Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

error in triangulation mesh of brain surface
by Fatemeh Ahmadi 08 Jun '21

08 Jun '21

External Email - Use Caution Hello Dear Dr. Fishel, I thank you for developing such a useful application, I use it for brain surface reconstruction, then I process the brain hemisphere surface by geometric method for my work, it seems that the triangulation mesh of brain surface obtained by Freesurfer is not good!How can I fix it? Thank you very much in advance,Regards. ---------------------Fatemeh Ahmadi,PhD Student in Computer Science,Department of Mathematics and Computer Science,Amirkabir University of Technology, Tehran, IranEmail: f.ahmadi(a)aut.ac.ir

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Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB exited for no reason
by 林鈺庭 08 Jun '21

08 Jun '21

External Email - Use Caution Dear Developer and Eugenio, Huge thanks for your help in the previous emails. We finally completed the analysis. However, when we run the code to gather the volumes, it shows no error but we can't find the path of the file either in FreeSurfer root (/application/freesurfer/subjects) or in the subject data direction(/data/S013). I'm wondering if there is any way to set the writing path for this process. Could you provide some advice? Thank you! *The terminal looks like this:* *[root@2981d0ea233a data]# quantifyHAsubregions.sh hippoSf T1 results.txt /data/S013Gathering results from subjects in: /data/S013 Using the prefix name: hippoSfUsing the suffix name: T1And writing them to: results.txt * Best regards, Josephine <freesurfer-request(a)nmr.mgh.harvard.edu> 於 2021年5月29日週六下午3:26寫道： > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1RrTJ4CP_-55U_c70cFRrBNM6YsunQmbfzjwS_VfF7t4Dw… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: mri_hippocampal-subfields error: MATLAB exited for no > reason (Iglesias Gonzalez, Juan E.) (Iglesias Gonzalez, Juan E.) > 2. Re: Hippocampal Subfield error (Daniel Davidson Callow) > 3. Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.) > 4. Re: Hippocampal Subfield error (Daniel Davidson Callow) > 5. mri_glmfit-sim with grf (ERROR: need --csd with --csd-out) > (Di?genes Bispo) > 6. Group comparison with MD (Antti Cajanus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 May 2021 19:29:14 +0000 > From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB > exited for no reason (Iglesias Gonzalez, Juan E.) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <7A66B3DD-56D6-4754-B9B5-84A215B1F480(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Multiple subjects or all of them? > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1GdciW0unJf79By6yzNdaCZgdWfXJEeLsraM57FUyfY3trP… > > > On May 28, 2021, at 12:26, ??? <ytlin923(a)g.ntu.edu.tw> wrote: > > > > External Email - Use Caution > > > > Dear Dear FreeSurfer Developers, > > > > (We?re the message 3) > > This happened to multiple subjects. Our computer got 16GB MHz DDR4 , We > thought it met the requirements to run the module based on the > documentation on freesurfer wiki , or didn?t it? :( > > > > > > Best regards, > > Josephine > > > >> freesurfer-request(a)nmr.mgh.harvard.edu ? 2021?5?29? ??12:03 ??? > >> Send Freesurfer mailing list submissions to > >> freesurfer(a)nmr.mgh.harvard.edu > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> > https://secure-web.cisco.com/19MxmZ-YngtXyjI8JhMif3nT9Tvss_ZmhVPTJcv7XmEmCX… > >> or, via email, send a message with subject or body 'help' to > >> freesurfer-request(a)nmr.mgh.harvard.edu > >> > >> You can reach the person managing the list at > >> freesurfer-owner(a)nmr.mgh.harvard.edu > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of Freesurfer digest..." > >> > >> > >> Today's Topics: > >> > >> 1. (no subject) (Daniel Davidson Callow) > >> 2. Hippocampal Subfield error (Daniel Davidson Callow) > >> 3. Re: mri_hippocampal-subfields error: MATLAB existed for no > >> reason (Iglesias Gonzalez, Juan E.) > >> 4. Re: Choosing projfrac/projdist and checking mri_vol2surf > >> output (M Pope) > >> 5. Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.) > >> 6. PVC to calculate myelin maps (Marina Fern?ndez) > >> 7. Re: PVC to calculate myelin maps (Glasser, Matthew) > >> 8. PVC to calculate myelin maps (Marina Fern?ndez) > >> 9. Re: PVC to calculate myelin maps (Glasser, Matthew) > >> 10. (no subject) (Francisca Ferreira) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 28 May 2021 07:52:44 -0400 > >> From: Daniel Davidson Callow <dcallow(a)umd.edu> > >> Subject: [Freesurfer] (no subject) > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Message-ID: > >> <CAFMVdsfJ9Scx1sQ+CC6BMobLtKQT6501=vTR9KKxVA4OB_rOxg(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> External Email - Use Caution > >> > >> Hello, > >> > >> I am running into errors when running > >> > >> segmentHA_T2.sh ${subj} > >> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1 > >> > >> Approximately 10% of my subjects are being processed but for some > reason, > >> the majority fail to execute. Here is an output from the error log. > >> ------------------------------ > >> USER dcallow > >> HOST compute-4-32.bswift.umd.edu > >> < > http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV… > > > >> PROCESSID 4033 > >> PROCESSOR x86_64 > >> OS Linux > >> Linux compute-4-32.bswift.umd.edu > >> < > http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV… > > > >> 2.6.32-754.35.1.el6.x86_64 > >> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux > >> ------------------------------ > >> > >> #-------------------------------------------- > >> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 > EDT > >> 2021 > >> ------------------------------------------ > >> Setting up environment variables > >> --- > >> INFO: error loading libraries in default configuration, trying with MCR > >> libraries only > >> LD_LIBRARY_PATH is > >> > .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering > >> norm.mgz to additional volume > >> makeIsotropic WARNING: not different enough, won't reslice! > >> No more processes. > >> ERROR: could not open > >> > /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh > >> for reading > >> ERROR: loading > >> > /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh > >> as MGH > >> Warning: File > >> > '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh' > >> not found. > >> [^H> In myMRIread at 64 > >> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H > >> Attempt to reference field of non-structure array. > >> > >> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211) > >> > >> > >> > >> MATLAB:nonStrucReference > >> @#@FSTIME 2021:05:27:21:39:51 > >> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U > 8.61 > >> P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L > $@#@FSLOADPOST > >> 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 > >> 31.22 29.74 28.95 > >> Linux compute-4-32.bswift.umd.edu > >> < > http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV… > > > >> 2.6.32-754.35.1.el6.x86_64 > >> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux > >> > >> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT > 2021 > >> > >> I am also getting a matlab_crash_dump file > >> > >> ------------------------------------------------------------------------ > >> Segmentation violation detected at Thu May 27 21:51:52 2021 > >> ------------------------------------------------------------------------ > >> > >> Configuration: > >> Crash Decoding : Disabled > >> Current Visual : None > >> Default Encoding : US-ASCII > >> GNU C Library : 2.12 stable > >> MATLAB Architecture: glnxa64 > >> MATLAB Root : /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux > >> MATLAB Version : 8.4.0.150421 (R2014b) > >> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 > >> 04:45:43 EDT 2020 x86_64 > >> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel > >> Software OpenGL : 0 > >> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java > >> HotSpot(TM) 64-Bit Server VM mixed mode > >> Window System : No active display > >> > >> Fault Count: 1 > >> > >> > >> Abnormal termination: > >> Segmentation violation > >> > >> Stack Trace (from fault): > >> [ 0] 0x00007f2b30f06213 > >> /lib64/libpthread.so.0+00033299 pthread_join+00000035 > >> [ 1] 0x00007f2a9f4d847d > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 2] 0x00007f2a9f4d8cac > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 3] 0x00007f2a9f5cae63 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 4] 0x00007f2a9f5af896 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 5] 0x00007f2a9f5a6b8d > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 6] 0x00007f2a9f5a6fd0 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 7] 0x00007f2a9f5aad00 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 8] 0x00007f2a9f5a5c3c > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 9] 0x00007f2a9f44fb03 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 10] 0x00007f2a9f42b9cc > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 11] 0x00007f2a9f42b132 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 12] 0x00007f2b21dcfc0a /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538 > >> mexRunMexFile+00000090 > >> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644 > >> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308 > >> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… > >> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 16] 0x00007f2b2260fb70 > >> /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 22] 0x00007f2b2263952e /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… > >> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 24] 0x00007f2b2260fb70 > >> /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 30] 0x00007f2b2263952e /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… > >> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 32] 0x00007f2b225ecbf0 > >> /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> inCallFcnWithTrap+00000086 > >> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> > >> This error was detected while a MEX-file was running. If the MEX-file > >> is not an official MathWorks function, please examine its source code > >> for errors. Please consult the External Interfaces Guide for information > >> on debugging MEX-files. > >> > >> If this problem is reproducible, please submit a Service Request via: > >> > http://secure-web.cisco.com/1lsmxJ1l6wT0WmnW3q7zuS6JngCO6upWHYdXR6E3TNhC0oD… > >> > >> A technical support engineer might contact you with further information. > >> > >> Any insight or help you can provide is greatly appreciated. > >> *Daniel Callow* > >> *PhD Student, Neuroscience and Cognitive Science* > >> Exercise for Brain Health Lab > >> University of Maryland, College Park > >> dcallow(a)umd.edu <dcallow(a)gmail.com> > >> 443-254-6298 > >>

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PhD position: Engineer with focus on neuroimaging and electrophysiology (Prof. Sergiu Groppa, Mainz, Germany)
by Gonzalez-Escamilla , Gabriel 07 Jun '21

07 Jun '21

External Email - Use Caution Summary The group of “Movement Disorders, Neurostimulation and Neuroimaging“at lead by Prof. Sergiu Groppa (http://secure-web.cisco.com/1tr-tFZBabpdpNrk71yEbb8w2Ivj1W1_4BhAobu3hxyuGPb…) is seeking a highly motivated scientist (PhD position). The successful candidate will be involved in the conduct of the study and the analysis and publication of newly acquired and already existing datasets. Be part of a very diverse team in an inspiring and socially relevant environment, which is also highly dedicated to supervision, teaching, and personal support. A further advantage will be to be part working on an international and interdisciplinary environment at the Department of Neurology, part of the Focus Program Translational Neurosciences (http://secure-web.cisco.com/1llcPlfajmjH7BjRkb-JU9qDHiMnP9IOG_uP389OixL38A4…) and Neuroimaging Centre (http://secure-web.cisco.com/1T6W87YYlSbWhZcXicP8zK5VUB4fcMz0VprkkSaV0oTtWli…) in Mainz. Expected close collaborations with national and international partners. Planned activities Develop and apply advanced multi-modal neuroimaging analysis strategies tailored to patients with movement disorders (e.g., Parkinson’s disease), including 1. Functional MRI; 2. Diffusion MRI; 3. Structural MRI; and possibly 4. Electroencephalography; and 5. Electromyography. Qualifications * Master’s degree (or equivalent) in basic life sciences, neuroscience, biomedical engineering or similar disciplines. * Proficiency in English. * Experience with the brain imaging software packages (e.g., Freesurfer, FSL, mrtrix, SPM, etc.). * Experience in pipeline development with BASH scripts, MATLAB, and python. Possibly in high-performance computer clusters (HPC). * Experience with electrophysiology and the analysis of brain signals is advantageous, but not essential. How to apply The position will be open until filled. Please submit your application (.doc, .docx or .pdf only) to Prof. Sergiu Groppa (segroppa(at)uni-mainz.de) the following: * A covering letter outlining your suitability for the role and a statement of research interests; * Short (max. 4 pages) curriculum vitae which should include: * Full name, address, telephone number and email address; * Details of education, professional training and qualifications; * Employment history, including current and professional or industry experience; * Research interests and list of publications. * Master’s degree certificate * The names and e-mail addresses of two referees * A proof of English proficiency. SIncerely yours, --- Dr. rer. nat. Gabriel Gonzalez-Escamilla Movement Disorders and Neurostimulation, Biomedical statistics and multimodal signal processing unit, Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine-Main-Neuronetwork (rmn2), Johannes-Gutenberg-University, Langenbeckstr. 1 55131 Mainz, Germany Tel: +49 6131 17 7865 Email: ggonzale(a)uni-mainz.de<mailto:ggonzale@uni-mainz.de> Webpage: http://secure-web.cisco.com/11PkRGNy-TQZpRnCeTwsDXXbaXO_nJcnGZufh-lotpYT7OP…<http://secure-web.cisco.com/1LKLCMr2JO0ElLwI08Y1IlE3cqCIk_J6fHK-mggdhDQ957l…> ü SAVE PAPER - THINK BEFORE YOU PRINT

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retinotopy with different phases
by Manenti, Giorgio 07 Jun '21

07 Jun '21

External Email - Use Caution Dear Experts, I am running my polar angle and eccentricity following the freesurfer retinotopy analysis. Saddly, i figured out that my eccentricity script has a shorter cycle compared to the polar angle (38sec vs 40sec pro cycle). I was wondering if it would be possible to save the collected data by “cutting/downsampling” the polar angle excluding the extra seconds pro cycle like using the time-point exclusion flag, or if it is possible to run the analysis over two different cycle durations ? Many thanks for your help! Giorgio

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error when running permutation analysis
by Star Xi 07 Jun '21

07 Jun '21

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MGH/Harvard: Postdoc in brainstem diffusion and PET imaging in aging/dementia position
by Jacobs, H (NP) 05 Jun '21

05 Jun '21

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work with Dr. Heidi Jacobs. The Jacobs lab is part of the Gordon Center for Medical Imaging at MGH and focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers and cognitive assessments. This postdoc will be involved in a new NIA-funded project working on new methods in PET and diffusion imaging to examine tau propagation in aging and Alzheimer’s disease. Our team and this project is embedded within the Harvard Aging Brain Study (HABS). Ideal start date is around July/August 2021. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and be able to work in a stimulating and inspiring environment. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is equipped with a large-scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference, OHBM), and manuscript preparation for publication in high impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should have a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, Medical Physics, Computer Science, Biomedical Engineering or related disciplines. Strong analytical, quantitative and programming skills as well as expertise in diffusion imaging are essential. Prior experience in PET is advantageous. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease dementia or aging would be beneficial. MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. [cid:image001.png@01D75A2F.104EC740]Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Assistant Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> Or go to: https://secure-web.cisco.com/1OvpD6SmTk_zFW5k8ELsjQ7xsiWYB3zS0hiR--mIJ0yDWj… , job nr 3153522

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Cerebellum Segementation
by A.R. Sekar 04 Jun '21

04 Jun '21

External Email - Use Caution Hello Experts! This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. It would be great if you could give me advice and any feedback about the pipeline. Thanks for your help! Regards, Akila

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nalysis of covariance between functional connectivity data (FS-FAST) and cortical thickness
by stdp82＠virgilio.it 04 Jun '21

04 Jun '21

External Email - Use Caution Hi, how can I perform vertex by vertex (surface) analysis of covariance between functional connectivity data (FS-FAST) and cortical thickness, regressing out the effect of groups? My mean concern is how buid the fsgd file. Stefano

2 1

A problem about Freesurfer
by 胡俊涛 04 Jun '21

04 Jun '21

External Email - Use Caution Can I use Freesurfer to process MRI image data of mice? Thank you!

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freesurfer-7.1.1-centos8.rpm :: problems
by Eric Deveaud 04 Jun '21

04 Jun '21

External Email - Use Caution Hello, I installed freesurfer-7.11 from centos8 rpm on stock docker centos8 image: there is some problems // misses with this installation 1) some scripts are python and uses /usr/bin/env python which is not available by default on centos8 currently freesurfer rpm specfile should have a dependency to python2, and associated python required modules, ie: dipy graph_tools holoviews plotly statsmodels pyyaml in that case, following files sheebang should be modified slicedelay dsh mcparams2reg rca-config2csh shebang should be /usr/bin/env python2 instead of /usr/bin/env python other solution will be to port those scripts to python3 and use fspython 2) some scripts are tclsh ones but no tclsh installed. eg unpackimadir2, unpacksdcmdir. fsgfget please add tcl rpm dependency to rpm specfile 3) tools depending on MRC matlab runtime segmentSubjectT2_autoEstimateAlveusML segmentSubjectT1_autoEstimateAlveusML segmentSubject segmentSubjectT1T2_autoEstimateAlveusML SegmentThalamicNuclei SegmentSubfieldsT1Longitudinal irepifitvol.glnx64 and fs_spmreg.glnxa64 are linked versus libmwmclmcrrt.so.8.3 which is not provided by mcr runtime R2014b but version 8.4 is. and by the way libncurses-devel is required as rpm dependency 4) some tools uses commands that are not available show_tal, tal_compare uses mri_show which is not avaialble 5) qdec tcl have invalid environement configuration Singularity> qdec Tcl_Init error: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 /usr/local/freesurfer/7.1.1-1/lib/tcl8.4 /usr/local/freesurfer/lib/tcl8.4 /usr/local/freesurfer/7.1.1-1/library /usr/local/freesurfer/library /usr/local/freesurfer/tcl8.4.6/library /usr/local/tcl8.4.6/library /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 you may want to add $FREESURFER_HOME/lib/tktools/tcl8.4 to TCL_LIBRARY regards Eric

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