Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

QDEC cluster output
by Lara Foland-Ross 18 Oct '19

18 Oct '19

External Email - Use Caution Hi Freesurfer experts, I’m running a simple qdec analysis to examine group differences in surface measures between a patient and control group, controlling for age and TBV. I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs), I get the following output in my terminal window: ~~~~~~~~~~~~ # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 7.365 125481 2114.03 -34.4 4.1 1.6 0.01660 0.01500 0.01820 4933 insula 2 3.851 73048 1830.45 -8.4 30.1 29.4 0.03440 0.03210 0.03670 3210 superiorfrontal 3 -3.248 128137 4923.73 -8.1 -64.0 5.8 0.00010 0.00000 0.00020 7680 lingual Simulation complete. ~~~~~~~~~~~~ However, when I click on “Find clusters and go to max”, the output in my terminal window changes to be as follows: ~~~~~~~~~~~~ Generating cluster stats using min threshold of 1.3... Found 3 clusters Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -4.0000 33 4923.73 -12.0 -67.1 34.7 7680 precuneus 2 1.7799 9 2114.03 -26.3 23.8 -6.0 4933 lateralorbitofrontal 3 1.4634 21 1830.45 -6.6 33.8 49.8 3210 superiorfrontal ~~~~~~~~~~~~ Lastly, I see that the x/y/z coordinates of the peak coordinates listed above are on the very edge of the corrected cluster. Yet, visual inspection of the peaks from uncorrected significance maps suggest that the peaks it is quite far from the “hottest” parts of the uncorrected significance maps. My questions are: 1. Why are these values different, and what values should I report? 2. Are the peaks listed above the center of gravity? Or highest p value of the cluster? Curious as to why the heatmap values are so different from the values above. Many thanks, Lara

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 18 Oct '19

18 Oct '19

External Email - Use Caution Dear Douglas, Did you get the subjects? I hope I loaded them correctly. Best regards, Marina.

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mri_pretess: Cannot allocate memory
by Peled, Noam 17 Oct '19

17 Oct '19

Dear group, When trying to run mri_pretess, I'm getting this error: znzTAGskip: tag=809120822, failed to calloc 1802706944 bytes! Cannot allocate memory Here is the full command I'm using (in the Martinos center, using ver6 stable): mri_pretess /autofs/space/thibault_001/users/npeled/subjects/mg27/mri/aseg.mgz 54 /autofs/space/thibault_001/users/npeled/subjects/mg27/mri/norm.mgz /autofs/space/thibault_001/users/npeled/subjects/mg27/tmp/274f23/54_filled.mgz Thanks! Noam

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Tracula question
by Alan Francis 17 Oct '19

17 Oct '19

External Email - Use Caution Dear Anastasia - I tried running tracula preproc. However, it gave me an error message. Could you please shed some light on this? Thank you, Alan [airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 trac-preproc -c /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local -log /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log -cmd /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable6/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Oct 15 10:01:10 EDT 2019 mri_convert --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals orientLAS /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -18.7806 mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) -> (-0.996936, 0.0343122, -0.0703008) normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) -> (0.0173889, 0.973389, 0.228497) normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) -> (-0.0762703, -0.226574, 0.971003) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) Reslicing using nearest writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz... INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals eddy_correct /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz 0 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0000 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0001 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0002 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0003 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0004 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0005 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0006 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0007 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0008 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0009 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0010 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0011 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0012 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0013 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0014 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0015 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0016 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0017 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0018 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0019 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0020 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0021 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0022 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0023 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0024 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0025 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0026 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0027 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0028 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0029 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0030 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0031 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0032 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0033 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0034 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0035 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0036 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0037 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0038 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0039 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0040 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0041 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0042 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0043 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0044 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0045 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0046 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0047 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0048 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0049 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0050 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0051 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0052 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0053 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0054 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0055 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0056 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0057 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0058 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0059 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0060 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0061 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0062 mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.ecclog /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/data.nii.gz mri_convert --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz mri_convert.bin --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) keeping frame 63 ERROR: valid frame numbers are between 0 and 62 Linux airhunger.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Oct 15 10:17:55 EDT 2019 -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> * *afrancis(a)mclean.harvard.edu <afrancis(a)mclean.harvard.edu>*

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FreeSurfer mal list - please remove me
by Adam Rytina 17 Oct '19

17 Oct '19

External Email - Use Caution Hello all, few days ago I subscribed to the FreeSurfer list in order to get e-mails regarding the FreeSurfer issues. I will not use FreeSurfer anymore. Hence, please, could you remove me from this list? Thanks a lot Adam

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freeview: load multiple volumes with a single option
by Jang, Ikbeom 16 Oct '19

16 Oct '19

Dear FreeSurfer community: I am a beginner and tying to load multiple volumes in Freeview with a single option applied to all the volumes. For example, I would like to set grayscale window as min=0 and max=100 for all volumes. Is there a simple command line which does that efficiently? The command line below works if I provide the option for each volume: freeview -v sitename/mri/subj0401/brainmask.mgz:grayscale=0,100 \ sitename/mri/subj0402/brainmask.mgz:grayscale=0,100 \ ... \ sitename/mri/subj0425/brainmask.mgz:grayscale=0,100 However, the command line something like this does not: freeview -v sitename/mri/subj*/brainmask.mgz:grayscale=0,100 Thanks in advance, Ikbeom

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recon-all skull stripping
by Inglese, Marianna 16 Oct '19

16 Oct '19

External Email - Use Caution To whom it may concern, I am using recon-all to segment many T1s. As I can see, one of the automatic step performed by recon-all is the skull stripping. Would it be possible to know the threshold used for the stripping? I guess it is the same threshold everytime. I would like to apply the skull stripping only on other T1s and need to get the same result. Thank you very much for the help. Yours faithfully, Marianna Inglese Research fellow, Imperial College London Department of Surgery and Cancer

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Postdoctoral Positions in Pediatric Neuroimaging at the Waisman Center, University of Wisconsin Madison
by Doug Dean III 16 Oct '19

16 Oct '19

External Email - Use Caution Postdoctoral Research Associate Waisman Center, University of Wisconsin–Madison, Madison WI The Waisman Laboratory for Brain Imaging & Behavior at the Waisman Center, University of Wisconsin–Madison, is seeking highly motivated postdoctoral researchers to work on neuroimaging research studies of young children and individuals with intellectual and developmental disorders (IDDs). Areas of research include the development and evaluation of image acquisition and analyses for brain imaging studies of infants, young children, and individuals with autism, Down syndrome and fragile X syndrome. The Alexander and Dean labs at the Waisman Laboratory for Brain Imaging & Behavior have multiple projects using MRI and functional near infrared spectroscopy (fNIRS). Work is ongoing to develop rapid, quiet and motion-correction imaging methods to improve studies in these challenging populations. Studies are also under way to characterize brain structure, microstructure and function change during early brain development and how development is affected in IDDs. The postdoctoral research associates will have opportunities to participate in activities related to neuroimaging methods development and evaluation, study data collection and analyses, research publications, grant writing and are expected to make positive scholarly contributions to our interdisciplinary and highly collaborative research programs. Desired Qualifications: Ph.D. in medical physics, neuroscience, engineering and/or a related field. Prior experience with imaging techniques (e.g. MRI, DTI, fMRI, PET, fNIRS) is preferred. Experience with brain image analysis software tools, MATLAB, Python, C++ and/or other computer programming is highly desirable. Pulse sequence programming experience would be a plus but not required. The candidate is expected to have an emerging track record of publishing in academic journals, strong analytic skills, and capable of working within a collaborative environment. Interested candidates should send: 1) curriculum vitae; 2) cover letter outlining research interests, experience, and career goals; and 3) a list of three references to either Dr. Andy Alexander at alalexander2(a)wisc.edu<mailto:alalexander2@wisc.edu> or Dr. Douglas Dean at deaniii(a)wisc.edu<mailto:deaniii@wisc.edu>.

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Postdoc Position at UPenn
by Mackey, Allyson P 16 Oct '19

16 Oct '19

External Email - Use Caution Postdoctoral Fellowship in Pediatric Neuroimaging at the University of Pennsylvania Drs. Allyson Mackey and Dylan Tisdall are seeking a postdoctoral fellow for an NIH-funded study on early childhood brain development. The goals of the study are to develop motion-resilient structural and functional MRI sequences, and to validate the new sequences in 100 children between the ages of 3 and 5. Children will be recruited from high-poverty, high-opioid use neighborhoods of Philadelphia. This study is part of the HEALthy Brain and Child Development (HBCD)<https://heal.nih.gov/research/infants-and-children/healthy-brain> planning initiative. Ultimately, HBCD will enroll pregnant mothers and follow children for at least 10 years, and will include data on children’s experiences, brain structure and function, and social, emotional, and cognitive development. The postdoctoral fellow will join the Changing Brain Lab<http://www.allysonmackey.com/> at the University of Pennsylvania, an interdisciplinary research group that studies how young children’s experiences change their brains. We are interested in the development of academically-relevant skills including reasoning, curiosity, creativity, and persistence. The CBL is part of a vibrant psychology and neuroscience community at Penn, and is affiliated with mindCORE<https://mindcore.sas.upenn.edu/>, the Center for Neuroscience and Society<https://neuroethics.upenn.edu/>, and the Positive Psychology Center<https://ppc.sas.upenn.edu/>. Imaging is conducted at the Center for Functional Neuroimaging<https://cfn.upenn.edu/facilities.htm>, which includes research-dedicated 3T Siemens Prisma and 7T Siemens Terra scanners. We welcome candidates with doctoral degrees in a wide variety of fields, including physics, engineering, statistics, neuroscience, and psychology. Applicants should have strong publication records, experience with pediatric neuroimaging, strong statistical training, and excellent computational skills. To apply, please send a cover letter describing your doctoral research and your goals for postdoctoral training, as well as your CV to Allyson Mackey at mackeya(a)upenn.edu<mailto:mackeya@upenn.edu>. As the position involves collaborating with multiple advisors, graduate students, and research assistants, please provide contact information for someone who has mentored you, and for someone you have mentored. Applications will be reviewed as they are received.The position is for one year, renewable for up to 3 years total. Ideal start date is on or before February 1st, 2020. -- Allyson Mackey, Ph.D. Assistant Professor Department of Psychology University of Pennsylvania 425 S. University Avenue Levin Building, Room 354 Philadelphia, PA 19104 215-573-3074

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FS-FAST: cluster size from 1st level analysis
by Keri Woods 16 Oct '19

16 Oct '19

External Email - Use Caution Hi From the 1st level analysis of an fMRI study I'm trying to extract the size of the clusters of activation from each subject, but don't know how to go about this. I know that for the group analysis you can get the cluster sizes from the output from mri_glm-sim. Is there a way to run the multiple comparison correction on the first level analysis in order to get this table? Or is there another way of getting the cluster sizes? Any help would be much appreciated. Thank you, Keri

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