureshi P please don't print this e-mail unless you really need to

2 1

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

2 1

"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

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