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Fwd: REMINDER: OHBM 2016 Call For Council Nominations Deadline Nov. 9
by Douglas N Greve 05 Nov '15

05 Nov '15

-------- Forwarded Message -------- Subject: REMINDER: OHBM 2016 Call For Council Nominations Deadline Nov. 9 Date: Thu, 05 Nov 2015 11:36:37 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear OHBM Member: Your opportunity to nominate individuals to serve as OHBM's leaders is *Monday, November 9th. * We invite you to nominate individuals with proven scientific leadership expertise, strategic thinking and planning skills, strong problem solving skills, results oriented, visionary, strong ethics, have a global perspective and are available to participate and commit time. Knowledge of OHBM activities and consistent attendance at the Annual Meeting is desired. Please complete the *Call for Nominations* <http://www.humanbrainmapping.org/i4a/forms/index.cfm?id=25> form no later than *Monday, November 9^th at* *11:59 PM US CST*. Self-nominations are welcome and encouraged. Councilors are not eligible for re-election for any council position for three years after serving one term. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. *Not Eligible Until 2018/2019* * Steve Smith, 2014-2015 Chair * Jia-Hong Gao, 2014-2015 Treasurer * Simon Eickhoff, 2014-2015 Secretary * Pedro Valdes Sosa, 2014-2015 Program Chair *Not Eligible Until 2017/2018* * Susan Bookheimer, 2013-2014 Chair * Julian Doyon, 2013-2014 Treasurer * Thomas Nichols, 2013-2014 Secretary * Peter Bandettini, 2013-2014 Program Chair * Klaas Enno Stephan, 2013-2014 Education Chair We look forward to your involvement in the identification and election of your association’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>. <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3662> *Save the Date! June 26-30, 2016* <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3662> *Current 2015-2016 Council Members <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3313>* *Call for Communications Committee Members <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3685>*

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segmentation question
by Ahtam, Banu 05 Nov '15

05 Nov '15

Dear All, I am new to freesurfer and would appreciate your help with the following questions. I tried to look through the previous posts but couldn’t find the answers to all my questions. Thank you in advance. Best, Banu My question: I wanted to look at certain language related regions in the brain such as Heschl’s gyrus, Wernicke’s area, and planum temporale. I am looking at the lh.aparc.stats file right now. I see that there is a label for superior temporal gyrus which would involve all these three regions. I was wondering if Heschl’s gyrus, Wernicke’s area, and planum temporale are also segmented and labelled separately. In the previous posts, I saw that anterior portion of transverse temporal corresponds to Heschl’s gyrus, and under lh.aparc.stats file it is labelled as transversetemporal. I am still not sure about planum temporale and Wernicke’s areas though. I saw planum temporale in the lh.aparc.a2009s.stats file (it is called G_temp_sup-Plan-tempo, if I am correct). However, I am not sure if it is a good idea getting values from two different stat files (planum temporale from this one, and the rest from the other). Also, could you tell me if Wernicke’s area is segmented, and if so how is it labelled? -------- Banu Ahtam, DPhil Post-doctoral Research Fellow Boston Children's Hospital Fetal-Neonatal Neuroimaging & Developmental Science Center http://childrenshospital.org/FNNDSC

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Job: OHSU Fair Neuroimaging Lab Research Associate
by Eric Earl 05 Nov '15

05 Nov '15

Damien Fair's Neuroimaging Lab is looking for a candidate with expertise in neuroimaging, particularly in the field of MRI. While the main focus of this position is in neuroimaging, candidates with experience in bioinformatics and software development are highly encouraged to apply. The position will support a large federally funded longitudinal study to assess the short- and long-term impact of substance use on brain development (Adolescent Brain Cognitive Development Study). The work will also include support for other federally funded imaging studies on the development of attention, learning, and cognition, for both human and animal model brain imaging. The incumbent will be heavily involved in programming and software development for these integrated structural and functional brain imaging studies. The incumbent will also be involved with data collection and analysis. A successful applicant must be able to work well independently, also in a team, and to communicate clearly in a collaborative environment with a diverse range of experiences and disciplines. She/he must also have familiarity with different tools to process and analyze large datasets of structural and functional neuroimaging data, as well as a documented history of software development and support. The selected applicant will implement and execute reusable data processing pipelines, develop and improve current workflows and QA pipelines that will be released to external labs and assist in the standardization of data sharing infrastructure across different institutions. The applicant will be responsible for managing software development, support, documentation, and using software engineering best practices. Links: ABCD Study<http://addictionresearch.nih.gov/adolescent-brain-cognitive-development-stu…> Job Posting IRC50111 (best viewed in Internet Explorer)<https://ais.ohsu.edu/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelfServ…..>

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R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 05 Nov '15

05 Nov '15

Hi Dough, in summary: I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the MRS_MASK.mgz and run: fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean - cfg MRS_MASK.config fcseed-sess -s Control22_FS -cfg MRS_MASK.config ...Writing to /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.fcseed- sess.12305/avgwf.mgh Segmentation fault Therefore, according with your suggestion, I have now run: fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log ERROR: cound not find session -cfg The doug.log is attached. Thanks, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 4-nov-2015 16.58 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST > >First, when running fcseed-config, don't give it the full path, just the >path relative to subject/mri (in this case only MRS_MASK.mgz) > >However, I don't think that is the problem. Please run > >fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log > >and send me doug.log > > > > > >On 11/04/2015 04:14 AM, stdp82(a)virgilio.it wrote: >> Hi list, this error is still occurring: >> >> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz >> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz >> fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz - fsd >> rest -mean -cfg MRS_MASK.config >> fcseed-sess -s -cfg MRS_MASK.config >> >> During >> >> fcseed-sess -s subj -cfg MRS_MASK.config >> >> Voxel Volume is 64.5752 mm^3 >> Generating list of segmentation ids >> Found 1 segmentations >> Computing statistics for each segmentation >> 0 1 0 0.000 >> MRIalloc(0, 1, 1): bad parm >> Reporting on 0 segmentations >> Computing spatial average of each frame >> >> Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. >> fcseed-sess.97908/avgwf.mgh >> Segmentation fault >> >> I have read your previous message and you can check the MRS voxel >> features. >> MRS voxel mask is in subj directory where I have run recon all - all. >> >> data_type FLOAT32 >> dim1 256 >> dim2 256 >> dim3 256 >> dim4 1 >> datatype 16 >> pixdim1 1.000000 >> pixdim2 1.000000 >> pixdim3 1.000000 >> pixdim4 0.010747 >> cal_max 0.0000 >> cal_min 0.0000 >> file_type NIFTI-1+ >> >> >> The features are same of other subject that runs fine. >> data_type FLOAT32 >> dim1 256 >> dim2 256 >> dim3 256 >> dim4 1 >> datatype 16 >> pixdim1 1.000000 >> pixdim2 1.000000 >> pixdim3 1.000000 >> pixdim4 0.010747 >> cal_max 0.0000 >> cal_min 0.0000 >> file_type NIFTI-1+ >> >> Thank you very much. >> >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: stdp82(a)virgilio.it >>> Data: 16-ott-2015 23.15 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL >>> >>> I'd like to open with FSLview the sig.nii.gz which is produced by >>> selxavg3-sess. >>> If I use mri_surf2vol, which is the template to added in -- template? >>> It should be in Tailairach space? Where can I find the template that >> I >>> should added? >>> Thanks, >>> >>> Stefano >>> >>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >>> data_type FLOAT32 >>> dim1 27307 >>> dim2 1 >>> dim3 6 >>> dim4 1 >>> datatype 16 >>> pixdim1 1.000000 >>> pixdim2 1.000000 >>> pixdim3 1.000000 >>> pixdim4 1100.000000 >>> cal_max 49.1815 >>> cal_min -12.3855 >>> file_type NIFTI-1+ >>> >>> >>> >>> >>> >>> >>> >>> Thanks, >>> >>> Stefano >>> >>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 29-set-2015 22.09 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>>> >>>> Do you mean surface-based analysis? You'd have to put them back >> into >>> the >>>> volume using mri_surf2vol, write them out as nifti and then run >>> fslview >>>> on them >>>> >>>> On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >>>>> Hi list, >>>>> >>>>> I would like to import FS-FAST results (conjunction maps) in >>> FSL, >>>>> opening them by fslview. >>>>> Could you provide me any suggestion? >>>>> >>>>> Thank you very much >>>>> Best regards, >>>>> >>>>> >>>>> 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 >>> >> >> >> _______________________________________________ >> 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 >

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MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx
by Erik Lindberg 05 Nov '15

05 Nov '15

Dear Freesufer experts, I have trouble loading a contrast matrix - however I am not sure if something is going wrong earlier ... and this is causing this problem. Below is the error messages that I get plus the contrast matrix and the .fsgd file I am trying to run. I checked this previous mesages on this topic - and excluded the possitility that it would be related to windows formating or something like that. Can you see what is wrong? Would the most grateful for any advice on this Thanks! Error message: Saving mask to rh.Abeta_Gender_Apoe_age.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx Abeta_Gender_Apoe_age.fsgd: GroupDescriptorFile 1 Title Abeta_Apoe_Gender Class AbetaNegativeApoeNegativeMen Class AbetaNegativeApoeNegativeWomen Class AbetaNegativeApoePositiveMen Class AbetaNegativeApoePositiveWomen Class AbetaPositiveApoeNegativeMen Class AbetaPositiveApoeNegativeWomen Class AbetaPositiveApoePositiveMen Class AbetaPositiveApoePositiveWomen Variables Age Input 0d93d314-d7fe-4615-9b00-ea8011255a81 AbetaPositiveApoeNegativeWomen 9.6133333333 Input 36643d8d-caf1-47be-9025-e5662092a0c1 AbetaPositiveApoeNegativeWomen 5.6133333333 Input 12ee5f59-b7de-431c-9c93-fc737465cf24 AbetaPositiveApoePositiveWomen 6.6133333333 AAA.mtx: {1 1 1 1 -1 -1 -1 -1}/4 0 mris_preproc --fsgd Abeta_Gender_Apoe_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.Abeta_Gender_Apoe_age.10.mgh mris_preproc --fsgd Abeta_Gender_Apoe_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi rh \ --out rh.Abeta_Gender_Apoe_age.10.mgh mri_glmfit \ --y lh.Abeta_Gender_Apoe_age.10.mgh \ --fsgd Abeta_Gender_Apoe_age.fsgd doss \ --C AAA.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.Abeta_Gender_Apoe_ager.glmdir mri_glmfit \ --y rh.Abeta_Gender_Apoe_age.10.mgh \ --fsgd Abeta_Gender_Apoe_age.fsgd doss\ --C AAA.mtx \ --surf fsaverage rh \ --cortex \ --glmdir rh.Abeta_Gender_Apoe_age

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Re: [Freesurfer] how to obtain individual's pial_lgi value
by Yang, Daniel 04 Nov '15

04 Nov '15

Hi all, Found an answer here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.ht… It works for me! Best, Daniel From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Daniel Yang <daniel.yj.yang(a)yale.edu<mailto:daniel.yj.yang@yale.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, November 4, 2015 at 3:30 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] how to obtain individual's pial_lgi value Dear FreeSurfer Experts, When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option. Could you please advise how I can obtain an individual’s pial_lgi value, give a label? Many thanks! Daniel

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Jobs: Postdoctoral Fellow - Neuropsychology/Clinical Neuroscience/Imaging
by Emily Rogalski 04 Nov '15

04 Nov '15

http://www.alzforum.org/jobs/postdoctoral-fellow-neuropsychologyclinical-ne… Employer Cleveland Clinic-Lou Ruvo Center for Brain Health Location Las Vegas, Nevada Principal Investigator Please send your CV to Sarah Banks, bankss2(a)ccf.org and Ryan Walsh, walshr(a)ccf.org. Description The Cleveland Clinic Lou Ruvo Center for Brain Health in Las Vegas, Nevada is looking for an outstanding postdoctoral researcher to join the team as soon as possible. The researcher will work with two clinical and translational researchers, Ryan R. Walsh and Sarah Banks, on a recently awarded NIH grant (duration of funds: five years) assessing the neuropsychological and neuroimaging correlates of Alzheimer’s and Parkinson’s diseases. The study utilizes cutting-edge neuroimaging and analytic techniques involving both MRI and PET to assess cross-sectional and longitudinal patterns of cognitive disruption and neuroimaging changes in these patients. As part of the funding mechanism, the researcher will also collaborate with Jeff Cummings, and there is potential for collaboration with another five-year, fully funded project involving multi-modal MRI imaging in Parkinson’s disease, as well as experts in fMRI and PET both at the Cleveland Clinic and other institutions. The Cleveland Clinic Lou Ruvo Center for Brain Health is developing an excellent research team, featuring accessible, affable clinician-scientists in neurology and neuropsychology—a multidisciplinary team, in a small and specialized environment. It has state-of-the-art scanning technology, and a robust neuroimaging core led by Dietmar Cordes, a dedicated MR physicist and his team of research engineers, physicists, and mathematicians. This position will be excellent for anyone who has recently graduated and is looking to rapidly build his or her academic career in a position with no immediate need to obtain external funding. Requirements The ideal candidate will hold a Ph.D. in neuroscience, psychology, or similar field and have an interest in and experience with neurodegenerative disease, cognition, and neuroimaging. He or she will enjoy working in a multidisciplinary team, be productive, and enjoy contributing to every stage of data collection, analysis, and presentation. He or she will hit the ground running, working on existing data sets to answer research questions related to those posed in the grant, and also develop their own projects. Once sufficient data has been accrued from the grant projects, prospective data analysis and manuscript preparation will account for much of the researcher’s time. As such, great communication and writing skills, in addition to statistical knowledge and ability, will be important. -- Emily J Rogalski, PhD Associate Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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preproc-sess and stc question
by Gay,Charles Wysaw 04 Nov '15

04 Nov '15

Hi - 1) I am trying to perform preprocessing steps on functional task data that was acquired on a Phillips scanner using an interleaved acquisition. There are 42 slices and the order is [0,6,12,18,24,30,36,1,7,13,19,25,31,37,2,8,14,20,26,32,38,3,9,15,21,27,33,39,4,10,16,22,28,34,40,5,11,17,23,29,35,41]. I've tried -slice order followed by the sequence but that didn't seem to work. And I wasn't able to find anything in stc-sess -help that explained how to enter the exact sequence order. If you could show me how to add/change the tutorial code below, that would be great. Thanks. 2) Do I need to modify the onsets in the paradigmfile? Thanks, Chaz preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run

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Extracing values from ces.nii
by Afzal, Afsana 04 Nov '15

04 Nov '15

Hi, I'm trying to extract the contrast values from ces.nii.gz after first-level analysis. My goal is to average the contrast values for each voxel across subjects for a given condition and see where an individual from a separate population falls within the distribution of contrast values. The ces.nii file I'm working with has the following dimension: (27307, 1, 6, 1), which I interpreted as containing information about 27307 voxels in a 3D matrix. What does the information in the 6 rows for each voxel represent? I was expecting to get a single raw b-value for each voxel. The structure is consistent with sig.nii and t.nii files as well. Thanks for any help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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how to obtain individual's pial_lgi value
by Yang, Daniel 04 Nov '15

04 Nov '15

Dear FreeSurfer Experts, When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option. Could you please advise how I can obtain an individual’s pial_lgi value, give a label? Many thanks! Daniel

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