Freesurfer

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30091 discussions

Fwd: recon-all error
by Patrícia Klobušiaková 04 Apr '17

04 Apr '17

Hello FreeSurfer Developers, I have installed Freesurfer on Windows using VMware - CentOS 64-bit (the one from FSLuser Linux installation). Everytime I run recon-all, there is an error. The same error occurs when I try to rum mri2mesh command in SIMNIBS toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and logfile attached. Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help. Best, Patricia

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Position in Genetics and Neuroimaging
by Juan Domingo Gispert López 04 Apr '17

04 Apr '17

The Barcelonaβeta Brain Research Centre (BBRC), research institution of the Pasqual Maragall Foundation (PMF) and the Centre for Genomic Regulation (CRG) invites applications for a full-time research position to study the genetic modulation of cerebral phenotypes based on genome-wide associations with neuroimaging data, as part of its clinical research program. The primary responsibility of this position includes the analysis and interpretation of genome-wide association studies (GWAS) data in association with quantitative phenotypes extracted from neuroimaging modalities. The candidate will be working under the guidance of the Principal Investigators Roderic Guigó of the CRG and the Neuroimaging Group Principal Investigator of the BBRC, Juan-Domingo Gispert. The aim of this project is to improve our understanding of genetic modulation of cerebral phenotypes in healthy subjects and to identify spatially varying patterns of genetic control that may not be evident from summary variables. For additional details please visit: https://recruitment.crg.eu/content/jobs/position/research-position-genetics… -- *Juan D Gispert* Head Neuroimaging Research *Barcelona**β**eta **Brain Research Center - Fundació Pasqual Maragall* T. (+34) 93 326 31 90 C/ Wellington, 30 08005 Barcelona *www.fpmaragall.org <http://www.fpmaragall.org/>*

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Re: [Freesurfer] FW: MPRAGE images dimension different {Disarmed}
by John Anderson 03 Apr '17

03 Apr '17

Dear Dhaval, when your recon-all finishs the process you will get images 256^3 and 1mm isootropic. The you can simply follow the instructions mentioned here https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your images back to native space. All the best, John > > On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah <dshah(a)bnac.net> wrote: > Hi All, > > I am new and a very basic question about freesurfer processing. > > I ran recon-all on a high res-T1 image(128x128x80 matrix size), but > after recon-all the folder mri contains resulted (brain.mgz and > orig.mgz) T1 images has (127x128x128 matrix size). > > 1) how come the dimensions are changed? Is it normal? > 2) how can i keep the dimensions same as the original? > 3) is it possible that i will always get the higher matrix size image > data? > > for simplicity, i converted resulted orig.mgz to nii format and loaded > it in to fslview. Please find the first image (Original) and the > second image (after recon-all but orig.mgz). > > Your help is greatly appreciated. > > -- > Kind regards, > Dhaval Shah > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > Buffalo Neuroimaging Analysis Center > State University of New York at Buffalo > Department of Neurology > 100 High St., D-2, Buffalo, NY 14203 > [MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be dshah@bnac.net//http://mbl.bnac.net](http://dshah@bnac.net/http:/mbl.bnac.net) > > > > > -- > Kind regards, > Dhaval Shah > > MRI Research fellow,MRI Physicist,Clinical Trial Research Staff > Buffalo Neuroimaging Analysis Center > State University of New York at Buffalo > Department of Neurology > 100 High St., D-2, Buffalo, NY 14203 > [MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be MailScanner has detected a possible fraud attempt from "dshah(a)bnac.net" claiming to be dshah@bnac.net//http://mbl.bnac.net](http://dshah@bnac.net/http:/mbl.bnac.net) > > _______________________________________________ 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. -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203 dshah(a)bnac.net // http://mbl.bnac.net

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MPRAGE images dimension different
by Dhaval Shah 03 Apr '17

03 Apr '17

Hi All, I am new and a very basic question about freesurfer processing. I ran recon-all on a high res-T1 image(128x128x80 matrix size), but after recon-all the folder mri contains resulted (brain.mgz and orig.mgz) T1 images has (127x128x128 matrix size). 1) how come the dimensions are changed? Is it normal? 2) how can i keep the dimensions same as the original? 3) is it possible that i will always get the higher matrix size image data? for simplicity, i converted resulted orig.mgz to nii format and loaded it in to fslview. Please find the first image (Original) and the second image (after recon-all but orig.mgz). Your help is greatly appreciated. -- Kind regards, Dhaval Shah MRI Research fellow,MRI Physicist,Clinical Trial Research Staff Buffalo Neuroimaging Analysis Center State University of New York at Buffalo Department of Neurology 100 High St., D-2, Buffalo, NY 14203dshah@bnac.net//http://mbl.bnac.net

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mri_vol2vol --mni152reg flips volume
by Melanie Ganz 03 Apr '17

03 Apr '17

Hi all, my colleague Vincent wanted to register a volume in MNI305 to MNI152, unfortunately the final image appears flipped up-down and anterior-posterior when using the --mni152reg flag with mri_vol2vol. For example, trying to resample fsaverage orig.mgz to MNI152 using mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mni152reg --o fsaverage.orig.MNI152.nii.gz ends up yielding the attached image (red is the output file and background is FSL MNI152 template). Anything obvious he's doing wrong? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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2 postdoctoral positions in cognitive neuroscience at UC San Francisco
by Roeland Hancock 03 Apr '17

03 Apr '17

Direct all inquires to brainlens(a)ucsf.edu *Joint Affective Neuroscience Postdoctoral Position at UCSF and Stanford University in California, USA* The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for Neurosciences in collaboration with the Stanford Mood and Anxiety Disorders Lab in the Dept of Psychology (http://goo.gl/dc96Cx PI: Ian Gotlib PhD) is looking for an exceptional postdoc in the field of affective neuroscience, with skills such as advanced neuroimaging, computational and programming, as well as organizational skills. Training in genetics and psychophysiology is a plus. The primary project that the postdoc will be responsible for is the examination of intergenerational neuroimaging using a ‘natural’ cross-fostering design that allows dissociation of genetic, prenatal and postnatal environment on brain networks that are transmitted across generations. Related articles from our lab can be found here - Yamagata et al. J Neurosci 2016 (http://goo.gl/vMK8iy) Ho et al. Trends in Neurosci 2016 (http://goo.gl/SyXLcK) and Scientific American (http://goo.gl/YTiH6D) There are other funded opportunities to be involved in such as research that examines the impact of anxiety and stereotype on psychophysiology and cognitive processes. The position can begin immediately. Please email brainlens(a)ucsf.edu with your CV, and with brief paragraphs of research interests, career goals and why you feel you are a good fit for the lab. Please add “[Postdoc job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 3 letters of reference forwarded. *Language Neuroscience Postdoctoral Position at UCSF in California, USA* The Hoeft Lab (http://brainLENS.org <http://brainlens.org/> PI: Fumiko Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for Neurosciences is looking for an exceptional postdoc in the field of language neuroscience, with skills such as advanced neuroimaging, computational and programming as well as organizational skills. Training in genetics is a plus. The primary project that the postdoc will be responsible for is the examination of intergenerational neuroimaging using a ‘natural’ cross-fostering design that allows dissociation of genetic, prenatal and postnatal environment on brain networks that are transmitted across generations. Related articles from our lab can be found here - Yamagata et al. J Neurosci 2016 (http://goo.gl/vMK8iy) Ho et al. Trends in Neurosci 2016 (http://goo.gl/SyXLcK) and Scientific American (http://goo.gl/YTiH6D) There are other funded opportunities to be involved in such as research that examines the Neural Noise Hypothesis of dyslexia (Hancock, Pugh and Hoeft, TiCS, in press) and the abundance of archival data on neuroimaging of language and literacy. The position can begin immediately. Please email brainlens(a)ucsf.edu with your CV, and with brief paragraphs of research interests, career goals and why you feel you are a good fit for the lab. Please add “[Postdoc job]” and your full name in the Subject of the email. Qualified candidates will be asked to have 3 letters of reference forwarded.

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2 postdoctoral positions in cognitive neuroscience at UC San Francisco
by Roeland Hancock 03 Apr '17

03 Apr '17

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v6 Hippocampal subfields on a cluster
by Ryan Muetzel 03 Apr '17

03 Apr '17

Dear Experts, I am trying to run the Hippocampal and brainstem MCR code on a cluster. When I schedule a job with anywhere between 2-4GB of RAM per dataset (i.e., per core), I am getting both java and matlab errors (from java, it is a GC out of memory error, and from matlab it is a vague segmentation fault). If I schedule the job with 6+GB of RAM, things run just fine. My sense is that there are maybe some multi-core/thread or memory settings in either java or the MCR that are causing trouble here? Or does this process really need 6GB of RAM? If the RAM requirements are closer to the 2-3GB range, do you happen to know of any flags I can/should pass to java/MCR to limit the parallel/memory expectations? For example, I’ve tried: export _JAVA_OPTIONS="-XX:ParallelGCThreads=1”, but without any luck. Let me know if you have any suggestions! Al the best, Ryan

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recon-all freezes during mri_fix_topology, FS6.0, Linux, using T2pial and FLAIRpial flags
by Eirik Wixøe Svela 03 Apr '17

03 Apr '17

Hello everyone, We recently installed FreeSurfer 6.0 at our site and are currently working out which flags and options to use. To learn more about what would suit our needs, we ran a couple of subjects using various flag combinations in order to evaluate the output. One run was initiated on Tuesday Mar 28, and as Friday Mar 31, the recon-all script still had not completed. We obtained similar results on trying to process it again, cf. the attached log file, and also with other subjects on other workstations. It seems that the mri_fix_topology binary is causing this issue -- the top utility indicates that four instances (one for each subject-flag combination, four in total) were running at full blast (100% CPU usage), and recon-all.log reveals that recon-all is waiting for this step to conclude. I have searched the list, but the posts containing similar issues all seemed to pertain to much older versions of FreeSurfer. FreeSurfer was invoked using the following command: $ parallel -a recon-all_test3.txt -j32 The contents of recon-all_test3.txt: recon-all -i /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127 -T2 /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/sorted/Sag_T2_CUBE_1iso/z4884 -s top3T_0186.fs6.3T.T2pial -all -3T -parallel -T2pial recon-all -i /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_T1_BRAVO_1iso/z127 -FLAIR /net/data/uTOP/3T_BRAVO/dicom/top3T_0186/Sag_CUBE_Flair_TR8/z360 -s top3T_0186.fs6.3T.FLAIRpial -all -3T -parallel -FLAIRpial recon-all -i dicom/top3T_0065/Sag_T1_BRAVO_1iso/Sag_T1_BRAVO_1iso-1.dcm -FLAIR dicom/top3T_0065/Sag_CUBE_Flair_TR8/Sag_CUBE_Flair_TR8-1.dcm -s top3T_0065.fs6.3T.FLAIRpial -all -3T -parallel -FLAIRpial recon-all -i dicom/top3T_0065/Sag_T1_BRAVO_1iso/Sag_T1_BRAVO_1iso-1.dcm -T2 dicom/top3T_0065/Sag_T2_CUBE_1iso/Sag_T2_CUBE_1iso-1.dcm -s top3T_0065.fs6.3T.T2pial -all -3T -parallel -T2pial I would be grateful for any and all clues as to what's wrong here. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v.6.0.0-2beb96c 2) Platform: Ubuntu LTS 14.04. 3) uname -a: Linux picasso 3.13.0-79-generic #123-Ubuntu SMP Fri Feb 19 14:27:58 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: See attachment. Regards Eirik Svela Institute of Psychiatry, University of Oslo

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ExploreDTI Workshop!
by Szabolcs David 02 Apr '17

02 Apr '17

Thrilled to announce that we are going to hold an ExploreDTI workshop in Utrecht (July 4-6)! More details can be found here: http://www.exploredti.com/workshop. We hope to see you there! Cheers, Szabolcs

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