[Freesurfer] Post-doctoral Research Position at the Yale Alzheimer's Disease Research Unit
External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit and the Yale PET Center has an opening for a highly qualified and motivated individual at the post-doctoral level to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Ph.D. in neuroscience, biomedical engineering, or a related field. Qualifications: Strong experimental, analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Ph.D. or an M.D./Ph.D. with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.me...@yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Image Analyst Position at the Yale Alzheimer's Disease Research Unit
External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit at Yale University School of Medicine has an opening for a highly qualified and motivated individual to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Master’s Degree or a Bachelor’s Degree with significant experience in neuroimaging analysis. Qualifications: Strong analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Master’s Degree or a Bachelor’s Degree with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.me...@yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Post-doctoral Research Position at the Yale Alzheimer's Disease Research Unit
External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit and the Yale PET Center has an opening for a highly qualified and motivated individual at the post-doctoral level to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Ph.D. in neuroscience, biomedical engineering, or a related field. Qualifications: Strong experimental, analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Ph.D. or an M.D./Ph.D. with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.me...@yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt_recon error: MatrixReadTxt: could not scan value [1][1]
Hello FreeSurfer Developers, I'm trying to pre-process some diffusion data based on the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 I am getting the following warning followed by the program hanging -- Creating output directory /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon Loading y from /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon/dwi-ec.nii.gz ... done reading. MatrixReadTxT: could not scan value [1][1] WARNING: matlab elment type is 1869357167, which is not a matrix. could not allocate 543518770 x 1683973236 matrix Cannot allocate memory unsupported matlab format 1678398324 (unknown) Cannot allocate memory -- I would greatly appreciate your assistance. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 6.9 (Final) 3) uname -a: Linux ariespet.med.yale.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Mar 21 19:29:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) dt_recon.log: see attached Thank you, Adam dt_recon logfile Fri Jan 19 20:58:24 EST 2018 VERSION $Id: dt_recon,v 1.23 2015/12/09 20:02:53 zkaufman Exp $ setenv SUBJECTS_DIR /home1/am2359/fs6_data/fpeb_app_fs cd /home1/am2359/Desktop /home1/am2359/freesurfer_6/bin/dt_recon --i /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom/MR.1.3.12.2.1107.5.2.32.35071.2015070812382834753264293 --s fpeb001 --o /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon ariespet.med.yale.edu am2359 /pet/apps/fsl5.0/bin/eddy_correct ECRefTP 0 #@#--- Converting input Fri Jan 19 20:58:24 EST 2018 cd /home1/am2359/Desktop mri_convert /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom/MR.1.3.12.2.1107.5.2.32.35071.2015070812382834753264293 /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon/dwi.nii mri_convert.bin /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom/MR.1.3.12.2.1107.5.2.32.35071.2015070812382834753264293 /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon/dwi.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom/MR.1.3.12.2.1107.5.2.32.35071.2015070812382834753264293... Getting Series No INFO: Found 2584 files in /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom INFO: Scanning for Series Number 6 Scanning Directory INFO: found 1664 files in series INFO: loading series header info. RunNo = 5 INFO: sorting. sdfiSameSlicePos() eps = 0.01 INFO: (128 128 64), nframes = 26, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; FileName /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom/MR.1.3.12.2.1107.5.2.32.35071.2015070812364240080860825 Identification NumarisVersyngo MR B17 ScannerModel TrioTim PatientName FPEB001 Date and time StudyDate 20150708 StudyTime 120054.296000 SeriesTime123644.50 AcqTime 123641.007500 Acquisition parameters PulseSeq ep_b0 Protocol ep2d_dti_1b0_25d PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 85 InversionTime -1 RepetitionTime7900 PhEncFOV 256 ReadoutFOV256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows128 NImageCols128 NFrames 26 SliceArraylSize 64 IsMosaic 0 ImgPos128.4139 158.0412 -61.9693 VolRes 2. 2. 2. VolDim128 128 64 Vc -1. -0. 0. Vr -0. -1. 0. Vs -0. -0. 1. VolCenter 0.4139 30.0412 2.0307 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 INFO: no Siemens slice order reversal detected (good!). TR=7900.00, TE=85.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon/dwi.nii... Saving bvals and bvecs cd /home1/am2359/Desktop mri_probedicom --i /home1/am2359/fs6_data/fpeb_app_dicom/fpeb001/3d_dicom/MR.1.3.12.2.1107.5.2.32.35071.2015070812382834753264293 Manufacturer SIEMENS ScannerModel TrioTim SoftwareVersion syngo MR B17 ScannerSerialNo 35071 Institution Yale University School of Medicine SeriesDescription ep2d_dti_1b0_25d StudyUID 1.3.12.2.1107.5.2.32.35071.301507081121329210013 StudyDate 20150708 StudyTime 120054.296000 PatientName FPEB001 SeriesNo 6 ImageNo 887 AcquisitionType 2D ImageType ORIGINAL\PRIMARY\DIFFUSION\NONE\ND ImagingFrequency 123.165588 PixelFrequency 1776 ImagedNucleus 1H EchoNumber 1 FieldStrength 3 PulseSequ
[Freesurfer] Fwd: mri_glmfit-sim --surf question
Hello FreeSurfer Developers, I have run a glm on the left hemisphere to compare cortical thickness between 2 groups. After, I did a cluster-wise correction with permutation testing using this command mri_glmfit-sim --glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs It completes without error, but I have a question about the log file and --surf argument. My concern if about this part of the log file where it shows "--surf fsaverage lh white" (see section from log file and complete log file attached). White is the default I based on the help file for mri_glmfit. Should I be running with --surf fsaverage lh pial? Does this imply that the glm is performed on the white matter surface. I am then visualizing on the inflated pial surface so does this cause a problem? -- 1/1 Fri Mar 2 03:23:25 EST 2018 mri_glmfit --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 FWHM = 0.00 gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd INFO: gd2mtx_method is dods Reading source surface /home1/am2359/fs6_data/fpeb_ app_fs/fsaverage/surf/lh.white --- Thank you, Adam cd /home1/am2359/fs6_data/fpeb_app_fs /home1/am2359/freesurfer_6/bin/mri_glmfit-sim --glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs $Id: mri_glmfit-sim,v 1.60.2.4 2016/11/17 18:01:28 zkaufman Exp $ Fri Mar 2 03:23:25 EST 2018 Linux tauruspet.med.yale.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Mar 21 19:29:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux am2359 setenv SUBJECTS_DIR /home1/am2359/fs6_data/fpeb_app_fs FREESURFER_HOME /home1/am2359/freesurfer_6 Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.sv2a.group.thickness.10.mgh --fsgd dx_sv2a.fsgd --C sv2a_thickness_group.mtx --surf fsaverage lh --cortex --glmdir lh.sv2a_group.glmdir.10 DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 1000 1/1 Fri Mar 2 03:23:25 EST 2018 mri_glmfit --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 FWHM = 0.00 gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd INFO: gd2mtx_method is dods Reading source surface /home1/am2359/fs6_data/fpeb_app_fs/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home1/am2359/fs6_data/fpeb_app_fs cmdline mri_glmfit.bin --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white sysname Linux hostname tauruspet.med.yale.edu machine x86_64 user am2359 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/home1/am2359/fs6_data/fpeb_app_fs/lh.sv2a.group.thickness.10.mgh logyflag 0 usedti 0 FSGD lh.sv2a_group.glmdir.10/y.fsgd mask lh.sv2a_group.glmdir.10/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /home1/am2359/fs6_data/fpeb_app_fs/lh.sv2a.group.thickness.10.mgh ... done reading. INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.1 Found 149953 voxels in mask Reshaping mriglm->mask... search space = 74612.064358 DOF = 19 thresh = 2, threshadj = 1.69897 Starting simulation sim over 1000 trials mri_glmfit simulation done 20.274 Fri Mar 2 03:43:45 EST 2018 mri_surfcluster --in lh.sv2a_group.glmdir.10/sv2a_thickness_group/sig.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --cwsig lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --sum lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.summary --ocn lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --annot aparc --cwpvalthresh .05 --o lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh --no-fixmni --csd lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001-sv2a_thickness_group.csd --csdpdf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.pdf.dat --vwsig lh.sv2a_group.glmdir.10
