Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill
by gangli 09 Aug '16

09 Aug '16

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu) For more information, please visit: http://www.unc.edu/~gangl/contact.html.

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 09 Aug '16

09 Aug '16

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Error running hippocampal segmentation with FS6
by Lauri Tuominen 09 Aug '16

09 Aug '16

Dear freesurfers, I tried running hippocampal segmentation using the Dev version 6 on launchpad. I get the following error message: I ran the recon-all command yesterday and it worked fine. Cheers! Lauri Tuominen INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160805 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160809 INFO: SUBJECTS_DIR is /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6 -rw-rw-r-- 1 ljt22 dinahgp 490999 Aug 9 09:26 /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/recon-all.log Linux compute-0-57 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux `/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/recon-all' -> `/autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T2 only) left Tue Aug 9 13:11:58 EDT 2016 /usr/local/freesurfer/stable6/bin/segmentSF_T2.sh /usr/local/freesurfer/stable6/MCRv80 /usr/local/freesurfer/stable6 iaon /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR /autofs/space/colbert_001/users/ljt22/Feargen2/subjects/iaon/anat/012/T2.mgz left T2_analysis2 See log file: /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/hippocampal-subfields-T2.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Warning: application is running on a locale different from the original platform locale. Error using segmentSubjectT1_autoEstimateAlveusML Too many input arguments. MATLAB:TooManyInputs Warning: Unable to open display 'localhost:48.0'. You will not be able to display graphics on the screen. #-------------------------------------------- #@# Hippocampal Subfields processing (T2 only) right Tue Aug 9 13:12:06 EDT 2016 /usr/local/freesurfer/stable6/bin/segmentSF_T2.sh /usr/local/freesurfer/stable6/MCRv80 /usr/local/freesurfer/stable6 iaon /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR /autofs/space/colbert_001/users/ljt22/Feargen2/subjects/iaon/anat/012/T2.mgz right T2_analysis2 See log file: /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/hippocampal-subfields-T2.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threa/pbs/ljt22/pbsjob_59.o12129908

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hippocampus question
by Jasmin Alves 09 Aug '16

09 Aug '16

Dear Freesurfer, I have noticed that the subcortical grey matter volume output for the hippocampus differs slightly from other segmentation methods, I was wondering if this is due to what subfields of the hippocampus are included in the segmentation. I was curious which subfields Freesurfer includes as regional boundaries for the hippocampus. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Average Hippocampal Subfield Maps
by Jessica Sevick 09 Aug '16

09 Aug '16

Hello, I am wondering if it is possible to make average .mgz for the hippocampal subfields for a set of control images? Thanks, Jessica Sevick T: 403.944.8652 C: 587.576.6666

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Linking surface and volume coordinates in Freeview
by Isabelle Deschamps 09 Aug '16

09 Aug '16

Dear Freesurfer experts, In May 2016, one of the high priority on the Freeview Development board was to "Link the surfaces together (i.e. when you click on a vertex in the inflated surface, it should go to that vertex on the white and pial) & show identical vertex information in the Voxel Info panel. When clicking on a point on the 2D surface, automatically move the cursor in the 3D view to the closest point on the surface to that point in the volume." I couldn't find any information about whether this priority has been addressed yet or not. Would it be possible to have an update? Thank you in advance for the information, Isabelle

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Re: [Freesurfer] resample structural ROI in functional space?
by Kami Koldewyn 09 Aug '16

09 Aug '16

Never mind - for some inexplicable reason, I did not consider using mri_convert, which works splendidly for doing this. Sorry for posting when tired and before thoroughly exploring my options. -kami From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Kami Koldewyn <k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, 8 August 2016 19:33 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] resample structural ROI in functional space? Hi All, I have a set of ROIs that were created in structural space, currently saved as volume masks. I would like to transform these into functional space, re-sampled to the functional resolution. Can anyone suggest a good way to do this? -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 08 Aug '16

08 Aug '16

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Re: [Freesurfer] How does Optseq2 arrange order of conditions?
by 連志浩 06 Aug '16

06 Aug '16

Dear Douglas, I'm sorry that I didn't include previous correspondence in my email, from now on, I'll remember to include it. (I'm a new user of the FreeSurfer Mail Archive, I hope I include previous correspondence at this time.) Thanks for your reminding. Best Regards, Chih-Hao ________________________________ Date: Fri, 5 Aug 2016 11:45:55 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How does Optseq2 arrange order of conditions? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <57A4B4B3.1000601(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Please remember to include previous correspondence in your email. On 08/01/2016 04:22 AM, ? ?? wrote: > > Dear Douglas, > > Thanks for your explanation. These information are helpful to me. > > >I'm not sure what you mean. How can it be a delay if it is after > thetrial is over? > > I?m sorry for I didn?t describe my second question well. I think I can > take another situation to describe my question. > > If I have a experiment that present stimulus until participants > response, and I know the average RT of this experiment is 1500 ms > after pilot test. > > In this situation, should I +/- the duration of jitter/null condition > in terms of the duration of each stimulus? > > For example, if a part of sequence Optseq2 output is ? Con1 Null(500 > ms) Con2 Null(1500 ms)?, and one of participants takes 1000 ms to > response for Con1. > > Should I add 500 ms to the first Null? or I don?t need to anything? > > Thanks for your reading. > > Best Regards, > > Chih-Hao > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... -- 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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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internal capsule freesurfer
by 张献昌 06 Aug '16

06 Aug '16

Dear freesurfer developer, Hi, We recently processed some T1 data using Freesurfer .We want to extract internal capsule as roi. We found it appear in the ColorTableLUT as regions 155-158, but do not actually appear in any of the output parcellations.There is a message that Doug wrote some tools to do this in <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020985.…>. I would appreciate it if anyone can send me the script intcapseg and it would be better if there is a file describing how to use it. Thanks!! Best Regards!

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Freesurfer August 2016