Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

Extracting values via mri_segstats from middle of the cortex
by Yash Patel 11 Oct '17

11 Oct '17

Hi, I have a MT and T1W volume (processed through recon-all). I would like to extract all MT values that lie in the middle surface of the cortex, and run that through mri_segstats so I get average MT values for each cortical region in the DK-atlas. My workflow is as follows: 1. mri_vol2suf --mov <MT_vol> --hemi lh --projfrac 0.5 -- regheader <id> --reg <MT_reg_to_T1W.dat> --o <vol2surf.output.mgh> --interp nearest 2. mri_surf2vol --surfval <vol2surf.output.mgh> --hemi lh --fillribbon --identity <id> --template <T1W> --o <surf2vol.output.mgh. 3. mri_segstats --seg <aparc+aseg for subid.mgz> --i <surf2vol.output.mgh> --ctab --id <list of regions> --o <output.stats> Is this the correct way of going about it? I was wonder if its alright to use mri_vol2surf to get MT values on a T1W surface, and then mri_surf2vol to get the output from vol2surf into a T1W cortical ribbon. And finally run mri_segstats on the output of mri_surf2vol using the aprac+aseg for that subject. Thank you, Yash RRI, Baycrest Health Sciences University of Toronto

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UMN Informatics Institute - Neuroimaging Staff Scientist posting
by bryon mueller 11 Oct '17

11 Oct '17

The University of Minnesota Informatics Institute (UMII) <https://research.umn.edu/units/umii> seeks a skilled, staff scientist to serve the MR Neuroimaging research community at the University of Minnesota. The successful candidate is expected to: (1) carry out consultations with researchers across the University and serve in the role of a staff scientist who provides technical assistance across multiple research groups; (2) provide technical and analytic support in designing and supporting neuroimaging analysis pipelines that will be run on platforms of the Minnesota Supercomputing Institute (MSI); (3) appropriately document work so that researchers are able to prepare grants, research papers and reports based on the analysis; (4) simultaneously support different versions of analysis tools that might require different libraries and operating system versions; (5) develop new computational environments, such as Docker, for major neuroimaging analysis platforms (AFNI, FSL, etc.) in the HPC environment at MSI; and (6) build computational workflows that scale and work across a broad range of file system storage. The successful candidate will join a growing group of imaging analysts in the University of Minnesota Informatics Institute. The Imaging Informatics Manager at the University of Minnesota Informatics Institute will serve as the supervisor. On a daily basis, the analyst will work closely with MR neuroimaging researchers, and staff at the Minnesota Supercomputing Institute. This position is both posted as a Researcher 5 <https://z.umn.edu/umii-neuroimaging-job-5>, Research Scientist (minimum required qualification: PhD) under Job Opening 319904 <https://z.umn.edu/umii-neuroimaging-job-5> (https://z.umn.edu/umii-neuroi maging-job-5) and as a Researcher 3 <https://z.umn.edu/umii-neuroimaging-job-3>, Assistant Scientist, (minimum required qualification: Bachelor's degree) under Job Opening 319899 <https://z.umn.edu/umii-neuroimaging-job-3> (https://z.umn.edu/umii-neuroi maging-job-3). Qualifications Required: • Background in scientific image processing, analysis or multi-dimensional signal processing • Have proficiency in at least one programming language (Python, MATLAB, Java, C++, …) • Be familiar with the Linux operating system • Have excellent interpersonal and organizational skills • Be able to articulate processes verbally and in writing • Be highly motivated to learn new technical skills Additional requirements for the Researcher 5 position (Job Opening 319904): • Doctoral degree in a science or engineering field • Experience in MR neuroimaging image analysis (fMRI, DWI, or structural) • Significant research experience and ability to work independently • Experience working in a team environment with people with diverse expertise • Publications, software, or grant applications demonstrating creativity and independence Preferred: • (for Researcher 3 position) Master’s degree in a science or engineering field • (for Researcher 3 position) Experience in MR neuroimaging image analysis (fMRI, DWI, structural) • (for both positions) Experience in medical image analysis • (for both positions) Experience with container technology, such as Docker • (for both positions) Experience in HPC environments • (for both positions) Experience with neuroimaging analysis software packages such as FSL, AFNI, SPM • (for both positions) Experience working in a team environment with people with diverse expertise

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Overlap between Yeo networks and aparc2009 segments
by shahin＠nmr.mgh.harvard.edu 11 Oct '17

11 Oct '17

Dear Experts, We are looking for a way to measure the amount of overlap between each 'aparc 2009 segment' vs. 'Yeo 7 networks segments'. Currently I can do that by converting segments to labels and and then measuring the number of common vertices between them. But I was wondering if there is a more direct way to do it. Regards

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R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 11 Oct '17

11 Oct '17

You have suggested to use 0 0 0 0 .25 .25 .25 .25 to look the map where, considering the group differences, the covariate predicts the dependent variable (functional connectivity) in 4GV1. Below I'm reporting the contrast that I have used. Please could you check it and suggest correction? Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please? Thanks C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 C15) group.effect.intercept 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 C16) group.effect.slope > 0 0 0 0 1 -1 0 0 > 0 0 0 0 1 0 -1 0 > 0 0 0 0 1 0 0 -1 On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: > Thank you very much. > Where I should put 0 0 0 0 .25 .25 .25 .25? > Which are the contrast reported below that I should modify? > > C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 > C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 > C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 > C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 > C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 > C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 > C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 > C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 > C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 > C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 > C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 > C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 > C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 > C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 > C15) group.effect.intercept > 1 -1 0 0 0 0 0 0 > 1 0 -1 0 0 0 0 0 > 1 0 0 -1 0 0 0 0 > C16) group.effect.slope > 0 0 0 0 1 -1 0 0 > 0 0 0 0 1 0 -1 0 > 0 0 0 0 1 0 0 -1 >----Messaggio originale---- >Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 9-ott-2017 22.56 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance > >I don't know what you are asking > > >On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >> Thank you very much. >> Where I should put 0 0 0 0 .25 .25 .25 .25? >> Which are the contrast reported below that I should modify? >> >> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >> C15) group.effect.intercept >> 1 -1 0 0 0 0 0 0 >> 1 0 -1 0 0 0 0 0 >> 1 0 0 -1 0 0 0 0 >> C16) group.effect.slope >> 0 0 0 0 1 -1 0 0 >> 0 0 0 0 1 0 -1 0 >> 0 0 0 0 1 0 0 -1 >> >> >>> ----Messaggio originale---- >>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>> Data: 3-ott-2017 16.19 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance >>> >>> probably you want 0 0 0 0 .25 .25 .25 .25 >>> >>> >>> >>> On 10/3/17 10:10 AM, stdp82(a)virgilio.it wrote: >>>> Many thank for your response. >>>> Claryfing my question on point 3, >>>> When I look in group.effect.slope, the map show the group difference >> removing >>>> the effect of the covariate. >>>> Conversely, I would to obtain the map reporting only the effect of >> covariate >>>> on dependent variable (functional connectivity). >>>> Is possible to look on it? >>>> Regards >>>> Stefano >>>> >>>> >>>>> ----Messaggio originale---- >>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> Data: 2-ott-2017 16.58 >>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>> >>>>> >>>>> >>>>> On 10/01/2017 05:08 PM, stdp82(a)virgilio.it wrote: >>>>>> Hi, >>>>>> on 4 groups, 1 covariate (4GV1) >>>>>> >>>>>> I run mri_glmfit using the following .mtx >>>>>> >>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>>>> should be >>>>> >>>>> 0 0 0 0 1 0 0 -1 >>>>> >>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>> C15) group.effect.intercept >>>>>> 1 -1 0 0 0 0 0 0 >>>>>> 1 0 -1 0 0 0 0 0 >>>>>> 1 0 0 -1 0 0 0 0 >>>>>> C16) group.effect.slope >>>>>> 0 0 0 0 1 -1 0 0 >>>>>> 0 0 0 0 1 0 -1 0 >>>>>> 0 0 0 0 1 0 0 -1 >>>>>> >>>>>> Please: >>>>>> 1) Could you check whether the all .mtx are complete and corrected, in >>>>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs-gr3+gr4. >>>> slope? >>>>> they look correct, except for the one i noted >>>>>> 2) Could you explain the meaning of: >>>>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 differ >>>> from that of grp3 and 4 >>>>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>>>> group.effect.slope - interaction between group and covariate >>>>>> group.effect.intercept - is there an effect of group on the inercept >>>>>> 3) Which is the contrast identifying the effect of covariate on group >>>>>> differences? >>>>> not sure what you mean >>>>>> Thanks >>>>>> >>>>>> Best regards >>>>>> >>>>>> >>>>>> Stefano >>>>>> >>>>>> >>>>>> >>>>>>> ----Messaggio originale---- >>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> Data: 5-set-2017 22.59 >>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>>>> >>>>>>> you would need to create a contrast to look for the interaction. If you >>>>>>> have four gruops and 1 covariate, then it would be >>>>>>> >>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>> >>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>> >>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >>>>>>>> Hi, >>>>>>>> e.g., by considering two or more groups, I would like to map the >> clusters >>>>>>>> reporting the covariance between the functional connectivity or >> cortical >>>>>>>> thickness (dependent variable) and age, tacking in account the group >>>>>>>> differences. >>>>>>>> Instead, I'm not interested to map the group differences, taking in >>>> account >>>>>>>> the nuisance factors. >>>>>>>> Thanks, >>>>>>>> Stefano >>>>>>>> >>>>>>>>> ----Messaggio originale---- >>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>>>> >>>>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>>>> >>>>>>>>> >>>>>>>>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>> Hi list, >>>>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence >>>>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>>>> Anyway, where I should look if I want assess the the map showing the >>>>>>>>>> clusters in which the dependent variable is associated to covariate, >>>>>>>>>> tacking in account the group difference? Please could you suggest my >>>>>>>>>> the path? >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> Stefano >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> -- >>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>> MGH-NMR Center >>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>> Fax: 617-726-7422 >>>>>>>>> >>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >> edu/transfer/outgoing/flat/greve/ >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> 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 >>>>>>>>> http://www.partners.org/complianceline . 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. >>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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How to calculate WM lobar volumes
by Shatil, Anwar Shahadat 11 Oct '17

11 Oct '17

Dear All: I want to find the WM lobar volumes in a set of MS patients. I also have the processed images from freesurfer. To extract the lobar volumes I used below codes from one of the previous threads of Freesurfer (https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-April/023232.h…) 1. mri_annotation2label --s <sub1> --hemi rh --lobesStrict lobesfile 2. mri_aparc2aseg —s <sub1> --labelwm --annot lobesfile 3. mri_segstats --seg mri/lobesfile+aseg.mgz --sum wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject <sub1> --surf-wm-vol --ctab /Applications/freesurfer/WMParcStatsLUT.txt —etiv Now, I don’t know how to get the volumes or which LUT table to use in the overlay. Please correct me if I used the correct LUT file in --ctab. Your guidance would be highly appreciated. Thanks, Anwar This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Obtaining an old-style license or running old FreeSurfer without it
by Mike Schmidt 11 Oct '17

11 Oct '17

I am re-running some MRI scans with multiple versions of FreeSurfer. I am aware that FreeSurfer 5.2.0 is deprecated and don't intend to use its output, other than for comparisons with current versions. My problem is that I have copied a .license file (as mikeschmidt(a)schmidtgracen.com from February 2017) that works successfully with version 6.0.0 (known-good) into FreeSurfer 5.2.0's FREESURFER_HOME and FreeSurfer 5.2.0 finds the file, but says it is invalid. Renaming the .license file to license.txt resulted in it not being found at all. I've even retrieved an old license file (as mschmidt(a)umc.edu from prior to April 2015) from backup that I used to use (email address no longer exists), thinking I had used it with 5.2.0 in the past, but it is also reported as invalid. I've read in the forum that 6.0.0 uses a different license file format due to libcrypt changes. But I can't seem to get new or old licenses to work. Is it possible to register for a replacement old-style license? Or is there another way to get 5.2.0 to work? I applied for a new license today to test everything before asking for help, expecting it would work with v6.0.0 but not 5.2.0. Testing validated my assumption, leading me to believe I need to acquire a valid license in the old format in order to run FreeSurfer version 5.2.0. Is that possible? Thank you for any assistance, Mike Schmidt

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TRACULA - error
by Rizvi, Batool 10 Oct '17

10 Oct '17

Hi, I'm running tracula using the following command: (Note: I'm replacing actual paths with made up paths) trac-all -prep -c /path/to/my/config.sh And for some reason it stops running while working on the first subject (creates the folder for the first subject), with this error: if: Expression Syntax. It doesn't show any errors before this line. The line before this one was copying over the bvecs file to the new path (cp /path/to/my/bvecs.txt path/to/dmri/dwi_orig.bvecs) Is there something I'm doing wrong? Thanks, Batool

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Transformation between spaces
by Florence Campana 10 Oct '17

10 Oct '17

Dear freesurfer experts, I ran a spatial ICA in volume and would like to visualize the components in surface in order to assess the overlap between the independent components and my ROI (defined on surface). However after reading this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am concerned with transformations between the MNI 305 space and the surface space without totally understanding the nature of the distortions unfortunately. Would you mind explaining it briefly to me and let me know whether you think that the transformation of the components from the MNI305 space to the surface will lead to distorted results in the case of our spatial overlap estimates? (in which case I can define the ROI in volume and conduct all the analyses in volume). Thank you very much, Florence Campana

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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases
by Mehta, Chintan 10 Oct '17

10 Oct '17

Thank you Thomas!

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Postdoctoral Fellowship at Mayo Clinic in Imaging Biomarker Development
by Senjem, Matthew L., M.S. 10 Oct '17

10 Oct '17

Postdoctoral Fellowship at Mayo Clinic in Imaging Biomarker Development Position Summary: A Research Fellow is being sought in the Department of Radiology at Mayo Clinic in Rochester, Minnesota. The focus of the research for this position will be on multimodal imaging changes (DTI, ASL, fMRI) associated with cerebrovascular disease, dementia, and brain resilience. Successful candidates should have background knowledge in mathematics, electrical engineering, computer science, biomedical engineering, or statistics. Applicants should be able to demonstrate good communication skills through publications in peer-reviewed publications. The position is currently for three years. If interested, please send your CV to Prashanthi Vemuri, PhD (vemuri.prashanthi(a)mayo.edu<mailto:vemuri.prashanthi@mayo.edu>). The complete posting is available here - http://www.mayo-clinic-jobs.com/job/Rochester-Research-Fellow-Radiology-Job…

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Freesurfer October 2017