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ROI Analysis
by Larissa Bechtle 04 Jan '19

04 Jan '19

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Job Opportunity
by Smith, Arleen 04 Jan '19

04 Jan '19

External Email - Use Caution Good Day I would like to extend a job opportunity at the University of Texas at Dallas. Please forward to members of the listserv. The School of Behavioral and Brain Sciences at The University of Texas at Dallas is accepting applications at the Assistant Professor level to join the area of Cognition and Neuroscience. The University of Texas at Dallas (UTD) is a Carnegie R1 classification institution and was recently ranked #1 in the US among universities founded less than 50 years ago by Times Higher Education. Faculty in the area of Cognition and Neuroscience are based both on the main campus and at three research centers located in central Dallas near The University of Texas Southwestern Medical Center (UTSW), with which there are strong collaborative relationships. UTSW houses the Advanced Imaging Research Center, an inter-institutional facility that provides neuroimaging resources supporting the research of UTD faculty. Additional neuroimaging resources are under development under the auspices of UTD. Applicants must hold a PhD degree in psychology, neuroscience, or a related field, and will be expected to build and maintain a scientifically rigorous, extramurally funded research program. The research area of interest should broadly be in the study of human reinforcement learning and decision making relevant to the emerging field of computational psychiatry, applying functional and structural neuroimaging methods. We invite applicants with a strong empirical program in one or more of these areas, and who, in addition, have strengths in applying novel methodological or analytical approaches to cognitive neuroscience. The successful candidate will be expected to actively engage in the research and training activities of the Cognition and Neuroscience area in the School of Behavioral and Brain Sciences, including advising doctoral students, mentoring postdoctoral trainees, and developing collaborative research programs. Applicants should upload (1) a cover letter; (2) a curriculum vitae; (3) a statement of research plans (approximately 2-3 pages); and (4) the names and full contact information for three references via the online application at http://jobs.utdallas.edu/postings/11357. Review of applicants will begin immediately. Administrative questions may be addressed to the Program Office at 972-883-7260. The University of Texas at Dallas is an Equal Opportunity/Equal Access/Affirmative Action Employer committed to achieving a diverse and inclusive community. Thank You Arleen smith The University of Texas at Dallas School of Behavioral & Brain Sciences, GR41 800 West Campbell Road Richardson TX 75080-3021 Office: GR4.506 PH. 972-883-2357 Fax 972-883-2491 [Description: Description: UTD Signature] Life's most urgent question is: What are you doing for others - Martin Luther King Jr.

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post-doc opportunity: structural/functional brain connectivity and networks
by Barbara Kreilkamp 04 Jan '19

04 Jan '19

External Email - Use Caution Dear all, As a current post-doc in this lab, I am happy to announce this three-year post-doc opportunity availabile in Dr Simon Keller's lab at the University of Liverpool, United Kingdom. The successful applicant will be specialising in structural and functional brain connectivity and networks in human epilepsy. Please find more information here https://www.jobs.ac.uk/job/BPF608/postdoctoral-research-fellow-neuroimaging… and in the attachment. Please read this job description (link and attachment) and direct your informal inquiries to Dr Simon Keller (simon.keller(a)liverpool.ac.uk) Kind regards and a happy new year! Barbara

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-qcache error
by 塩浜直 03 Jan '19

03 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do group analysis for cortical thickness map using Qdec GUI. We've already have recon-all files that were made by “recon-all –s subjid –i subjid.nii –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Firstly, I try to run command “recon-all –s subject –qcache” for each subject floders. However, the program stopped with error 1 minutes after starting. Last line of recon-all.log showed as follows. #@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 I've searched the list but I can find no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: Free Surfer 6.0 2) Platform: macOS Mojave (64b Intel) 3) recon-all.log: see attached Tadashi Shiohama

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Re: [Freesurfer] map parcellations into DWI space?
by Greve, Douglas N.,Ph.D. 03 Jan '19

03 Jan '19

you might try this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 On 12/30/18 1:45 AM, Yerong Li wrote: > External Email - Use Caution > Dear FreeSurfer experts: > I am trying to map ./mri/aparc.a2009s+aseg.mgz and > ./mri/aparc+aseg.mgz into DTI file. > Let's say, we have a DTI file with its b-vectors: > ./bvals > ./bvecs > ./data.nii.gz > > I am trying to use the command from this webpage: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > So I used the command : > mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o > dk-in-rawavg.mgz --regheader aparc+aseg.mgz > > The output file seems not very reasonable. Could you help me with this? > > Yerong > ================================== > Can you be more specific about which files you want to map into your DWI > space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You > will need a registration file which you can obtain with bbregister > > > On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: >> >> External Email - Use Caution >> >> Dear FreeSurfer experts, >> I have a parcellation and a whole brain white matter files which are >> the outputs of FreeSurfer. >> I want to register them to my DWI. I mean I want my parcellation and >> white matter to be in the physical space of my DWI. >> Can FreeSurfer do it for me? >> If not , can you suggest me a toolbox that can do it fast? >> I would be grateful if u could help me. >> Cheers, >> Maedeh, >> >> >

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Diagnosing a recon error
by Maksimovskiy, Arkadiy 03 Jan '19

03 Jan '19

Dear Experts, I was wondering if someone might be able to help diagnose a recon error. I used the following command to initiate recon: recon-all -subject RMD002 -i /ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii -T2 /ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD002.nii -T2pial -3T -all The recon log indicates an error: recon-all -s RMD002 exited with ERRORS Attached is the log file. I used grep to search through it for “failed” or “error”, but am unable to see any indices of errors, other than this message at the bottom of the log. I would love to hear any info for what might have gone wrong. Thank you for all your help, Arkadiy

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Extracting cortical thickness from a significant cluster in an independent sample
by Tamara Sussman 03 Jan '19

03 Jan '19

External Email - Use Caution Hello Freesurfer Experts! Thank you in advance for considering this question. I did a cortical thickness analysis (surface-based), and found a significant cluster. I found the average cortical thickness in* this group*, in the .*y.ocn.dat* file, which is great. Now I want to find the average cortical thickness in the same cluster, in a separate group of subjects. I tried using mri_segstats, but it doesn't seem to work: mri_segstats --slabel $label --i $input --nonempty --excludeid 0 --avgwf test.dat --sum Test_SupParietal.sum The error I am getting is: ERROR: cannot do frame average without input volume Any thoughts about a better way to approach this analysis? Thanks again in advance! -T

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Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047
by 허정선 03 Jan '19

03 Jan '19

External Email - Use Caution Thank you for your reply. Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. And, there was a problem like the photo below, and only the recon-all.log could be attached to you. Thanks, Jeongson ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1812201012130.17732(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Jeongson it certainly looks like something went badly wrong. 2mm may be too thick - we typically recommend <=1.5mm for any voxel direction. Can you send us the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid? cheers Bruce On Thu, 20 Dec 2018, ??? wrote: > External Email - Use Caution > > Hello Freesurfer developers > I'm starting using FS and I have a problem running recon-all. > #recon-all -s /usr/local/freesurfer/subjects/20180108 -all > I've attached the output to a ERROR image file. > > We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. > freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 > > Any help is greatly appreciated. > > Thanks. > > Jeongson ------------------------------

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Which T1 volume to use for coregistration with PET volume
by Matthieu Vanhoutte 03 Jan '19

03 Jan '19

External Email - Use Caution Dear Freesurfer’s experts, I used mri_coreg command to coregister PET image onto T1 volume. Basically, this command coregister PET image onto orig.mgz volume (default target). However, I wonder if T1.mgz wouldn’t be a better target since it has been corrected for inhomogeneities and intensity normalized ? Thanks for helping ! Best, Matt

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mri glm fit matrix is ill-conditioned
by Sahil Bajaj 02 Jan '19

02 Jan '19

External Email - Use Caution Hi experts, I am running following command: mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir Both FSGD and Contrast files are also attached. After I run above command, I get following error (highlighted in red): mri_glmfit --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir gdfRead(): reading PAI_SUI_ONLY_MILD_DEP2.fsgd INFO: demeaning continuous variables Continuous Variable Means (all subjects) 0 SUI 52.4444 2.11403 1 Age 32.1111 7.23332 2 DEP 55.1111 7.83786 Class Means of each Continuous Variable 1 Male 52.0000 32.0000 54.0000 2 Female 52.6667 32.1667 55.6667 INFO: gd2mtx_method is dods Reading source surface /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral cmdline mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir sysname Linux hostname hyperion machine x86_64 user scanlab FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh logyflag 0 usedti 0 FSGD PAI_SUI_ONLY_MILD_DEP2.fsgd labelmask /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/label/lh.cortex.label maskinv 0 glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir Loading y from /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+08 Design matrix ------------------ 0.00000 1.00000 0.00000 1.68188 0.00000 -0.01536 0.00000 -1.67279; 1.00000 0.00000 -0.68326 0.00000 1.09063 0.00000 -0.77969 0.00000; 0.00000 1.00000 0.00000 -0.68326 0.00000 -1.39785 0.00000 2.02720; 0.00000 1.00000 0.00000 -0.68326 0.00000 1.22888 0.00000 -0.14176; 1.00000 0.00000 0.73582 0.00000 -0.29186 0.00000 0.62375 0.00000; 1.00000 0.00000 -0.68326 0.00000 -0.84486 0.00000 -0.26935 0.00000; 0.00000 1.00000 0.00000 1.68188 0.00000 -1.12135 0.00000 0.11341; 0.00000 1.00000 0.00000 -0.68326 0.00000 1.50538 0.00000 -0.65211; 0.00000 1.00000 0.00000 -0.68326 0.00000 -0.15361 0.00000 0.75134; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=1.034183 (col 7), Max=2.816108 (col 8) ... could not determine the cause of the problem Both fsgd and contrast files are created in LINUX, and I also normalized my data using DeMeanFlag 1 ReScaleFlag 1 as suggested here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49123.html Could you please help in resolving this issue? Thanks ! Sahil

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