Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

trac-all error with .nii.gz images, mri_probedicom
by Hao wen 20 Dec '16

20 Dec '16

Hello, FreeSurfer experts: I know that we are going to have a new version of FS 6.0.0, but with the curent newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) for FS5.3.0, I am working on UBUNTU14.0. To run tracula in parallel on my machine, here is my config file( for test, I have two subjects, and all are recon-alled, I stored all the image into .nii.gz(dwi.nii.gz, fmap_magnitude.nii.gz, fmap_phasediff.nii.gz),I use the magnitude and phase image to do the correction for the B0-inhomogeneity, the gradient table format are .bvec and .bval , Here is one of my config file: ### This is to define the CAPS version subjects_dir and subject_id for FreeSurfer setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/Freesurfer/Reconall/reconall_GENFI/clinica_reconall_result/prevdemals_67subjs/analysis-series-default/subjects set dtroot = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result set subjlist = ( sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0 ) ### This is to point to the dwi original data set dcmroot = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test set dcmlist = ( sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.nii.gz) ### This is to define the dwi gradient table(bvel and bvec) set bvecfile = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bvec set bvalfile = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bval ### This is to define the registration-based B0-inhomogeneity compensation with the magnitude and phase map images set dob0 = 1 set b0mlist = (sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_magnitude1.nii.gz) set b0plist = (sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_phasediff.nii.gz) # This is to define Echo spacing for field mapping sequence (from sequence printout), only used when doing registration-based B0-inhomogeneity compensation. set echospacing = 0.7 Here is the command to run the preprocessing: trac-all -path -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt But it gave me some errro from mri_probedicom: mri_probedicom --i /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010002VH/ses-M0/fmap/sub-PREVDEMALS0010002VH_ses-M0_phasediff.nii.gz > /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result/sub-PREVDEMALS0010002VH/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010002VH_ses-M0/dmri/b0info.dat Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Dec 20 18:22:04 CET 2016 The error is obvious, because the image here is not a dicom file, but I suppose tracula can deal with any format for mri_convert? In case you need the trac-all.log, I atttached one of them here. Really need your help, thanks in advance Hao

2 3

Talairach error in monkey brain
by Qi Ting 19 Dec '16

19 Dec '16

Dear Freesurfer experts, I'm using freesurfer to process my monkey brain data. It reported errors during Talairach registration step. So I added no-tal-check tag to run recon-all autorecon1 and used tkregister2 to manually edit registration. However, I couldn't let them perfectly fitted, especially deformation in sagittal view. But when I checked the final parcellation, I found it worked well. So I was wondering whether the Talairach registration step matters a lot for the final results? And whether I did correctly? Thanks in advance! with best regards, Ting Qi

1 0

Poorly Designed Matrix Two Stage Longitudinal Model
by Timothy Hendrickson 19 Dec '16

19 Dec '16

FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I'm curious, I've used the same format of design matrix on cross sectional without problem. Anyway here is the command line input: mri_glmfit --glmdir rh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir \ --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ --y rh.testretest.thickness-spc.stack.fwhm10.mgh \ --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_pairedAnalysis.DOSSDS.mtx \ --label rh.testretest.fsaverage.cortex.label \ --surf fsaverage rh The error message is attached within file error_designMtx_12_19_16.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. Any help would be extremely beneficial. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

1 0

TRACULA to define multiple bvals
by Hao wen 19 Dec '16

19 Dec '16

Hello, Freesurfer experts: I want to ask you in TRACULA, we can define multiple bvecs with the variable 'bveclist' in configuration file, so my question is if we have the same option for bval, or it is mandatory to have the same bvals for all the subjects??? I dont see any information about this... Thanks in advance Hao

2 3

3d brain vessels visualisation
by anand iyer 19 Dec '16

19 Dec '16

Hi Could you please help with this? I am able to create a 3D model of brain with T1 volume. I want to superimpose the surface vessels from a T1 GAD. How do i go about it? Thanks, Anand Anand Iyer

2 1

TRACULA trac-all preprocessing errors
by Hao wen 19 Dec '16

19 Dec '16

Hello, Freesurfer experts: I am new to Tracula, and I followed your tutorial with your tutorial data, and for the preprocessing pipeline, I got some errors when doing the tensor fitting, here is the command: trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial and I looked over the trac-all.log and found that the problem is from the command dmri_train, here is the errro log information: ' /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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 ERROR: fio_pushd: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni cwd /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial cmdline /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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.elmo.2005.25745.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 /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/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 sysname Linux hostname DELLEED1 machine x86_64 user wen Output directory: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni Output directory in test subject's space: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff Output base: 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 Training subject directory list: /tmp/subj33.elmo.2005.25745.txt Location of streamline files relative to base: 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 Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: [1] 1065 segmentation fault (core dumped) --outdir --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr ' and in the output structure /dlabel, I dont have the mni sub-folder, so I guess I have some problems when doning the tensor fitting. And I know in this process, we will need the aparc+aseg.mgz, but the in the tutorial data diffusion_recons , for the subject of elmo.2005, I dont find aparc+aseg.mgz in mri folder, and I just found aparc+aseg2diff.mgz image in Diff001, instead, you use this volume??? I am stuck at this step, any advice will be appreciated:) Thank in advance Hao Good day

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Own ROI for cortical thickness measurements
by andinie＠gmx.net 17 Dec '16

17 Dec '16

Dear Freesurfer-experts, I want to create my own ROI for purposes of cortical thickness measurements in Freesurfer. As input, I have a binary_volume_mask.mgz. But I'm lacking to get this mask as a label or volume into the FS structure. I already tryed the mri_vol2surf and mri_vol2roi, unfortunately without successs. Looking forward to hearing your suggestion, Best, Andreas Niebuhr ............................................................................ ..... Bitte denken Sie an Ihre Verantwortung gegenüber der Umwelt, bevor Sie diese E-Mail drucken. Die in dieser Nachricht enthaltenen Informationen können vertraulich sein und sind ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der vorgesehene Empfänger sein, so bitte ich Sie, den Absender unverzüglich zu informieren und die E-Mail zu löschen. Eine nicht autorisierte Verwendung, Verbreitung oder Kopie ist nicht gestattet. Ich weise darauf hin, dass über das Internet per E-Mail übermittelte Nachrichten verändert oder verfälscht werden können. Herkömmliche E-Mails sind nicht gegen den Zugriff Dritter geschützt, so dass unter Umständen auch die Vertraulichkeit nicht gewahrt sein kann. Von der Übermittlung sensibler Geschäftsdaten sollten Sie daher absehen.

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Please send email only once as list, not each email
by anand iyer 17 Dec '16

17 Dec '16

Hello I am signed up for receiving mails; and i get each individual one which is flooding my inbox can you please send all only once a day as a list? Thanks, Anand Iyer

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Regarding: dlPFC volume
by Dr Sampada Sinha 17 Dec '16

17 Dec '16

Dear freesurfer experts, I managed to create dlPFC ROI and successfully extracted the cortical surface parameters. I also want to have the whole volume of dlPFC (*not* the gray matter volume). Will it make any sense if I multiply dlPFC ROI surface area with its corresponding thickness to get a valid dlPFC volume? Thanks and regards, Sampada -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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Center Director Ad: Umass Amherst Human Magnetic Resonance Center
by Jacquie Kurland 16 Dec '16

16 Dec '16

Please post this ad: Human Magnetic Resonance Center Director (Tenured Associate or Full Professor) The Department of Psychological and Brain Sciences and Institute for Applied Life Sciences at the University of Massachusetts Amherst, invite applications for a tenured faculty position at the rank of associate or full professor to also serve as director of the newly-opened Human Magnetic Resonance (MR) Center, starting September 2017. The Human MR Center houses a state-of-the-art Siemens Skyra 3T and is part of the $95 million investment of the University and the Commonwealth into the new Institute of Applied Life Sciences (http://www.umass.edu/ials/) As a faculty member with a home in the Department of Psychological and Brain Sciences, the director will lead his or her own research lab and related student training. The director is expected to lead the MR Center in all its functions and to carry out his or her own neuroimaging research. As director, this person is expected to build and lead a highly productive center and support the development of MRI and MRS research of new and existing users. The director will also oversee Center staff including physicists and technicians. Applicants must have an MD or PhD in Psychology, Neuroscience, or related field, and a strong track record of research publications and federal funding focused on the development or use of state-of-the-art magnetic resonance techniques and approaches for the study of human brain structure and function. Preference will be given to a candidate with demonstrated leadership and extensive experience and involvement in a successful MR center. We seek relevant expertise in areas such as: anatomical or functional neuroimaging; development of new neuroimaging methodologies; or neuroimaging of cognition To apply, submit the following materials: Curriculum vitae, research statement, contact information for three references, and a letter of application that addresses the responsibilities and requirements described above. Applicants must submit all materials by the priority deadline of January 25, 2017, in order to ensure consideration. Please submit materials online to: http://umass.interviewexchange.com/jobofferdetails.jsp?JOBID=79603 For questions about the position, contact search committee co-chair, Rebecca Spencer, rspencer(a)umass.edu<mailto:rspencer@umass.edu>. The University is committed to active recruitment of a diverse faculty and student body. The University of Massachusetts Amherst is an Affirmative Action/Equal Opportunity Employer of women, minorities, protected veterans, and individuals with disabilities and encourages applications from these and other protected group members. Because broad diversity is essential to an inclusive climate and critical to the University's goals of achieving excellence in all areas, we will holistically assess the many qualifications of each applicant and favorably consider an individual's record working with students and colleagues with broadly diverse perspectives, experiences, and backgrounds in educational, research or other work activities. We will also favorably consider experience overcoming or helping others overcome barriers to an academic degree and career. Thank you in advance, Jacquie Kurland -- Jacquie Kurland, Ph.D., CCC-SLP Associate Professor Dept. of Communication Disorders (413) 545-4007 jkurland(a)comdis.umass.edu<mailto:jkurland@comdis.umass.edu>

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Freesurfer December 2016