Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

Qdec error in analysis
by AYUSHI SHUKLA 12 Jul '17

12 Jul '17

Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s <subjid> -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the qdec GUI, I get the following error- "Error in Analyze: Couldn't open /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." I went through the old questions with the same issue, however I could not figure a solution for my problem as when I check in the directory, the file is present. I have tried to re-run recon-all and recon-all -s as well, but it is still giving the same error. I was wondering if someone could help me with this issue. Warm Regards Ayushi Shukla

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Re: [Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume
by Taylor, Johnmark 12 Jul '17

12 Jul '17

The subject name when I call tksurfer, the subject name when I call tkmedit, and the subject name in the registration file are all exactly the same: red_badger. One thing I noticed is that in the left hemisphere everything seems normal (the activation is in the expected location); things only look weird in the right hemisphere. There's no possibility that the surface reconstruction could have been off the mark? Though it seems implausible that it would take the IPS and somehow warp it all the way onto the medial surface of the brain... Here are pictures of both the volume and surface views of the activation in question (it's the medial patch on the surface view, the patch with the red cursor in the volume view), in case they didn't load before for some reason. https://ibb.co/b8HFCv https://ibb.co/cWYcQF On Thu, Jul 6, 2017 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: error message while using autorecon1 (Hoopes, Andrew) > 2. Re: error message while using autorecon1 (Buckless, Colleen) > 3. Re: Additional surface area (Bruce Fischl) > 4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude) > 5. Re: error message while using autorecon1 (Hoopes, Andrew) > 6. Re: error message while using autorecon1 (Buckless, Colleen) > 7. Re: error message while using autorecon1 (Hoopes, Andrew) > 8. Re: recon-all on newborn (Lilla Zollei) > 9. Re: recon-all on newborn (Das S.) > 10. Re: Still confused by group analysis.. (Douglas Greve) > 11. Re: Raw Cortical thickness values (Douglas Greve) > 12. Re: Average myelination within ROI (Douglas Greve) > 13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve) > 14. Re: Recon-all: too many ('s (Douglas Greve) > 15. Re: Using multimodal slab input for hippocampus subfield > segmentation in FS6 (Douglas Greve) > 16. Re: Strange Discrepancy Between Activation Location on > Surface vs. Volume (Douglas Greve) > 17. Re: negative header after preproc-sess (Douglas Greve) > 18. Re: freesurfer(a)nmr.mgh.harvard.edu (Douglas Greve) > 19. Re: Building your own fsaverage (Douglas Greve) > 20. Re: Qdec error in analysis (Douglas Greve) > 21. Re: mri_glmfit error (mri_reshape number of elements) > (Douglas Greve) > 22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve) > 23. Re: GLM fitting for the cortical volume (Douglas Greve) > 24. Re: Subject with missing fMRI data (Douglas Greve) > 25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve) > 26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve) > 27. Re: content of "subjects_dir" (Douglas Greve) > 28. Re: Qdec error in analysis (AYUSHI SHUKLA) > 29. asegstats2table error (Elizabeth Dao) > 30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz(a)gmail.com) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Jul 2017 17:29:23 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] error message while using autorecon1 > To: "'freesurfer(a)nmr.mgh.harvard.edu'" > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466. > namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="Windows-1252" > > Hi Colleen, > If you source freesurfer, and run: > ls $FREESURFER_HOME/mni/bin > It should output a list of mni tools, including nu_correct. Is this what > you see? There's a possibility that your mni sub-directory isn't sourced. > Andrew > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh. > harvard.edu> on behalf of Buckless, Colleen <Buckless(a)kennedykrieger.org> > Sent: Wednesday, July 05, 2017 12:18 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: [Freesurfer] error message while using autorecon1 > > Hi All, > I am using the newest version of freesurfer, and I keep getting errors > when I run recon-all ?autorecon1. It appears that the error might have to > do with nu_correct, and I have attached the recon-all.log. > Any suggestions on how to fix this? > Thanks, > > Colleen Buckless > Research Assistant > Center for Neurodevelopmental and Imaging Research > Kennedy Krieger Institute > 443-923-2747 > Buckless(a)kennedykrieger.org > > ________________________________ > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not encrypted by > default. You have the right to request further emails be encrypted by > notifying the sender. Your continued use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying, distribution, or the taking of any action in reliance > on the contents of this information is strictly prohibited. If you have > received this e-mail in error, please immediately notify the sender via > telephone or return e-mail. > > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Jul 2017 17:36:47 +0000 > From: "Buckless, Colleen" <Buckless(a)kennedykrieger.org> > Subject: Re: [Freesurfer] error message while using autorecon1 > To: "'freesurfer(a)nmr.mgh.harvard.edu'" > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <6F20C54B58C269489AA5CC858A1F58AF95125F(a)GSP-MAIL1.kki.org> > Content-Type: text/plain; charset="us-ascii" > > Hi Andrew, > The output list includes nu_correct. > Thanks, > Colleen > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@ > nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew > Sent: Wednesday, July 05, 2017 1:29 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] error message while using autorecon1 > > Hi Colleen, > If you source freesurfer, and run: > ls $FREESURFER_HOME/mni/bin > It should output a list of mni tools, including nu_correct. Is this what > you see? There's a possibility that your mni sub-directory isn't sourced. > Andrew > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh. > harvard.edu> on behalf of Buckless, Colleen <Buckless(a)kennedykrieger.org> > Sent: Wednesday, July 05, 2017 12:18 PM > To: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: [Freesurfer] error message while using autorecon1 > > Hi All, > I am using the newest version of freesurfer, and I keep getting errors > when I run recon-all -autorecon1. It appears that the error might have to > do with nu_correct, and I have attached the recon-all.log. > Any suggestions on how to fix this? > Thanks, > > Colleen Buckless > Research Assistant > Center for Neurodevelopmental and Imaging Research Kennedy Krieger > Institute > 443-923-2747 > Buckless(a)kennedykrieger.org > > ________________________________ > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not encrypted by > default. You have the right to request further emails be encrypted by > notifying the sender. Your continued use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying, distribution, or the taking of any action in reliance > on the contents of this information is strictly prohibited. If you have > received this e-mail in error, please immediately notify the sender via > telephone or return e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. > nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=- > 6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_ > 41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_ > uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e= > > > 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhv > trs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3Mr > Y&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s= > fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e= . 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. > > > > > ------------------------------ > > Message: 3 > Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Additional surface area > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1707051351070.31440(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Michael > > you need to look in the volume to see what is causing it. I would guess > some dura that is being incorrectly included, but you will be able to tell > in the slice view > > cheers > Bruce > > > On Mon, 3 Jul > 2017, Michael Davies wrote: > > > > > Hello, when inspecting a subject i discovered an anomaly on top of the 3D > > surface i have not previously encountered on other subjects i have > > inspected. Could you please let me know if this would be problematic > when at > > the analysing group data please? > > > > > > Kind regards, Michael > > > > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 5 Jul 2017 13:53:57 -0400 > From: miracle ozzoude <miracooloz(a)gmail.com> > Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > ---------- Forwarded message ---------- > From: miracle ozzoude <miracooloz(a)gmail.com> > Date: Tue, Jul 4, 2017 at 10:23 AM > Subject: remove skull from gtmseg.mgz > To: Douglas N Greve <freesurfer(a)nmr.mgh.harvard.edu> > > > Hello Freesurfer, > > After running the first step of PETsurfer (https://surfer.nmr.mgh. > harvard.edu/fswiki/PetSurfer) I viewed the image it created using > freeview. When I change, the color map to Lookup Table, the image also > included the skull. How can I remove the skull from gtmseg.mgz/prevent it > from showing? Any help will be appreciated. Thanks. Please, see attached > image > > Best, > Paul >

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asegstats2table error
by Elizabeth Dao 12 Jul '17

12 Jul '17

Dear experts, I have completed recon-all with no errors. Now I would like to use the 'asegstats2table' command but I've received the error below. I would appreciate any help in solving this problem. I am using FreeSurfer v6.0.0 on a Linux CentOS machine. [TLA@CogmobCentOS MCI]$ asegstats2table --subjects 201.MR1 202.MR1 203.MR1 --meas volume --tablefile aseg_stats_all.txt 'import site' failed; use -v for traceback Traceback (most recent call last): File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line 4, in <module> import os File "/usr/local/lib/python2.7/os.py", line 398, in <module> import UserDict File "/usr/local/lib/python2.7/UserDict.py", line 84, in <module> _abcoll.MutableMapping.register(IterableUserDict) File "/usr/local/lib/python2.7/abc.py", line 109, in register if issubclass(subclass, cls): File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__ cls._abc_negative_cache.add(subclass) File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add self.data.add(ref(item, self._remove)) TypeError: cannot create weak reference to 'classobj' object Thank you in advance for your help! Liz

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Running segmentation on spatially normalized data
by Lauren Stephanie Hopkins 12 Jul '17

12 Jul '17

Hi all: We ran FreeSurfer's recon sequence of anatomy files that had already been aligned to the MNI template - so spatially normalized. We're doing all of our processing in AFNI and the resulting segmentation output files open in AFNI's orig space, not in tlrc space. So basically we can't overlay the segmentation files on our anat+tlrc files where they should already be aligned to each other. When we converted the file to a .tlrc file with the AFNI command 3dcopy we could then overlay the mask on the normalized anatomy but it was no longer aligned. So I suppose my question is - is there any way to have the segmentation files maintain their positioning or output in .tlrc space so they are still aligned to our anatomy files? Thanks for any insight. Lauren

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mri_glmfit-sim ERROR cannot find mc-z.csd file
by Aly Negreira 12 Jul '17

12 Jul '17

Hi Freesurfer Community, I'm using FsFast on my dissertation data and trying to run a monte carlo correction on my functional data in the volume. I keep running into the below error. In attempting to troubleshoot, it looks like Yuko ran into a similiar issue (see archived email from Fri Dec 9 @ 12:26:46 EST in 2011) just not sure how to fix it! Please advice....I just want my PhD already! Thank you! Aly ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd COMMAND: mri_glmfit-sim \ --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \ --cache 1.3 abs \ --cwp 0.05\ --3spaces MAC INFO: OS X El Capitan Version 10.11.6 FREESURFER VERSION: -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------

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Re: [Freesurfer] UPDATE: Matlab Problem LME
by Diers, Kersten /DZNE 12 Jul '17

12 Jul '17

Hi Clara, thanks for the additional information, this is helpful! If you are calling the scripts with [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95); then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices for which the analysis will be performed. 'lhcortex' should already be a subset of the vertices specified by 'lhsphere', i.e. excluding some portions of the medial wall. If you have zero-valued columns in your data matrix, one thing worth trying is to remove the corresponding indices from 'lhcortex', i.e. further restrict the analysis mask. This should be done before the initial covariance estimation, i.e. prior to calling lme_mass_fit_init or lme_mass_fit_EMinit. In addition, it is of course worthwhile to investigate the cause of the zero-columns. Best, Kersten

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changing resolution and FOV
by Linda Eva Heidinger 12 Jul '17

12 Jul '17

Hello freesurfer experts: I am doing the following steps in the script below: (1) Use recon -all to calculate the freesurfer T1 anatomical which requires a single DICOM file to be calculated from each subject. (2) Use the functional Bold time series data originally derived from DICOM files for that subject and preprocess them: correct for slice timing and do regular AFNI registration of the images using the first volume as reference but do not spatially smooth. (3) We then use this Bold series after preprocessing by converting AFNI to NifTi by using 3dAFNItoNIFTI and inputing it into bbregister which computes a spatial registration matrix between the bold image and the T1 anatomical. (4) We now compute a coregistration using mri_cvs_register from the individual brain to a template brain for the volumetric non-linear morphing. It requires an anatomical scan of the subject that has been processed in freesurfer as in step (1). In our case we will use the standard brain cvs_avg35_inMNI152 as the target/template. (5) Next, we move the bold image from the individual space into the standard or template space. We use the command mri_vol2vol where we input the AFNI Bold image converted to NifTi and the bbregister matrix and template in (4) above to obtain the Bold in this template space. The script that does this is given below: # FreeSurfer commands nmr-std-env setenv SUBJECTS_DIR <path to the directory where all MRI data for this study reside> setenv SUBJECT <my subject code> cd $SUBJECTS_DIR # First, run FS recon-all on the T1 (MEMPRAGE) anatomical as usual. recon-all -subjid $SUBJECT -i temp_${SUBJECT}/001.mgz -all -openmp 4 # Second, do co-registration at the individual level between the hires anatomical and the bold (functional) image. # In the below example the already motion corrected (and otherwise preprocessed) bold data for run 005 are in # $SUBJECTS_DIR/$SUBJECT/bold/005/005.mc.nii # Use boundary-based registration (bbregister) - this by far the most accurate tool. # Note: This is rigid 6 DOF. It is almost always best to use rigid DOF 6 for within-subject registration. bbregister --mov $SUBJECT/bold/005/005.mc.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg boldregister.dat --fslmat ${SUBJECT}_anat2bold.mat # Just in case, let us make FSL type coregistration matrices as well. convert_xfm -omat ${SUBJECT}_bold2anat.mat -inverse ${SUBJECT}_anat2bold.mat # Now, we will compute a group-level coregistration from the individual brain to a template brain for both volumetric non-linear morphing. # We will use the standard brain cvs_avg35_inMNI152 as the target/template. mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECT/cvs_CVS35MNI152 --openmp 8 # Finally, we can move the bold image from the individual spac into the standard space: mri_vol2vol \ --mov $SUBJECT/bold/005/005.mc.nii \ --targ $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \ --o Grand_Average/${SUBJECT}_CVS35MNI152_005.mc.nii \ --m3z $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \ --noDefM3zPath \ --interp nearest \ --reg $SUBJECT/bold/boldregister.dat \ --no-save-reg \ We have successfully run the script but the result: /${SUBJECT}_CVS35MNI152_005.mc.nii is too large (47 gigs) to run on our computers using four runs for the next step which is AFNI 3dDeconvolve. We would like to down sample this Bold aligned to the template image file to the resolution and FOV of the original Bold image file in step (2) above. I believe freesurfer converts everything to freesurfer space (1mm^3 256^3) but instead we want the matrix to be 128X130X32 or downsized. How would you do this? Thanks!

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FreeSurfer on Windows 10 64-bit
by Peter Stanwell 12 Jul '17

12 Jul '17

Dear all, I'm looking to set up FreeSurfer on a Windows 10, 64-bit OS. Has anyone tried this using the Linux BASH shell on the latest (anniversary) version of Windows 10? If so, any tricks to to watch out for? Best, Peter

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viewing mri_glmfit FDR corrected results
by marco mcsweeney 11 Jul '17

11 Jul '17

Dear FreeSurfer experts, I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons. My question is about how do I correctly get the FDR corrected results showing cluster number, size, MNI coordinates etc. as I would if I used QDEC? I have searched through the archives and have found what looks like the answer, but I'm not convinced that the method I used is correct. I used 1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs --cwpvalthresh .99 and 2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary However when I visualize the FDR corrected results with tksurfer or freeview I can see a couple of clusters not listed in the summary. Am I missing something? Thank you so much in advance. Any help or advice would be greatly appreciated. Best wishes Marco

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Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks
by Sheena Chand 11 Jul '17

11 Jul '17

Stanford University's Department of Psychiatry & Behavioral Sciences is seeking to hire full time post-doctoral fellows in Computational Modeling of Brain Networks for their Cognitive & Systems Neuroscience Laboratory. This lab is headed by Dr. Vinod Menon who has broad multidisciplinary expertise that spans several scientific disciplines and has published extensively on various aspects of human cognition and brain function. Explore our lab website for more information: http://med.stanford.edu/scsnl.html. Please, distribute job posting (below) appropriately in your department. We thank you for your support. POSTDOCTORAL FELLOWSHIP IN COMPUTATIONAL MODELING OF BRAIN NETWORKS The Stanford Cognitive and Systems Neuroscience Laboratory invites applications for a postdoctoral fellowship in human brain network analysis and modeling. We seek candidates with strong research backgrounds in one or more of the following areas: resting-state and task-evoked fMRI connectivity, structural HARDI-based connectivity, neurophysiological modeling of brain networks, Bayesian modeling, machine learning, and deep neural networks. Candidates must have strong computational skills and a PhD in computational neuroscience, computer science, physics, biomedical engineering or related fields. This is an exciting opportunity to work on multiple NIH- and Stanford-funded projects using multimodal (fMRI, optogenetic, DTI, EEG) brain imaging techniques in multiple clinical populations and normative groups. The successful candidate will develop a vigorous research program that contributes to, and complements, ongoing research studies. The candidate will have access to state-of-the-art brain imaging and HPC/GPU facilities.Please email a CV, statement of research interests and relevant background, and names of three referees to Drs. Vinod Menon and Aarthi Padmanabhan at scsnl.stanford+postdoc(a)gmail.com<mailto:scsnl.stanford@gmail.com> Best, Sheena _________________ Sheena Chand Research Administrative Assistant Department of Psychiatry & Behavioral Sciences Stanford University|School of Medicine Email: schand05(a)stanford.edu<mailto:schand05@stanford.edu> Desk: (650) 498-9821

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Freesurfer July 2017