Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arkadiy Maksimovskiy 23 Jun '16

23 Jun '16

Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Command line: mri_glmfit --y lh.BD_SD.thickness.10B.mgh --fsgd FSGD_Collapsed_Across_Smokers_demeaned.fsgd dods --C BDvsSD1.mtx --surf fsaverage lh --cortex --glmdir lh.BD_SD.glmdir The FSGD file (if using one) Design matrix: Design matrix ------------------ 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 9.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -2.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 -31.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -37.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 26.340 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -20.660; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 -22.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.849 0.000 0.000 0.000 0.000 0.000 -16.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 14.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 -27.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 4.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -30.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -28.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -23.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -27.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 13.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 5.340 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 36.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 -0.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 54.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 45.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 22.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 38.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 -12.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -12.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 16.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 50.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -35.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 59.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 25.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 32.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 14.340 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -23.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.849 0.000 0.000 0.000 0.000 0.000 -22.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 -1.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -22.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 3.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 35.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 -36.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -39.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -25.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -18.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -37.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 -14.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 4.849 0.000 0.000 0.000 0.000 0.000 -2.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -26.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 19.340 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 23.340 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 2.340 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 33.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 29.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -31.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.849 0.000 0.000 0.000 0.000 0.000 22.340 0.000 0.000 0.000; -------------------------------- FSGD File: GroupDescriptorFile 1 Title Title Class HDMale Class HDFemale Class SDMale Class SDFemale Class BDMale Class BDFemale SomeTag Variables BG_Proc BD_Clock Input 0286_recon BDMale -2.150943396 9.339622642 Input 0174_recon BDMale -2.150943396 -2.660377358 Input 0259_recon BDMale 1.849056604 -31.66037736 Input 0119_recon BDMale -2.150943396 -37.66037736 Input 0037_recon BDMale -2.150943396 26.33962264 Input 0027_recon BDFemale -0.150943396 -20.66037736 Input 0312_recon BDMale -1.150943396 -22.66037736 Input 0173_recon BDMale 3.849056604 -16.66037736 Input 0213_recon BDMale -1.150943396 14.33962264 Input 0371_recon BDMale 2.849056604 -27.66037736 Input 0109_recon BDMale 1.849056604 4.339622642 Input 0144_recon BDMale -0.150943396 -30.66037736 Input 0236_recon BDMale 0.849056604 -28.66037736 Input 0028_recon BDMale 0.849056604 -23.66037736 Input 0006_recon BDMale -2.150943396 -27.66037736 Input 0218_recon BDMale 2.849056604 13.33962264 Input 0361_recon BDMale -2.150943396 5.339622642 Input 0026_recon HDMale -2.150943396 36.33962264 Input 0098_recon HDMale -1.150943396 -0.660377358 Input 0273_recon HDMale -2.150943396 54.33962264 Input 0011_recon HDMale -1.150943396 45.33962264 Input 0304_recon HDMale -2.150943396 22.33962264 Input 0147_recon HDMale 1.849056604 38.33962264 Input 0166_recon HDMale -1.150943396 -12.66037736 Input 0170_recon HDMale 0.849056604 -12.66037736 Input 0275_recon HDMale -0.150943396 16.33962264 Input 0133_recon HDMale -0.150943396 50.33962264 Input 0021_recon HDMale -2.150943396 -35.66037736 Input 0013_recon HDMale -1.150943396 59.33962264 Input 0381_recon HDMale -0.150943396 25.33962264 Input 0380_recon HDMale -1.150943396 32.33962264 Input 0139_recon HDMale -2.150943396 14.33962264 Input 0252_recon SDMale -0.150943396 -23.66037736 Input 0209_recon SDFemale 3.849056604 -22.66037736 Input 0262_recon SDMale 2.849056604 -1.660377358 Input 0370_recon SDMale -2.150943396 -22.66037736 Input 0315_recon SDMale -0.150943396 3.339622642 Input 0244_recon SDMale -1.150943396 35.33962264 Input 0104_recon SDMale 1.849056604 -36.66037736 Input 0189_recon SDMale 0.849056604 -39.66037736 Input 0131_recon SDMale -2.150943396 -25.66037736 Input 0292_recon SDFemale -0.150943396 -18.66037736 Input 0266_recon SDMale -2.150943396 -37.66037736 Input 0069_recon SDFemale 1.849056604 -14.66037736 Input 0177_recon SDMale 4.849056604 -2.660377358 Input 0016_recon SDFemale 0.849056604 -26.66037736 Input 0372_recon SDMale -2.150943396 19.33962264 Input 0095_recon SDFemale 1.849056604 23.33962264 Input 0368_recon SDFemale 2.849056604 2.339622642 Input 0015_recon SDMale 1.849056604 33.33962264 Input 0321_recon SDMale -2.150943396 29.33962264 Input 0151_recon SDMale -0.150943396 -31.66037736 Input 0323_recon SDMale 3.849056604 22.33962264 DefaultVariable BD_Clock Note: In attempt to trouble-shoot, I demeaned this file, and am still getting the same error. My contrasts are: 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Thank you for your help, Arkadiy

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Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28
by Arkadiy Maksimovskiy 23 Jun '16

23 Jun '16

Hi Doug, Still no luck getting the script- the site does not load for some reason. Any chance you might be able to paste it into the message body? Thanks, - Arkadiy On Sun, Jun 19, 2016 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: GLM_Fit Question (Douglas Greve) > 2. Using Freesurfer commands in matlab (HARI GURAGAIN) > 3. change the algorithm (N Saf) > 4. Re: change the algorithm (Bruce Fischl) > 5. Re: registering to fsaverage (Trisanna Sprung-Much) > 6. Re: registering to fsaverage (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Jun 2016 23:54:18 +0200 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] GLM_Fit Question > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5765C30A.5080604(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > try now > > On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote: > > Hi Freesurfers, > > > > I am having a similar problem with the FSGD file as the user indicated > > at this thread: > > > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html > > > > I am trying to access the script that Doug wrote in order to fix it, > > however, the link to download the script does not seem to be working. > > I was wondering if someone might be able to upload it again. > > > > Thank you in advance for your help, > > > > Arkadiy > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Recon-all error at Talaraich transform
by Cook, Bernie 23 Jun '16

23 Jun '16

Hi all, In attempting to run a recon-all of the included subject "bert" on Mac OS X Yosemite and accompanying download, I'm receiving an error at the Talaraich transform step. However, it does not seem to be outputting a description of what is happening. With the computer I'm using, I often have to input an administrator password for something as simple as moving a file or running a "sudo" command. Would this potentially be failing because a certain permission is needed that is incapable of prompting the user for a password? If this could be the case, where might I move the file/how might I change permissions to access this? See below for the requested information. Thanks in advance. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.3.-0 x86_64 1) subject name: bert 2) command line: recon-all -s bert -all 3) error message: "recon-all -s bert exited with ERRORS at Thu Jun 23 09:48:07 EDT 2016" (during Talaraich transform) 4) script/recon-all.log: see attached [1455168447449_PastedImage] Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC | Undergraduate Research Assistant 440-623-4710 cook.1327(a)osu.edu<mailto:cook.1327@osu.edu>

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RA position available
by Bruce Fischl 23 Jun '16

23 Jun '16

The UCSF Department of Radiology and Biomedical Imaging is looking for a researcher with strong interests in neuroimaging interested in a Specialist position at UCSF. We are a neurodevelopment and neuroimaging lab. Specialists (research assistant) appointed at the junior rank must possess a baccalaureate degree (or equivalent degree) or four years of equivalent research experience (e.g., with instrumentation and research equipment, social science research methods, or creative activities). Specialists appointed at the Assistant or Associate rank must possess a master’s degree (or equivalent degree) or at least five years of experience demonstrating expertise in the relevant specialization. Specialists appointed at the full rank must possess a PhD degree or ten or more years of experience demonstrating expertise in the relevant specialization. The ideal candidate will have 1+ years of lab experience (beyond coursework lab experience) and familiarity with one or more of the following: Matlab, R, Linux/Unix, C+ or other statistical or MRI image analysis software such as Freesurfer or FSL. We are seeking candidates with a strong background in neurosciences or biomedical engineering who have the ability to perform independent research in addition to supporting the lab. Candidates interested in working in the lab for at least 2 years are preferred. Combining neuroimaging, genetics and computational methods, we are primarily interested in elucidating mechanisms underlying neurodevelopment. Working in close collaboration with local collaborators at UCSF and investigators at UCSD, University of Oslo, and Harvard University/Martinos Center, the specialist will assist in a) developing a novel automated MRI atlas of the human brainstem and cerebellum, b) validating this hindbrain atlas on neuroimaging pediatric datasets with brain malformations, and c) organize and analyze our large database of pediatric neuroimaging and genetics datasets that we have in-house. UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. To apply, please provide the following materials to Dr. Rahul Desikan (rahul.desikan(a)ucsf.edu) 1) CV (must contain previous research experience) 2) Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3) Three references

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X11 / mesa update broke tkmedit snapshots
by Flavin, John 22 Jun '16

22 Jun '16

Hi all, I run the pipelines for the CNDA and various other XNAT installations. We recently updated some of our packages, and our Freesurfer snapshots (generated with tkmedit using a tcl script) have broken. We're on Centos 6.8. The package that seems to cause the breakage is one of the mesa packages, probably mesa-libGL, upgraded from 10.4.3 to 11.0.7. (But it's hard to be sure that's the exact one because of the dependencies.) That mesa package gets pulled in as a dependency to an X11 update, specifically xorg-x11-server-Xorg upgraded from 1.15.0 to 1.17.4. We're working now on figuring out a strategy to downgrade these, and some others. It's a little hairy because there are a lot of dependent packages and a lot of affected machines. If anyone else has seen this, or knows how to fix it, I'd love to hear from you. John Flavin ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Viewing Select Labels
by badji atef 22 Jun '16

22 Jun '16

Hello, I tried to do the quick tutorial to be able to see specific anatomic region i.e the corpus callosum,I highlighted the aparc+aseg file and changed the threshold number with low=253 and high=255 but I don't get the same results at all. Should I change the frame too?and what about the replace In value with or replace Out value with ? FreeviewAnatomicalVolumes

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New Research Assistant Position in Neuroimaging Available at Washington University in St Louis
by Karl Friedrichsen 22 Jun '16

22 Jun '16

NEW RESEARCH ASSISTANT POSITION IN NEUROIMAGING AVAILABLE POSITION SUMMARY: Applications are invited for a research assistant position in the Ances Laboratory at Washington University in St. Louis. The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Results are expected to have broad implications not only for understanding the pathophysiology of neurodegenerative disorders but more generally for understanding the relationship between brain physiology, anatomy, and behavior. The laboratory utilizes state-of-the-art magnetic resonance imaging (MRI) research facilities and has an outstanding record of productivity. Funding is guaranteed for a minimum 2 year commitment PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the research assistant will be to archive/organize images (large multi-modal imaging datasets) and process/analyze multi-modal neuroimaging data. The research assistant will assist in various lab maintenance and organizational duties including tracking project progress, meet grant deadlines, and anticipate project needs. QUALIFICATIONS: The qualified candidate will have at least a Bachelor's degree in human biology, neurosciences, psychology, bioengineering, computer sciences, or other related fields. The qualified candidate must have computer skills and some basic knowledge of computer languages (e.g. C, C++, Matlab, Python). The research assistant must be dependable, have good attention to details, be well organized, self-motivated, and comfortable working as part of a team. Previous experience with fMRI data analysis programs is preferred but not necessary. Strong facility with statistical analyses is also desired. To apply, please send a letter of interest and CV to bances(a)wustl.edu. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110

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New Post Doctoral Position in Neuroimaging Available at Washington University in St Louis
by Karl Friedrichsen 22 Jun '16

22 Jun '16

NEW POST DOCTORAL POSITION IN NEUROIMAGING AVAILABLE POSITION SUMMARY: Applications are invited for a post doctoral position in the Ances Laboratory at Washington University in St. Louis. The primary focus of the lab is to understand how neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain organization and mediates symptoms. Results are expected to have broad implications not only for understanding the pathophysiology of neurodegenerative disorders but more generally for understanding the relationship between brain physiology, anatomy, and behavior. The laboratory utilizes state-of-the-art magnetic resonance imaging (MRI) research facilities and has an outstanding record of productivity. Writing manuscripts and applying for independent grants will be strongly encouraged. Funding is guaranteed for a minimum 2 year commitment. PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary responsibility of the post-doctoral fellow will be to conceive, design, and analyze studies pertaining to the effect of neurodegenerative disease on structural (e.g., volumetric imaging and diffusion tensor imaging [DTI]) and functional (e.g., blood oxygen level dependent [BOLD] imaging and arterial spin labeling [ASL]) brain organization. Anticipated activities entail development and implementation of new analytic strategies to facilitate understanding of disease in the human brain, integration of large multi-modal imaging datasets, and analysis of the relationship between brain imaging markers and cognition or clinical status. Strong written communication skills are required. Attention to detail, organizational capability, and the ability to handle multiple concurrent tasks are essential. The post-doctoral fellow is expected to be able to work independently as well as part of a team in a fast paced environment. PREFERRED EDUCATION/EXPERIENCE: A PhD in neuroscience, computer science, physics, engineering, mathematics, psychology, or related fields is requested. Previous experience is preferred in computational methods, scientific programming, and/or neuroimaging data analysis. Experience in computer programming (e.g. Matlab, shell scripting, Python, C), image processing (e.g. custom routines, FSL, AFNI, Freesurfer), and statistical analyses (R, SPSS) is beneficial. CRITICAL SKILLS AND EXPERTISE: The successful applicant will have a strong background in scientific computing (e.g., Unix/Linux experience). Academic proficiency in statistics is strongly desired. The applicant should have experience designing or adopting statistical approaches to address neurobiological questions. Preference will be given to applicants with a strong publication record or experience with writing grant applications. The successful candidate should be highly motivated with excellent analytical and interpersonal skills. To apply, please send a letter of interest and CV to bances(a)wustl.edu. Please arrange for three confidential letters of reference to be sent to the address below. Only applicants considered for employment will be contacted. Contact Information: Beau Ances MD, PhD Department of Neurology Washington University in Saint Louis Box 8111 660 South Euclid Ave Saint Louis, MO 63110 bances(a)wustl.edu

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Quality control with different pipelines
by Kirstie Whitaker 22 Jun '16

22 Jun '16

Hi everyone, I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released). If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does? Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits? Thank you again for the fantastic tools! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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LGI
by Walid Yassin 22 Jun '16

22 Jun '16

*Hello,* *I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error!* ******************************************************* Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! ******************************************************* *I checked the archives and saw a reply by Marie to someone who had the same problem.* *She recommended changing the info inside “SearchProjectionByPial.m" in the ~/Application/freesurfer/matlab directory to:* ******************************************************* function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(vertices list); ******************************************************* *Which i did, but i am still getting this error!* *Any recommendations on what to do next? I am running MATLAB_R2016.* *Thank you in advance,* *WY*

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