[Freesurfer] Several faculty jobs at University of Chicago in Aging + Alzheimer's and related dementias

dbMyxTVK2-BEuUAWnPq8HbY39qxTChBfaUeN2WTE94tfjXYCspSexf3zkFEsQ-ZrFouNqM_e9GXgIq2FWjfUhH_ZS-tqxA58GDpjFCsUn6zjj1OFbVrWipbYErwpGWX8kQYHZhOJsf6pZdsEwahYNqD5f35h43w2SHKTv8A-880LQ3_7dJNTeCQ5d91xie-sXJXvrR1FdfeB-mHCVRIFUtYODq3xnGM6pHEPmDWl__wu7uaR4VS8JgPUxVEFXY1hv3Fb7HKLw/https%3A%2F%2Fapply.interfolio.com%2F140371 -- *Adam Martersteck, PhD *

[Freesurfer] Job at University of Chicago, neuroimaging for aging/Alzheimer

have some prior experience with neuroimaging software libraries, and Python and/or R. Experience with high-performance cluster shell scripting and schedulers, and machine learning libraries are desirable. Apply through the portal, but feel free to reach out with questions ( marterst...@uchicago.ed

Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis

External Email - Use Caution On other thought: You may want to do Doug's suggestion of calculating the paired-diff in the longitudinal stream's subject-specific unbiased template space of each participant instead of doing it all in fsaverage. Then take the resultant file, the symme

[Freesurfer] Jobs at Northwestern’s Alzheimer’s Disease Center

rs.northwestern.edu%2Fpsp%2Fhr857prd_er%2FEMPLOYEE%2FHRMS%2Fc%2FHRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL%3FPage%3DHRS_APP_JBPST_FL%26Action%3DU%26FOCUS%3DApplicant%26SiteId%3D1%26JobOpeningId%3D45255%26PostingSeq%3D1> (BA, BS, less prior experience) *Adam Martersteck, PhD* Assistant Professor Northwestern U

Re: [Freesurfer] Advice? Re: Freeview 7.1.1 won't start on Mac: segmentation fault

External Email - Use Caution Hi Sam, I can tell from your crash report you have a LG HDR 4K, 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) plugged in. You might try unplugging any external monitors and just having your native laptop display on then starting FreeView and see

Re: [Freesurfer] Dividing surface overlays

External Email - Use Caution Hi Dylan, Give this a try: fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan < mtisd...@pennmedicine.upenn.edu> wrote: > External Email - Use Caution > > Hi all, > > I've generated tw

Re: [Freesurfer] PETsurfer

External Email - Use Caution PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the release notes here: https://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCft8AUJ0fOq2tnIi9H-neObzRYbNnzQ_f-6Te5NpdO_gdoIcUF7wBpGrIgl62EZEaig2VymVFjCNARkn

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

will appear on each monitor. Under the Display tab try checking the box > "default for display" for any external monitor and not the "scale" option > for the hardware to scale the image up/down in size. > > - R. > > On Aug 2, 2021, at 16:08, Adam Martersteck wrote: &

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

0p or unplug the monitor, I can open FreeView without error. Hope this helps other people out there. My graphics card on the 13" MacBook Pro is the Intel Iris Plus Graphics (1536 MB) from the Quad-Core Intel i5. On Mon, Aug 2, 2021 at 10:28 AM Adam Martersteck wrote: > I should add: I&

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

tKLbhrUhl8OTrwNFjiqhXcjsJb86Yz-6R-DTgfHSEAzWDL0QgznDOjerB7-xv-KJYP9ECT_vGza0i7LICmv8c0YsLHQn7E8y2Bl3u8WH2t_ntW9Bbu7Zowx9ubjV4nrif-rv2oBgs3t4dO1En3qw4YxfrHuldvBQUvKX32TAyKrafsDcqI42e4hmx1fb3P-FTEwsLgeSqUyPcDTSVwcYI51XgdwgrICJqOfSNQtzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html >>

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

qFaFbqFoDVkvD1kx1BZxSteV2e5Q6jrFPf-YEcIImmcloqwIqP8Lh2lnSy5aLFUp8K9mERr6dYmb0OhnvW_rEkD7__biFcC5PAxgQXOLA-8GdeO0SES2PBZDvT6wg4_mvqRFFPHORULo23A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html > > - R.. > > On Jul 29, 2021, at 14:34, Adam Martersteck wrote: > > External Email -

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly

External Email - Use Caution Here's a log from a completely clean install of FreeSurfer 7.2.0. On an Intel processor MacBook Pro, running macOS Big Sur (11.4). __Starting with a completely clean install of FreeSurfer 7.2.0__ Copied license file over from 7.1.1. (Confirmed license

[Freesurfer] 2 surface mri_glmfit as independent variables

External Email - Use Caution Hi FreeSurfer team, I have a question about running mri_glmfit with 2 different surface modalities as the independent variable and a single value per participant as the dependent variable. I'm trying to examine the unique and shared contribution of the

Re: [Freesurfer] fsaverage label into functional space

External Email - Use Caution To confirm, your label is starting on the fsaverage surface. You can open tksurfer fsaverage ?h pial and open the label and it shows up? From my experience using fcseed-sess & fcseed-config using FS v6.0.0 what you want to do is move the label from fsa

[Freesurfer] Accessing the FS mail archive online

External Email - Use Caution Hi Freesurfer team, Just in case this hasn't been brought to your attention -- it looks like the online mail archive requires a martinos center login. Accessing links to past questions and answers via google or just https://mail.nmr.mgh.harvard.edu/pip

[Freesurfer] Advantage of having skull for longitudinal processing?

External Email - Use Caution Hi Freesurfer team, I'm thinking of pre-skullstrip'ing my brains prior to being input into FreeSurfer. My fear was this information in the skull might be useful during mri_robust_register or mri_robust_template for longitudinal analyses: Martin discu

[Freesurfer] Postdoc or Research Associate/Scientist at Northwestern in Chicago

External Email - Use Caution *Apologies for cross-posting* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease Imaging Core is seeking a research associate or postdoctoral fellow. Prior experience with Alzheimer's disease is *not a requirement

Re: [Freesurfer] mri_convert

External Email - Use Caution mri_convert can do lots of things but I would actually try mri_probedicom to get the DICOM timings. If you have AFNI installed you could also try dicom_hinfo which has more examples in the AFNI wiki than mrI_probedicomi. You could just loop over dicoms

Re: [Freesurfer] PET PVC transforms and MG voxels

External Email - Use Caution Hi Freesurfer team, Just wanted to bump this to see if anyone had any thoughts. Thanks, Adam On Tue, Jan 29, 2019 at 10:21 AM Adam Martersteck wrote: > Hi FreeSurfer team, > I have two comments/questions about PET PVC & Doug’s 2016

[Freesurfer] Postdoctoral Fellow at Northwestern's Alzheimer's Disease Center

External Email - Use Caution *Apologies for cross-posting* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease is seeking candidates for a postdoctoral fellowship in Neuroimaging of Aging and Dementia. The fellow will focus on analyzing multimod

Re: [Freesurfer] Computation time

External Email - Use Caution Hi Dawn, See https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Step-wiseDirectives-1 for an approximate beakdown of computational time per step. The parallel flag in FS v6 will decrease this to about 3 hours total on a 4 core machine. (time varies d

Re: [Freesurfer] T2pial correction options

External Email - Use Caution Re-posting to see if anyone has had this problem before and solutions they've implemented. > Hi Freesurfer team, > > We’re having some trouble with the T2pial option. We are currently getting > the Martinos Center ABCD project Tisdall/van der Kouwe vN

[Freesurfer] T2pial correction options

External Email - Use Caution Hi Freesurfer team, We’re having some trouble with the T2pial option. We are currently getting the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and T2SPACE at 0.8mm^3, bandwidth matched for distortion. Linked below are 2 gifs were we

Re: [Freesurfer] bbregister error

External Email - Use Caution Are you sure you're terminal is setup in tcsh or csh? If you're using bash instead, you want "export SUBJECTS_DIR=/project/bil/Nada" Take a look at: https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or https://surfer.nmr.mgh.harvard.edu/f

Re: [Freesurfer] resting state motion censoring

number of TRs). And if frame 119, 120, and 121 where to be excluded: then it would be a *m* by 3 matrix with column 1, row 119 set to 1; row 120 column 2 set to 1; row 121 column 3 set to 1. Is that all correct? Thanks, Adam On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck wrote: > Hi Fre

Re: [Freesurfer] resting state motion censoring

add. > If I don't get back in a couple of weeks, send me a reminder. > > > On 02/14/2018 12:13 PM, Adam Martersteck wrote: > > Just a quick follow-up question, > > For FD/DVARS or other "censoring" criteria -- using -tpexclusion > > worked great for sur

Re: [Freesurfer] resting state motion censoring

as N Greve wrote: > Yes,you need a time point exclusion file (-tpexclude filename option to > mkanalysis-sess). Run mkanalysis with -help to get more info on how to > create it. > > On 01/25/2018 04:43 PM, Adam Martersteck wrote: > > Hi Freesurer experts, > > > > I

[Freesurfer] resting state motion censoring

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in

Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

Hi Dr. Yeo, Just a related question -- do you have an opinion on if one of the network solutions corresponds to the language network? I realize they are all bilateral, with no significantly left lateralized one. But do you think one of the DMN solutions (such as Default B in the paper you linked,

Re: [Freesurfer] Long-stream comparing differing resolutions

Just bumping to the top to see if anyone has ideas about comparing 0.8mm vs. 1mm data using the long stream. Dear FS Experts, I’m trying to compare multiple T1-weighted sequences taken across multiple scanners in the same day in 15 individuals using the longitudinal stream. One question we had

[Freesurfer] Long-stream comparing differing resolutions

Dear FS Experts, I’m trying to compare multiple T1-weighted sequences taken across multiple scanners in the same day in 15 individuals using the longitudinal stream. One question we had was how different cortical thickness estimates would be using a 0.8mm^3 resolution vs. our standard 1mm^3 MPRA

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

fer 6.0 with some of the analyses > > > > > > > > > > Dear Batool, > > Sorry for missing your message. > > > And dear Adam: > > > Thanks for covering me! That’s exactly my standard answer to that question > ;-) > > > > > > > > >

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce" e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results

Re: [Freesurfer] PET PVC - CSF estimation

Hi, Just want to bump this to the top now that the weekend is over! Thanks for any insights about the CSF estimation, Adam On Fri, Oct 21, 2016 at 1:03 PM, Adam Martersteck wrote: > Thanks for replying Doug, > > Yes, I would like to use my own mask if the choroid plexus is inc

Re: [Freesurfer] PET PVC - CSF estimation

o that I could input my own estimation (just the ventricles)? Thanks! Adam On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve wrote: > What do you mean? You have your own CSF segmentation and you want to use > that instead of the one created by gtmseg? > > > > On 10/20/2016 11

[Freesurfer] PET PVC - CSF estimation

Hi FreeSurfer team, Hopefully Doug or someone familiar with the new PET PVC implementation can answer a few things I can't seem to find on http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC publications (2013 or 2016). 1) Is the choroid plexus included in the binarized the

Re: [Freesurfer] bbregister problems with PET data

t is > between the hemispheres? Is that typical for this tracer or is this a > phenomena with this subject (or population)? > > On 03/30/2016 03:41 PM, Adam Martersteck wrote: > > Hi Freesurfer team, > > > > I’m encountering a problem using bbregister on PET data: > >

[Freesurfer] bbregister problems with PET data

Hi Freesurfer team, I’m encountering a problem using bbregister on PET data: -- When I attempt to register a PET volume to T1-space the asymmetric tracer uptake of the PET throws off proper registration. (Treating the PET as a T1 because of the non-specific white matter uptake > grey matter sign

[Freesurfer] v5.3 fsaverage (accidentally) in v5.1 directory

Hi Freesurfer team, *Short question: *Will (accidentally) using the fsaverage v5.3 subject in our v5.1 directory influence our reconstructions? *Long question:* Our server has 2 different freesurfer environments. A recon was accidentally run on a single v5.1 subject in the v5.1 directory with fr

[Freesurfer] Using N3 MNI and N3 FS corrections

Hi Freesurfer users, I have a question about using the N3 algorithm twice for processing ADNI data: Is it okay for data to have undergone the ADNI N3 correction (Boyes et al. 2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through the Freesurfer pipeline and undergo FS N3 correc

Re: [Freesurfer] problems with Surface-based Interhemispheric Registration

arc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot) Hope that was helpful! Adam Martersteck On 01/28/2014 11:26 AM, Adam Martersteck wrote: > > Hi Freesurfer team, > > I noticed that the xhemireg file is missi

[Freesurfer] xhemi - xhemireg file

Hi Freesurfer team, I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg I'm assuming the xhemireg for v5.3.0 (found in v5.3.0's $FS_HOME/bin/xhemireg) is identical and I can use that with v5.1.0? Thanks, Adam ___

[Freesurfer] reg.dat for ICBM152 to MNI305 (fsaverage)

verage without any further alteration? >> If not: Different linear transform from MNI-305 to ‘fsaverage MNI-305’? Thanks! Adam Martersteck Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11

[Freesurfer] freeview v5.3 reposition surface

the mris_make_surface command after saving the new surface(s)? Thanks, Adam Martersteck Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11 Chicago, IL

[Freesurfer] FS 5.1: white matter holes in wm.mgz

curious if anyone had ever run into this error and a solution for avoiding it in the future. Thanks in advance for the help! Adam Martersteck Cognitive Neurology and Alzheimer’s Disease Center brain.northwestern.edu ___ Freesurfer mailing list