Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

PairedAnalysis Longitudinal data
by Maria A Infante 14 May '17

14 May '17

Hi, I have a question about the paired-diff.fsgd file listed on the freesurfer wiki. I have 3 groups and 2 time points. How is the subject1pair computed? GroupDescriptorFile 1 Class Main Variables Age Input subject1pair Main 30 Input subject2pair Main 40 Input subject3pair Main 50 Input subject4pair Main 60

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Longitudinal hippocampal subfields analysis
by Manuel Delgado 14 May '17

14 May '17

Dear all, I set out to perform a longitudinal analysis of hippocampal subfields. I have already edited the cross and/or the bases when necessary and obtained the longs. Then I have obtained the hippocampal subfields by the automated pipeline: recon-all -s <subject> -hippocampal-subfields-T1. Now I am going to create the qdec table to proceed with the analysis, but I don't know whether I have to smooth the data by recon-all -long <tpid> <baseid> -qcahe before the analysis, or given that hippocampal subregions have been extracted by using its own pipeline it is not necessary to do any smoothing. Thanks -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN

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Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60
by Weisholtz, Daniel S.,M.D. 12 May '17

12 May '17

Dear Bruce, Thank you for your help. I was able to view the defects. It does seem to be an extensive defect—possibly retained dura? I’m not sure of any other way to fix it. Do you think that the poor quality of the source image makes it impossible to generate any kind of surface using free surfer? Best, Dan On May 11, 2017, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Message: 9 Date: Thu, 11 May 2017 11:38:42 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer Digest, Vol 159, Issue 12 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1705111132360.28473(a)door.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1705111132360.28473@door.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-7" Hi Dan that's a pretty low-contrast, severely motion-corrupted scan. We did pretty well given the input I think. To visualize the defects you can cd into the subject's mri dir and run: fv -v brain.mgz wm.mgz:colormap=heat -f \ ../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overlay_threshold=1,100 \ ../surf/lh.inflated.nofix:overlay=../surf/lh.defect_labels:overlay_threshold=1,100 then click the "use overlay color" button for the lh.orig.nofix surface. You can also change the display paramters in "configure overlay" to find a specific defect by setting the min/max to a narrow range around the one you are interested in (this will put it in the middle of the range and color it orange) cheers Bruce On Thu, 11 May 2017, Weisholtz, Daniel S.,M.D. wrote: Dear Bruce, Thank you so much for your suggestions. Unfortunately, I was not able to open lh.defect_labels in freeview. ?When I try, Freeview crashes. ?There are no rh surfaces in the surf folder, so I presume this means the problem occurred in the left hemisphere. I was able to view the inflated.nofix and orig.nofix but I?m still not exactly sure what the problem is, and I would be grateful if you could take a look at the subject folder. I will upload it to the ftp site. It is called s117. Thank you! Best, Dan On May 10, 2017, at 10:43 AM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Message: 9 Date: Tue, 9 May 2017 15:54:12 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1705091553090.16219(a)door.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1705091553090.16219@door.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-15" Hi Daniel you can load the ?h.defect_labels as an overlay on either the? inflated.nofix or orig.nofix surface and use it to find the location of? that defect. Usually this means something big is wrong - it should be? obvious looking at the inflated.nofix I would think. If you can't find it,? upload the subject to our ftp site and I'll take a look Bruce On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote: Hello Freesurfer Developers, I am trying to run recon-all -all and the procedure is freezing while trying to correct what appears to be a large defect (vertices=36706). The source T1 image is not great quality due to rippling artifact, but I have inspected brainmask.mgz, wm.mgz, and aseg.mgz and I cannot identify a large defect. The dura was not completely removed, and I tried improving this by using various watershed thresholds as well as using gcut. I also tried manually removing the remaining dura, but none of this was helpful. ?I also tried using -T2FLAIR, but this did not seem helpful either.? I am attaching the recon-all.log. This does not include the edits I made to brainmask.mgz. That was done on a separate attempt. This does include the -T2FLAIR, as you can see in the recon-all.log file. 1) FreeSurfer version:?freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: OS X Yosemite 10.10.5 3) recon-all.log attached I very much appreciate any assistance you can provide. Happy to send any of the data if it would be helpful. Sincerely, Dan Weisholtz

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Reminder: Fully Funded PhD Studentship in Social Neuroscience at Bangor University, UK {Disarmed}
by Kami Koldewyn 12 May '17

12 May '17

***Note: I will be attending the VSS meeting in Florida. If you are attending the meeting and would like to meet to discuss this post, please contact me to arrange a time!*** Join the Developmental Social Vision Lab<https://goo.gl/8IOZ3z> as a PhD Student! Applications are invited for a 3-year, fully funded PhD position in the lab under the supervision of Dr. Kami Koldewyn. The post is part of a European Research Council funded Starting Grant focused on Developmental Social Neuroscience. The project, ‘Becoming Social’, investigates developmental change in social perception, social learning and the social brain in late-childhood/early adolescence. The successful applicant will work with the Becoming Social team to design and carry-out research that focuses on understanding how we perceive, process and understand the social interactions we observe. Methods used may include behavioural, eye-tracking and neuroimaging (e.g. fMRI, DWI) measures and the PhD student will be very involved, both conceptually and technically, in the design and construction of research questions and the tasks to address them. Closing date for applications: 1st June , 2017. Start date: 1st October, 2017. For full details see this document: PDF of advertisement<https://goo.gl/SJu8Go> To apply, visit: https://jobs.bangor.ac.uk/ Job #BU01420<https://goo.gl/p2xIhx> For more information or discuss eligibility please contact: Kami Koldewyn at k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk> 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] TRACULA tract reconstruction
by Antonin Skoch 12 May '17

12 May '17

Dear Joelle, regarding the conversion to .bvecs, could you please show the example of difference between bvecs converted by mri_convert of FreeSurfer and mrconvert of mrtrix3? Do you have most recent version of mrtrix3? There have been a quite extensive discussion on implementation of FSL .bvec convention in mrtrix3 in spring 2016: http://www.mrtrix.org/2016/04/15/bug-in-fsl-bvecs-handling/ However, there have been quite a big effort to settle this issue and I am pretty convinced that the recent versions should have this issue resolved. Maybe you can also post this to the mrtrix community forum, they are usually responding very quickly and each post gives detailed attention. Regards, Antonin Skoch ??Dear Tracula experts, I am applying Tracula on a longitudinal data set, and have some questions I am hoping you could help me with: Firstly, upon visual inspection, several tracts appear to be quite messy, or small (on the default freeview threshold) for most subjects. However, the -stat step from Tracula does not necessarily flag these tracts as outliers. What is then the best way to decide whether tracts are not correctly reconstructed and need to be rerun separately once more? Can I rely on the flagged outliers? Or should I rerun all the tracts that do not look ok after visual inspection? And in the last case, for tracts that look small, are they considered as correctly reconstructed if looking ok at lower thresholds than the default of freeview? Second, concerning the rerunning of poorly reconstructed tracts, I was wondering if there might be a more automated way to configure the dmrirc file in order to adapt it for each subject/each tract to rerun (and its corresponding control points). Third, I was wondering if there is a recommended software for obtaining bvecs and bvals. For the moment I used mrconvert (from MRtrix, using the -export_grad_fsl option) and the new mri_convert from freesurfer 6.0. As they give different outputs, I was wondering if this may impact the reconstruction. Lastly, would you recommend using freesurfer 5.3 or 6.0 for applying the longitudinal stream of Tracula? Related to this, is it recommended to use the same freesurfer version to obtain the long/base images, and to run Tracula? Thank you for your time, Best regards, Joëlle van der Molen

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REPOSTED: 3.5 year Postdoc in Social Neuroscience at Bangor University, UK
by Kami Koldewyn 12 May '17

12 May '17

***Note: I will be attending the VSS meeting in Florida. If you are attending the meeting and would like to meet to discuss this post, please contact me to arrange a time!*** Applications are invited for a 3.5-year, full time postdoctoral position with Dr. Kami Koldewyn in the Developmental Social Vision lab<https://sites.google.com/view/devsocialvislab/> in the School of Psychology at Bangor University<https://www.bangor.ac.uk/psychology/> (Wales, UK). The post is part of a European Research Council funded Starting Grant focused on Developmental Social Neuroscience. The project, ‘Becoming Social’, investigates developmental change in social perception, social learning and the social brain in late-childhood/early adolescence. The successful applicant will be the coordinator of the first major research stream of the Becoming Social project, which focuses on understanding the typical adult system and developing tasks and methods that will be applied throughout the five-year project in the longitudinal developmental streams. Methods used may include behavioural, eye-tracking and neuroimaging (e.g. fMRI, DWI) measures and the postdoctoral researcher who fills this post will be very involved, both conceptually and technically, in the design and construction of research questions and the tasks to address them. Duties will include working to develop tasks and materials that will be used across the entire project (including not only typical adults but children/adolescents aged 9-16 both with and without an Autism Spectrum Disorder). The postdoctoral researcher will be a key member of the Becoming Social team and will work closely with other team members. A PhD or equivalent in a relevant field (e.g., Psychology, Neuroscience, Cognitive Science, Biomedical Imaging/Engineering or Computer Science), as well as outstanding written and spoken communication skills are essential. In addition, this particular post requires significant technical and/or neuroimaging abilities. The successful candidate needs to be comfortable with tackling new imaging and analysis methods and have the technical chops to do so. Closing date for applications: 5th June, 2017. Proposed start date: As soon as possible - (though exact timing is flexible for the right candidate). For full details see this document: PDF of advertisement<https://goo.gl/Q4y9fM> To apply, visit: jobs.bangor.ac.uk — Job BU01403<https://goo.gl/1EwTD2> For more information, to discuss eligibility or to arrange a meeting at VSS, please contact: Kami Koldewyn at k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk> 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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Postdoctoral Position: Developmental Neuroimaging
by emma jane 11 May '17

11 May '17

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position is supported by a recently awarded NICHD Center Grant (i.e., a CAPSTONE Center for Multidisciplinary Research in Child Abuse and Neglect; PI: Dr. Jennie Noll) and will be based in the Child Maltreatment Solutions Network (http://solutionsnetwork.psu.edu/) and the Prevention Research Center (www.prevention.psu.edu) both of which are located on the University Park campus in State College, PA. The primary responsibility of this position will be to provide neuroimaging research support (e.g., experimental design, implementation and data analysis) to a longitudinal project that will consider the biological embedding of child maltreatment in multiple biologic systems (e.g., neuroendocrine, autonomic, genetic, epigenetic, immunologic) and the impact of embedding on health outcomes, including neurodevelopmental trajectories. Candidates must have a PhD in psychology, neuroscience, or an allied field, or have completed all requirements for a PhD by the time of appointment. Applicants must have expertise in human subjects MRI, preferably with developmental cohorts. Preference will be given to those candidates with experience working with children who have experienced maltreatment or other high-risk groups. The successful candidate will be expected to contribute to experimental design and coordination of the neuroimaging aspects of the project and data analysis. Candidates must demonstrate expertise in functional and structural MRI analysis methods using standard processing packages (e.g., SPM, AFNI, FSL, Freesurfer etc.) and experience with longitudinal and complex datasets would be advantageous. The postdoctoral researcher will also be expected to contribute to manuscript preparation and presentation of study-related outcomes at key scientific meetings. Extensive mentorship will be provided to the successful candidate in order to facilitate the transition to an independent research career. This position will provide an opportunity to interact with several vibrant research communities at Penn State, including the Social Sciences Research Institute (www.ssri.psu.edu) and the Social, Life and Engineering Science Imaging Center (www.imaging.psu.edu) among others. The initial appointment will be for one year, with the possibility of renewal in subsequent years. Salary and benefits are based on NIH guidelines, commensurate with experience and qualifications. Interested candidates should upload a CV, cover letter, statement of research interests, and 2-3 relevant publications. In addition, applicants should arrange for 3 professional references to be submitted separately to Dr. Emma Jane Rose (Associate Director for P-TRAN) at emmajanerose(a)psu.edu. Review of applications will begin immediately and will continue until the position is filled. For further information about this appointment, please contact Dr. Emma Jane Rose at emmajanerose(a)psu.edu or 814-865-0114. Apply online at https://psu.jobs/job/69051 CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://www.police.psu.edu/clery/, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. … -- *Emma Jane Rose PhD.* *Assistant Research Professor & * *Associate Director for the **Program for Translational Research on Adversity and Neurodevelopment (P-TRAN)* *Edna Bennett Pierce Prevention Research Center* *The Pennsylvania State University* *308 Biobehavioral Health Building* *University Park, PA 16802* *www.prevention.psu.edu <http://www.prevention.psu.edu/>* *www.npscoalition.org <http://www.npscoalition.org/>*

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Segmentation faults with unpacksdcmdir and dcmunpack
by Dillon, Daniel G. 11 May '17

11 May '17

Hi everyone. I’m unpacking dicoms collected on a 3T Tim Trio and I’m getting segmentation errors (see below) with two of ~80 subjects when using either unpacksdcmdir or dcmunpack (I’ve tried both commands with FreeSurfer 5.3.0 and 5.3.1, running on the Harvard NCF cluster). I’m not sure what to try next, hoping to get some advice . . . I don’t know that anything went wrong with the scans but it’s odd that only these two subjects are failing. Any ideas for a fix? Thanks in advance, Dan Dillon Here’s the command and output with unpacksdcmdir: unpacksdcmdir -src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -cfg 151027_RMD057/151027_RMD057.cfg $Id: unpacksdcmdir,v 1.19.2.1 2007/09/19 14:34:42 greve Exp $ /net/rcss2/srv/export/ncf_anl/share_root/anl01/RMD -src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -cfg 151027_RMD057/151027_RMD057.cfg Wed May 10 12:20:08 EDT 2017 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2017/05/10-16:20:08-GMT BuildTimeStamp: Dec 16 2007 07:41:05 CVS: $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ User: ddillon Machine: ncfc22.rc.fas.harvard.edu<http://ncfc22.rc.fas.harvard.edu><http://ncfc22.rc.fas.harvard.edu/> Platfor m: Linux PlatformVersion: 2.6.32-642.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ncfc22.rc.fas.harvard.edu<http://ncfc22.rc.fas.harvard.edu><http://ncfc22.rc.fas.harvard.edu/> Linux ncfc22.rc.fas.harvard.edu<http://ncfc22.rc.fas.harvard.edu><http://ncfc22.rc.fas.harvard.edu/> 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed May 10 12:20:08 EDT 2017 Log File is 151027_RMD057/unpack.log INFO: Logfile is 151027_RMD057/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is 151027_RMD057/dicomdir.sumfile INFO: status file is 151027_RMD057/parse.status Scanning directory Wed May 10 12:20:09 EDT 2017 mri_parse_sdcmdir --sortbyrun --d 151027_RMD057/RAW/ --o 151027_RMD057/dicomdir.sumfile --status 151027_RMD057/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Wed May 10 12:22:14 EDT 2017 ------------------------------------------ 5 T1_MEMPRAGE ok 192 192 144 1 151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm 6 T2_SPACE ok 192 192 144 1 151027_RMD057.MR.INVESTIGATORS_Dillon.6.1.20151027.152735.4qpapf.dcm 17 REVMEM_01 ok 72 72 47 290 151027_RMD057.MR.INVESTIGATORS_Dillon.17.1.20151027.152735.7xk08n.dcm 19 REVMEM_02 ok 72 72 47 290 151027_RMD057.MR.INVESTIGATORS_Dillon.19.1.20151027.152735.xgrals.dcm 21 PST_01 ok 72 72 47 170 151027_RMD057.MR.INVESTIGATORS_Dillon.21.1.20151027.152735.1trnf8q.dcm 23 PST_02 ok 72 72 47 170 151027_RMD057.MR.INVESTIGATORS_Dillon.23.1.20151027.152735.1q4ykwt.dcm 25 PST_03 ok 72 72 47 170 151027_RMD057.MR.INVESTIGATORS_Dillon.25.1.20151027.152735.3k8rgn.dcm 27 PST_04 ok 72 72 47 170 151027_RMD057.MR.INVESTIGATORS_Dillon.27.1.20151027.152735.wkcxen.dcm unpacking config ------------------ {5 3danat nii T1.nii} {6 3danat nii T2.nii} {17 RevMem nii f.nii} {19 RevMem nii f.nii} {21 PST nii f.nii} {23 PST nii f.nii} {25 PST nii f.nii} {27 PST nii f.nii} ----------------------------------- --------------------------------------------------------- Run 5 ----------------------------------------- Wed May 10 12:22:14 EDT 2017 5 3danat nii T1.nii mri_convert 151027_RMD057/RAW//151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm 151027_RMD057/3danat/005/T1.nii --sdcmlist 1 51027_RMD057/3danat/005/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation Here’s the command and output with dcmunpack: dcmunpack -src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -run 5 3danat nii T1.nii /ncf/tools/current/apps/arch/linux_x86_64/freesurfer/5.3.1/bin/dcmunpack -src 151027_RMD057/RAW/ -targ 151027_RMD057 -fsfast -run 5 3danat nii T1.nii -rwxr-xr-x 1 nrgadmin nrg 23416 Feb 19 2015 /ncf/tools/current/apps/arch/linux_x86_64/freesurfer/5.3.1/bin/dcmunpack --------------------------------------- 1 5 3danat T1 0 0 --------------------------------------- Searching for matching files Wed May 10 13:34:44 EDT 2017 Wed May 10 13:34:44 EDT 2017 Found 1549 total files. Interrogating each and every one of them. Be patient. If you have collected the data in the Martinos center, this will run faster if you kill this job and re-run with -martinos Found 8 unique series: 5 6 17 19 21 23 25 27 Subject 151027_RMD057 Date 20151027 Time 152735.343000 Institution 5 T1_MEMPRAGERMS 1.54 2200 7 1.1979166269302\1.1979166269302 ROW 651 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.124.20151027.152735.14a3j6a.dcm 6 T2_SPACE 327 2800 120 1.1979166269302\1.1979166269302 ROW 651 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.6.109.20151027.152735.hkvqu7.dcm 17 REVMEM_01 30 3000 75 unknown COL 2240 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.17.53.20151027.152735.q6qzzg.dcm 19 REVMEM_02 30 3000 75 unknown COL 2240 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.19.118.20151027.152735.csj5a8.dcm 21 PST_01 30 3000 75 unknown COL 2240 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.21.141.20151027.152735.61ysw7.dcm 23 PST_02 30 3000 75 unknown COL 2240 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.23.108.20151027.152735.1g8omw.dcm 25 PST_03 30 3000 75 unknown COL 2240 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.25.149.20151027.152735.waf4h2.dcm 27 PST_04 30 3000 75 unknown COL 2240 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.27.167.20151027.152735.b9fgot.dcm mri_convert 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.124.20151027.152735.14a3j6a.dcm 151027_RMD057/3danat/005/T1.nii --nskip 0 --ndrop 0 nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.124.20151027.152735.14a3j6a.dcm... Getting Series No INFO: Found 1550 files in 151027_RMD057/RAW INFO: Scanning for Series Number 5 Scanning Directory INFO: found 144 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. INFO: (192 192 144), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.997 -0.028 -0.069 3.361; 0.019 0.992 -0.128 -12.399; 0.072 0.127 0.989 0.552; 0.000 0.000 0.000 1.000; FileName 151027_RMD057/RAW/151027_RMD057.MR.INVESTIGATORS_Dillon.5.1.20151027.152735.1oe820t.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName 151027_RMD057 Date and time StudyDate 20151027 StudyTime 152735.343000 SeriesTime 153542.390000 AcqTime 153336.015000 Acquisition parameters PulseSeq tfl3d4_ns Protocol T1_MEMPRAGE PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.54 InversionTime 1100 RepetitionTime 2200 PhEncFOV 230 ReadoutFOV 230 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 90.5719 127.9491 99.4836 VolRes 1.1979 1.1979 1.2000 VolDim 192 192 144 Vc 0.0126 -0.9958 -0.0903 Vr -0.0730 0.0892 -0.9933 Vs -0.9973 -0.0191 0.0716 VolCenter -2.5393 22.0298 -18.9494 TransferSyntaxUID 1.2.840.10008.1.2.4.90 UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault

2 2

Trying to get functional scan working
by Brad Matushewski 11 May '17

11 May '17

Hello Freesurfer crowd. I am working on try to get my first fMRI scan working. I have come a long ways in terms of setting things up but have reached a road block that I have unable to get past. I have been following along the slides from the power point presentation "FSFAST Part 2". I got as far as slide #32: Preprocessing Command". Specifically, I entered the following command: preproc-sess -sf sessids -surface fsaverage lhrh -mni305 -fwhm 5 -pre-run Things started to happen but finished rather quickly. I looked through the text output and it would appear that it cannot find the bet.fsl tools(?). I looked at the directory to where it was looking at it IS in there (i.e. /usr/local/freesurfer/bin/bet.fsl) I also labelled things exactly as outlined: (i.e. /usr/local/freesurfer/subjects/handedness/project/Sess01) I have attached a couple text files from the output logs. What can I try next? [Logo] Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447

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mri_label2label with close operation
by Hengda He 11 May '17

11 May '17

Hi Freesurfer Developers, I'm trying to map the vertices of caudal middle frontal in one subject into the space of another subject by using mri_label2label. And I used the method mentioned in this https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2015-November/042298.… We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I noticed the mri_label2label in v5.1 has the bug of getting holes in the mapped labels( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42600.html) So I am using the /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin from freesurfer-x86_64-unknown-linux-gnu-dev5-20160513. For example, we have source Labels(aparc-lh-003_5thCol.label), which are all in SurfaceRAS coordinates: #!ascii label , from subject FreeSurfer vox2ras=TkReg 8 104996 -35.679 16.281 25.156 1 104997 -36.480 16.439 25.362 2 104998 -37.443 16.702 25.369 3 105705 -41.554 16.840 28.930 4 105716 -40.445 17.153 28.046 5 105720 -39.570 17.200 26.959 6 131017 -29.315 12.915 45.422 7 131030 -31.304 12.514 46.455 8 By running this: /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh We got mapped Labels(aparc-lh-003_5thCol_Reg2MNI.label), which are all in SurfaceRAS coordinates: 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000 But the mapped labels I got from the mri_label2label in v5.1 and that from using mri_label2label.bin in dev are quite similar to each other when applying the method to around 3500 labels. So I am wondering if the bug of getting holes was fixed by providing morphological operations in the updated mri_label2label like close operation. If it is true, I am confused about the mapped labels from mri_label2label with close operation. For example, with the same source labels above, I ran /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI_close2.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh --close 2 And we got mapped Labels(aparc-lh-003_5thCol_Reg2MNI_close2.label): 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000 1045 -1.690 -91.572 -40.145 0.0000000000 118251 -18.413 75.394 63.061 0.0000000000 118258 -21.026 75.715 61.847 0.0000000000 119092 -19.797 75.786 62.165 0.0000000000 The problem is that four additional labels 1045, 118251, 118258 and 119092 are not actually on the white matter surface but seem to be right on a sphere(ex. label 1045, 1.690^2+91.572^2+40.145^2=100^2). But I checked all other mapped labels like 119096, they are on the WM surface in the SurfaceRAS coordinates. I am using CentOS release 6.9. Thanks! All the Best, Hengda

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Freesurfer May 2017