Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

How to overlay FSL GFEAT statistical maps onto a fsaverage surface
by Yang, Daniel 03 Aug '13

03 Aug '13

Hi FreeSurfer Expert, So GFEAT results are in MNI152 standard space. Is there a way I can visualize the GFEAT results on a fsaverage surface? For example, if I do the following, would that be okay? tksurfer fsaverage lh inflated -annot aparc.annot \ -ov fbert.gfeat/cope1.feat/stats/zstat1.nii.gz \ -ovreg fbert1.feat/reg/freesurfer/anat2std.register.dat \ -fthresh 2.3 -fmid 3.3 -fslope 1 Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Segmentation Abnormalities Label
by Zhu, Alyssa 02 Aug '13

02 Aug '13

Hi, Is there a way to get the various intensity abnormality labels (100-117) seen in the FreeSurferColorLUT.txt file (e.g. via a different command line option)? Thus far we've only been getting the WM-hypointensities (77) and non-WM-hypointensities (80) labels. I read in another thread that some labels are no longer used in current versions (my lab is using v5.1). Is that the case here? Thanks, Alyssa

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make the annotation more transparent in freeview?
by Yang, Daniel 02 Aug '13

02 Aug '13

Hi FreeSurer Expert, I am wondering if there is a way that the annotation can be made somewhat transparent in freeview so that I can still see the functional activation on top of the annotation? Thanks, Daniel

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Re: [Freesurfer] Trac-all question
by Anastasia Yendiki 02 Aug '13

02 Aug '13

It can have any name you want. You just have to type the right name next to the "-c ..." On Fri, 2 Aug 2013, Alan Francis wrote: > Sorry. I have another question. Should I name the config file dmrirc.txt or > is there any other name? > thank you so much, > > Alan > > > On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis <alandarkenergy(a)gmail.com> > wrote: > Thanks Anastasia. > > > On Fri, Aug 2, 2013 at 2:26 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Alan - All the "set ..." commands for tracula need to > be in a configuration file. You then pass that > configuration file as an argument to the "-c" option of > trac-all. See tutorial: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Hope this helps, > a.y > > On Fri, 2 Aug 2013, Alan Francis wrote: > > Hi Anastasia and others: > I have been trying to run Trac all on five brains. > It keeps giving me the > error message: > > ERROR: run list is longer than subject list > > My run list is equal to the subject list: Here is > the environment: > > Thanks for your help, > > Alan > Martinos Center for Biomedical Imaging > > __________________________________________________________________ > > -------- > freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > -------- > > Setting up environment for FreeSurfer/FS-FAST (and > FSL) > FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ > FSFAST_HOME > /usr/local/freesurfer/stable5_3_0//fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR > /usr/local/freesurfer/stable5_3_0//subjects > MNI_DIR > /usr/local/freesurfer/stable5_3_0//mni > FSL_DIR /usr/pubsw/packages/fsl/current > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : setenv SUBJECTS_DIR /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : setenvSUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data > /diffusion_r > econs/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set dtroot = /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set dtroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ > r > econs/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set subjlist = (101/ 102/ 103/ 104/ 105/) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set dcmroot = /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set dcmroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ > r > econs/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set dcmlist=(101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001 > . > nii \ > ?102/Diffusion_Recons/20080911_101015358000-000010-000001DIFFUSIONHighResva > l > erabi1002s010a001.nii \ > ?103/Diffusion_Recons/20080911_140753578000-000010-000001DIFFUSIONHighResva > l > eraBI1003s010a001.nii \ > ?104/Diffusion_Recons/20080915_160812745000-000010-000001DIFFUSIONHighResVa > l > eraBI104s010a001.nii \ > ?105/Diffusion_Recons/20080917_190940899000-000016-000001DIFFUSIONHighResVa > l > eraBI105s016a001.nii \ > ? ) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set runlist = (101/ 102/ 103/ 104/ > bem/ mri/ stats/ > touch/ > Diffusion_Recons/ scripts/ surf/ > trash/ > label/ src/ tmp/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set runlist = (101/ 102/ 103/ 104/ 105/) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set bvecfile = /autofs/space/dbvecs.txt > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set bvecfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ > r > econs/bvecs.txt > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set bvalfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_ > r > econs/bvals.txt > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set doeddy = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set dorotbvecs = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set usemaskanat = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set thrbet = 0.3 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set doregflt = 0 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set doregbbr = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set doregmni = 1 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set doregcvs = 0 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set mnitemp = > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set cvstemp = cvs_avg35 > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set cvstempdir = $FREESURFER_HOME/subjects > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set pathlist = ( lh.cst_AS rh.cst_AS \ > ? lh.ilf_AS rh.ilf_AS \ > ? lh.unc_AS rh.unc_AS \ > ? fmajor_PP fminor_PP \ > ? lh.atr_PP rh.atr_PP \ > ? lh.cab_PP rh.cab_PP \ > ? lh.ccg_PP rh.ccg_PP \ > ? lh.slfp_PP rh.slfp_PP \ > ? lh.slft_PP rh.slft_PP ) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 > 5) > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : trac-all -prep -c /autofs/space/d > dali_001/ dali_002/ dali_003/ > csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_ > Data/diffusion_ > recons] : trac-all -prep-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion > _r > econs/ > > ERROR: run list is longer than subject list > > > > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > >

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Trac-all question
by Alan Francis 02 Aug '13

02 Aug '13

Hi Anastasia and others: I have been trying to run Trac all on five brains. It keeps giving me the error message: ERROR: run list is longer than subject list My run list is equal to the subject list: Here is the environment: Thanks for your help, Alan Martinos Center for Biomedical Imaging __________________________________________________________________ -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/ FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects MNI_DIR /usr/local/freesurfer/stable5_3_0//mni FSL_DIR /usr/pubsw/packages/fsl/current csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set dtroot = /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set dtroot = /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set subjlist = (101/ 102/ 103/ 104/ 105/) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set dcmroot = /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set dcmroot = /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set dcmlist = (101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.nii \ ? 102/Diffusion_Recons/20080911_101015358000-000010-000001DIFFUSIONHighResvalerabi1002s010a001.nii \ ? 103/Diffusion_Recons/20080911_140753578000-000010-000001DIFFUSIONHighResvaleraBI1003s010a001.nii \ ? 104/Diffusion_Recons/20080915_160812745000-000010-000001DIFFUSIONHighResValeraBI104s010a001.nii \ ? 105/Diffusion_Recons/20080917_190940899000-000016-000001DIFFUSIONHighResValeraBI105s016a001.nii \ ? ) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set runlist = (101/ 102/ 103/ 104/ bem/ mri/ stats/ touch/ Diffusion_Recons/ scripts/ surf/ trash/ label/ src/ tmp/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set runlist = (101/ 102/ 103/ 104/ 105/) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set bvecfile = /autofs/space/dbvecs.txt dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set bvecfile = /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set bvalfile = /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvals.txt csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set doeddy = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set dorotbvecs = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set usemaskanat = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set thrbet = 0.3 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set doregflt = 0 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set doregbbr = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set doregmni = 1 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set doregcvs = 0 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set cvstemp = cvs_avg35 csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set cvstempdir = $FREESURFER_HOME/subjects csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set pathlist = ( lh.cst_AS rh.cst_AS \ ? lh.ilf_AS rh.ilf_AS \ ? lh.unc_AS rh.unc_AS \ ? fmajor_PP fminor_PP \ ? lh.atr_PP rh.atr_PP \ ? lh.cab_PP rh.cab_PP \ ? lh.ccg_PP rh.ccg_PP \ ? lh.slfp_PP rh.slfp_PP \ ? lh.slft_PP rh.slft_PP ) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/d dali_001/ dali_002/ dali_003/ csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/ ERROR: run list is longer than subject list

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trac-all inquiry
by David Soto 02 Aug '13

02 Aug '13

Hi, I have successfully run recon-all in my dataset and now am attempting to use trac-all on my diffusion data obtained on a Siemens scanner. Diffusion dicoms were transformed to .nii using MRIConverter and then to .mnc using nii2mnc output.nii output_t.mnc. I am trying to run trac-all on a single subject and for this I have created the configuration file attached (tracula02ST) As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui and within each subject the T1 serving as input for recon-all are in mri/orig while the diffusion images are in a folder call diffdata (named output_t.mnc) which also contains the bvecs and bvals files, which were transposed and organised according to the tutorial (named as bvecs_t.txt and bvals_t.txt) When I run: trac-all -c tracula02ST.txt I get: ERROR: no analysis step (-{prep,bedp,path}) has been selected THEN I run: trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so and then gives the long output text below with an error message. Segmentation fault (core dumped) foreach: No match. The trac-all.log is attached also. Could you please help? Cheers David -- http://www1.imperial.ac.uk/medicine/people/d.soto/ wmen-dsoto3:~/Documents/fmri/rsdtianawmgui> trac-all -prep -bedp -path -c tracula02ST.txt INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui Actual FREESURFER_HOME /usr/local/freesurfer trac-paths -c /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/dmrirc.local -log /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.log -cmd /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Aug 2 09:44:20 BST 2013 /usr/local/freesurfer/bin/dmri_paths --outdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cst_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cst_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ilf_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ilf_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.unc_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.unc_AS_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fmajor_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fminor_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.atr_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.atr_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ccg_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ccg_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cab_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cab_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slfp_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slfp_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slft_PP_avg33_mni_bbr /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slft_PP_avg33_mni_bbr --dwi /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz --grad /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs --bval /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals --mask /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz --bpdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz 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/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids --seg /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 Segmentation fault (core dumped) foreach: No match. wmen-dsoto3:~/Documents/fmri/rsdtianawmgui>

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Alternative methods of controlling for grey matter exclusion
by Gonzalo Iribarne 02 Aug '13

02 Aug '13

Hello Freesurfer Experts, I am attaching snapshots of problem areas I continue to work with in reconstructing surfaces from children T1 weighted scans. In several different participants, movement is often a factor in creating striated movement artifacts along the outer edge of cortex. I have previously edited white matter and added control points that have sufficiently moved the pial surface, but there are several occasions where "white" high intensity voxels appear outside grey matter surfaces, yet visually seem too close to the edge to designate as white matter with control points/wm edits. In other instances, there are several areas excluded from grey matter boundaries that have no "white matter" voxels near enough to help extend the surface. Can bias field/normalization be used in making corrections for excluded grey matter/noisy high intensity voxels? Thank you in advance, Gonzalo Iribarne [image: Inline image 2][image: Inline image 3][image: Inline image 1]

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 02 Aug '13

02 Aug '13

Hi Anastasia Thank you for your answer. Yes, those files exist. I also extracted the bvec an bval files with anotther software then dcm2nii and i keep getting the same kind of error. Also, about the 6 diffusion direction, those data i sent you, are just testdata for running tracula. sincerely Florian >>> Anastasia Yendiki 02.08.13 0.41 Uhr >>> Hi Florian - Do these files exist? /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals The format of the bvecs and bvals that you sent seems fine, but (and this has nothing to do with the error you're getting) I have to warn you that you may not be able to get good results running probabilistic tractography on this data. It looks like you're acquiring the same 6 diffusion directions, repeated 8 times. Six directions is the absolute minimum for reconstructing the tensor model, but will probably not be sufficient for the crossing fiber model that bedpostx reconstructs (and is used by tracula). Your scan time is better spent acquiring 48 different directions, rather than the same 6 directions 8 times. a.y On Mon, 29 Jul 2013, Borsodi Florian wrote: > Hello, > > I have been trying to run tracula on my data and i keep getting the same > kind of error repeatedly. > For my imput I am using dicoms from a Siemens scanner with a stadard > diffusion protocol. However, tracula cannot read the bvec and bval data out > of the dicom header. Therefore, I implemented bvec and bval files into the > config file. > After doing so, I got the error which says that tracula cannot find the > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > I have tried many options, but still cannot find a solution. > I am hoping to get some troubleshooting help. > > I have atteched my log- and config- files, as well as my bvec and bval > files. > To uphold patient confidentiality, I have encode the name patient's data as > "AAAAAA". > > I believe the problems are the bvec and bval files or their structures. The > log-file lete me assume this, especially the lines 202 - 205, 264 - 268 and > 1480 - 1484. > > Thank you in advance for your help, and your speedy response. > > With kind regards, > > Florian Borsodi > Department of Neurology > Medical University of Graz > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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GLUT: Fatal Error
by Amy Bilderbeck 02 Aug '13

02 Aug '13

I'm getting started on my first Freesurfer project (previously using SPM and FSL only). I'm working via the jalapeno cluster at FMRIB (University of Oxford) which runs, I believe, the latest version of FreeSurfer. I've run into a number of early problems, including whilst working on the tutorial data. I will describe what I hope is a basic problem. I cannot get tkmedit to work, and see the error message GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: :7.0 (my display number for my VNC connection is 7) I have, I think, launched FreeSurfer correctly in the terminal before running the tkmedit command, using either . $FREESURFER_HOME/SetUpFreeSurfer.sh SUBJECTS_DIRecho SUBJECTS Or tcsh source . $FREESURFER_HOME/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs So, I can see previous threads suggesting I have not launched FreeSurfer correctly but I suspect FreeSurfer is indeed launched, or perhaps because I need to be using X11/xming. But of course I am unsure. Any tips? Dr. Amy Bilderbeck University of Oxford, Dept of Psychiatry Warneford Hospital, OX3 7JX

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Re: [Freesurfer] optseq2
by Douglas Greve 01 Aug '13

01 Aug '13

On 8/1/13 8:03 PM, Claire Wilcox wrote: > Thanks much! Good to know:). > > Can you clarify the second option? Do you mean just specify one event, and then change the name to one of four possibilities (low cs, low us, high cs, high us)? That prob wouldn't work as we would love to optimize contrast bw low and high cs/us. Yes, this is what I mean. :( > > We actually also want to keep the cs and us separate (and jitter time between) so that we can look at activation associated with cs separate from us, so sadly your first idea won't work either. > > Sent from my iPhone > > On Aug 1, 2013, at 5:35 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote: > >> Hi Claire, you can't do this type of design in optseq because optseq >> requires that there be no constraints of which stimulus can follow >> itself or another stimulus (obviously this does not work for your >> design). If you take a CS-US pair as a stimulus, then that should work. >> Also, you could spec just one condition and randomly recode stimuli as >> CS and US. It is not perfect, but you'd get the random timing, and it is >> probably good enough. >> >> doug >> >> >> On 8/1/13 6:44 PM, Claire Wilcox wrote: >>> hello, >>> i'm struggling with how to specify a schedule and then ask optseq2 to identify an optimal timing schedule. specifically i have a conditioned cue and an unconditioned stimulus. the high threat CS always needs to follow with a high pain US and low threat CS with a low pain CS. how can i specify such a schedule in optseq2? i've been trying a number of combinations of below, but am failing miserably with lots of varying warnings and error messages and inability to read files or 'Bus error' >>> >>> what should the --in input schedule file format look like? that might be the missing link .. although that's hard to say for sure. >>> >>> many thanks, >>> claire >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> >

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