Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

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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wm edits not incorporated on recon-all rerun
by Octavian Lie 01 Apr '17

01 Apr '17

Dear All, I am stuck. Several brains I segment need both wm and pial edits, typically deleting incorrectly incorporated voxels, such as dural voxels for pia, and basal temporal hyperintensity artifact or bright dural voxels included due to partial volume effects for wm. I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz for wm. Rerunning recon-all led as expected to pial correction, however wm edits did not end up in ?h.white, despite increasingly desperate efforts and commands: recon-all -autorecon2-wm -autorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all Please advise, I could FTP one subject to you for suggestions. Again, edits here are all voxel deletions and not additions to wm.mgz. Thank you, Octavian

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display ROI mean values for FS atlas
by X K 01 Apr '17

01 Apr '17

Hi, I am doing a project with the Desikan-Killiany atlas. After some ROI analysis, I've got some values for each area. Now I want to display these values in the brain 3D space. The values are Z statistic scores, so there are both positive and negtive values (I want Z=0 to be in the middle of the color bar). In addition, I want to have a color bar about the plot. Attached please find one example data for the displaying. Please help if you have experience about this method. Thanks. Best, Xiangzhen

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Freesurfer April 2017