Freesurfer

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applyMorph gives (10000 10000 10000) coordinates
by Peled, Noam 07 Feb '19

07 Feb '19

Hey all, I'm trying to morph patients' invasive electrodes into a template brain. I'm not sure why, but sometimes, the applyMorph gives me the (10000 10000 10000) coordinates for a subset of the electrodes, where the rest are ok. In the output, for those electrodes I can see it writes "not valid", but still gives reasonable coordinates and not (10000 10000 10000) For example: applyMorph --template /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz --transform /autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d point_list /autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt /autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt a Where in the output file you can see the (10000 10000 10000) coordinates. I attached the applyMorph output. btw, I'm using the Freesurfer dev version Thanks, Noam  LZ

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*** Call for PhD Applications ***
by Giada Lettieri 07 Feb '19

07 Feb '19

External Email - Use Caution *2019/20 PhD Programs at the IMT School for Advanced Studies LuccaDeadline for applications – April 23rd 2019, 12 pm CEST* Applications are now being accepted for the 2019/20 PhD Programs at the IMT School for Advanced Studies Lucca (*www.imtlucca.it <http://www.imtlucca.it>*), one of the six Schools of Excellence in Italy and one of the highest rated graduate schools in Europe according to the most recent U-Multirank survey. Highly motivated candidates from all disciplines are invited to apply for one of the 32 fully-funded scholarships within two doctoral Programs that integrate scientific competences of economics, engineering, computer science, neuroscience and behavioral psychology, physics, applied mathematics, statistics, history and sciences of cultural heritage. One of the four field-specific tracks is *Cognitive, Computational and Social Neurosciences*, which is under the “Cognitive and Cultural Systems” PhD Program. This research-based, multidisciplinary track focuses on cognitive, computational and social neurosciences, and integrates basic neuroscience methods, including molecular biology and genetics, with traditional experimental psychology and cognitive neuroscience. Students will attend multiple courses, including fundamentals in cognitive psychology, behavioral and social neuroscience, neuropsychology, psychophysiology, neural basis of perception, neural basis of consciousness, philosophy of science, critical thinking, structural and functional neuroimaging, and basic/advanced methods for data analysis. In particular, the CCSN track is designed to train researchers who will contribute to knowledge in (multi)disciplinary areas such as *multisensory perception, supramodality and cross-modality; sleep and consciousness; action recognition and motor control;neuroplasticity and learning; organization of semantic concepts; neurolinguistics; social and antisocial behavior; decision-makingprocesses in economics and financial environments; aesthetic perception*. During their doctoral studies, students are encouraged to carry out their research with the School’s Research Units. For conducting their experimental activities, students can rely on both in-house and outsourcing facilities. The IMT School has a Cyberphysics Lab equipped for behavioral, psychophysics and EEG (64 and 256 channels amplifiers) research. Functional and structural MRI studies can be conducted at any of the partner MRI scanner sites in Pisa (1.5 and 7 Tesla) and Massa (3 Tesla); EEG and fMRI acquisition could be combined. Courses are led by world-renowned researchers and provide students with all the theoretical skills and advanced tools required for rigorously tackling a multitude of analysis, design and management problems within the broad framework of systems analysis in economic, social, scientific, technological and cultural domains. Specialized faculty and staff create a network that provides key guidance and support throughout the PhD Program. Working closely with faculty, both in the classroom and in the development of research, students reach the highest levels of scholarly achievement. IMT School PhD graduates will be able to use the skills they acquired during their studies to recognize and resolve complex problems, to choose the most appropriate method or instrument to utilize when approaching these problems, even in disciplines outside of their primary field of research. All students are based in the recently restored San Francesco complex, a fully integrated Campus in the historical center of the beautiful Tuscan city of Lucca. The Campus includes renewed residential facilities, an on-site canteen, study and living rooms, a state-of-the-art library and outdoor recreational spaces, which foster a unique cultural, professional and social environment for our doctoral program. Eligible students, in addition to *free room and board*, will also receive a research scholarship which amounts to approximately *€15,300/year*. The scholarships are fully-funded for up to four years, with a possibility of graduating after the third year. The PhD Programs at the IMT School attracts students from around the world, providing a truly international environment. English is the official language of the School. Moreover, all students will have the opportunity to spend periods abroad at research institutes, laboratories or universities, both within the Erasmus+ framework and through ad hoc mobility agreements. Most IMT School PhD Graduates have reached prominent roles in academics, governmental institutions, public and private companies or professions across the globe. To find out more about the School, the admission requirements and how to apply, please see *https://www.imtlucca.it/en/programma-dottorato/overview <https://www.imtlucca.it/en/programma-dottorato/overview>* *Deadline for applications – April 23rd 2019, 12 pm CEST* -- *Giada Lettieri* PhD student Cognitive, Computational and Social Neuroscience *MOlecular MInd LABoratory <http://momilab.imtlucca.it/>* IMT - School for advanced studies Piazza S. Francesco 19, 55100, Lucca, Italy Mob: +39 389 0461034 <https://scholar.google.it/citations?user=ysqHTIwAAAAJ&hl=en>

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Announcing HCP Course 2019, July 8-12 in Portland, OR!
by Jennifer Elam 06 Feb '19

06 Feb '19

External Email - Use Caution We are pleased to announce the <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…>2019 HCP Course: "Exploring the Human Connectome" <https://store.humanconnectome.org/courses/2019/exploring-the-human-connecto…>, to be held July 8 – 12, 2019 at the University Place Hotel and Conference Center <https://www.uplacehotel.com/> at Portland State University in Portland, Oregon, USA. This 5-day intensive course will provide training in acquisition, processing, analysis and visualization of whole brain imaging and behavioral data using methods and tools developed by the WU-Minn-Oxford Human Connectome Project (HCP) consortium. FreeSurfer is a major part of the HCP structural processing pipeline, has been critical to the processing of the HCP Young Adult project's over 1100 released high quality imaging datasets, and continues to be used in the processing of forthcoming Lifespan HCP data. The course is designed for those interested in: - using HCP-style data currently available from the young adult HCP and HCP Lifespan (Development and Aging) projects - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data (including legacy data) using HCP pipelines and methods - using Connectome Workbench <https://www.humanconnectome.org/software/connectome-workbench.html> tools and sharing data using the BALSA <https://balsa.wustl.edu/> imaging database - learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data - positioning yourself to capitalize on HCP-style data forthcoming from large-scale projects currently collecting data (e.g., Lifespan HCP development and aging longitudinal data and Connectomes Related to Human Disease projects) - learning how to obtain data from the NIMH Data Archive (NDA) and setup processing in an Amazon Web Services (AWS) environment Participants will learn how to acquire, analyze, visualize, and interpret data from four major MR modalities (structural MR, resting-state fMRI, diffusion imaging, task-evoked fMRI) plus magnetoencephalography (MEG) and extensive behavioral data. Lectures and labs will provide grounding in neurobiological as well as methodological issues involved in interpreting multimodal data, and will span the range from single-voxel/vertex to brain network analysis approaches. The course is open to students, postdocs, faculty, non-profit and industry participants. The course is aimed at both new and current users of HCP data, methods, and tools, and will cover both basic and advanced topics. Prior experience in human neuroimaging or in computational analysis of brain networks is desirable, preferably including some familiarity with FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki> and Freesurfer <https://surfer.nmr.mgh.harvard.edu/> software. For more info and to register visit the <https://store.humanconnectome.org/courses/2017/exploring-the-human-connecto…>HCP Course 2019 website <http://store.humanconnectome.org/courses/2019%20%20%20%20%20%20%20%20%20/ex…> . If you have any questions, please contact us at: hcpcourse(a)humanconnectome.org We look forward to seeing you in Portland! Best, 2019 HCP Course Organizers -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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Re: [Freesurfer] fs on GPU? Segmentation fault error!
by fsbuild 06 Feb '19

06 Feb '19

External Email - Use Caution Hello Vin, The latest/dev branch of freesurfer builds on Ubuntu 16 without cuda, but I have not tried compiling it for cuda on 16.04.  My understanding is that cuda builds are not officially supported.   I would first make sure that everything builds and runs w/o cuda. I would try not to manually copy/change the installation of cuda libraries,. i.e., if you need a specific version then I would install that version (rather than use the cp command to clobber version 5 with version 8, which may not be entirely backwards compatible and so could also cause run time errors).   If you know what you have for graphics/GPU hardware, then you should be able to lookup online what versions of cuda it supports, e.g., for Nividia hardware, https://developer.nvidia.com/cuda-gpus You can also get a currently supported cuda version to install for Ubuntu 16.04 from this link, https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch… - R. vin rasa February 6, 2019 at 12:17         External Email - Use Caution        Freesurfer Wizards, Any thoughts on this? Thanks in advance ## I renamed: /usr/local/cuda-8.0/lib64$ sudo cp libcudart.so.8.0 libcudart.so.5.0 in the next step: recon-all -i $sub_dir/$i/"$i".nii -all -sd $output_dir $i -use-gpu.. Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 9.20 Runtime : 8.0 Acquiring CUDA device Using default device CUDA device: TITAN Xp Segmentation fault Linux Dond-12 1.25.0-13-generic #36~16.04.1-Ubuntu SMP Wed Aug 15 17:21:05 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2 exited with ERRORS at Mi 6. Feb 18:14:50 CET 2019 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer TRACULA with FAD
by Alex Dufford 04 Feb '19

04 Feb '19

External Email - Use Caution Hello Freesurfer experts, I am interested in running an along the tract analysis with the outputs from tracula. I am interested in using https://www.nitrc.org/projects/fadttster/ to do so. I was wondering where to find the 'arc length' for the fibers and if there is anything else I should consider in try to analyze the fibers with FADttster. Thank you! Best, Alex -- Alexander Dufford M.A. Developmental Psychology Graduate Student Family and Child Neuroscience Laboratory University of Denver Office Phone: 303-871-3096 http://www.du.edu/ahss/psychology/fcnlab/

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(no subject)
by Jordan Fowler 04 Feb '19

04 Feb '19

External Email - Use Caution Here is the message displayed: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Jordans-MacBook-Air-2:~ jordanfowler$ > cp $FREESURFER_HOME/subjects/sample-001.mgz . -bash: /Applications/freesurfer/subjects/sample-001.mgz: Permission denied

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free surfer install issues
by Jordan Fowler 04 Feb '19

04 Feb '19

External Email - Use Caution I have recently installed the free surfer software and when testing that it is installed correctly using the examples listed on the website I get a permission denied message. How can I go about fixing this? Attached is the terminal output from trying to run the first example. Thank you, Jordan Fowler

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gray matter volume of the entorhinal cortex
by Laboratorio de Neurociencia Funcional 04 Feb '19

04 Feb '19

External Email - Use Caution Dear Freesurfers, gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume measure of the EC would be more precise? I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how probabilistic maps of EC were built based on ex vivo MRI contrast? Thank you in advance. Best, Jose L. Cantero

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Re: [Freesurfer] Surface to Volume conversion
by Bunting, Emma 04 Feb '19

04 Feb '19

External Email - Use Caution Hi Bruce, I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for participant 124 and got these outputs... For sig.mgh: Volume information for sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 For sig.lh.nii.gz: Volume information for sig.lh.nii.gz type: nii dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -68267.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -2.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 13653.5000 0.0000 0.0000 1.0000 -3.0000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 13653.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 3.0000 -0.0000 -0.0000 -0.0000 1.0000 Please let me know if you need any other information in order to help with our problem, Best wishes, Emma ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 25 January 2019 17:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 179, Issue 41 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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: Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS (Hoopes, Andrew) 2. Re: FSFAST poor registration (Greve, Douglas N.,Ph.D.) 3. Re: Surface to volume conversion (Bruce Fischl) 4. Re: Functional connectivty walkthrough step 8 error (Greve, Douglas N.,Ph.D.) 5. Re: cortical thickness calculation based on hammersmith segmentation (Greve, Douglas N.,Ph.D.) 6. Re: FSFAST poor registration (Keri Woods) 7. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi) 8. Re: Orientation by direction cosines (Greve, Douglas N.,Ph.D.) 9. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi) 10. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi) 11. Re: Functional connectivty walkthrough step 8 error (Greve, Douglas N.,Ph.D.) ---------------------------------------------------------------------- Message: 1 Date: Fri, 25 Jan 2019 16:24:14 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2A2251F1-6E66-4125-9A96-76700348245B(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" I believe this python2 issue has been fixed in the dev version found here https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mr… best, Andrew ?On 1/25/19, 10:08 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Falk thanks for catching the typo. I fixed it - nice to have an easy thing to fix for a change :) Bruce On Fri, 25 Jan 2019, falk.luesebrink(a)med.ovgu.de wrote: > > External Email - Use Caution > > Dear Juergen, > > > > Thanks for your quick reply! Actually the spelling error is in the error message. Taken from > http://martinos.org/~mreuter/long/long_mris_slopes > > > > # extensive error checks > > # if options.fsgd is None and > > if options.qdec is None: > > # print 'ERROR: Specify --fsgd or --qedc' > > parser.print_help() > > print '\nERROR: Specify --qedc (and other required arguments)\n' > > sys.exit(1) > > > > # if options.fsgd is not None and options.qdec is not None: > > # print 'ERROR: Specify either --fsgd or --qedc, not both' > > # sys.exit(1) > > > > At least Martin is consistent with his typo. :D > > > > Best, > > Falk > > > > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von Juergen Haenggi > Gesendet: Freitag, 25. Januar 2019 10:35 > An: Freesurfer Mailinglist <freesurfer(a)nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS > > > > External Email - Use Caution > > Dear Falk > > > > I have no idea, but recognised that the error refers to --qedc and not to --qdec. > > maybe there is a spelling error somewhere that is related to your problem. > > > > HTH > > Cheers > > J?rgen > > ----------------------------------------------------------------------------------------------------- > > University of Zurich > > Dr. J?rgen H?nggi, Ph.D. > > Department of Psychology > > Division Neuropsychology > > Binzmuehlestrasse 14, PO Box 25 > > 8050 Zurich, Switzerland > > > > 0041 44 635 73 97 (phone office) > > 0041 76 445 86 84 (phone mobile) > > 0041 44 635 74 09 (fax office) > > BIN 4.D.04 (office room number) > > > > j.haenggi(a)psychologie.uzh.ch (email) > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > http://www.juergenhaenggi.ch (private website) > > > > This email (and any attachment/s) contains confidential and/or privileged > > information. If you are not the intended recipient (or have received this > > email in error) please notify the sender immediately and destroy this > > email. Any unauthorised copying, disclosure or distribution of the > > material in this email is strictly forbidden. > > ----------------------------------------------------------------------------------------------------- > > > > > > > > On 25 Jan 2019, at 10:26, falk.luesebrink(a)med.ovgu.de wrote: > > > > External Email - Use Caution > > > > Dear all, > > > > Has anyone run the longitudinal pipeline successfully using the WSL? I?m running it with Ubuntu 18.04.1 LTS > and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. > > > > I?m trying to process my first longitudinal data set following the instructions of the tutorial as close as > possible. The data has been processed without issues and now I want to do the statistical analysis. When I > run: > > long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc > --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR > > > > I get the following error: > > File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448 > > print '\nERROR: Specify --qedc (and other required arguments)\n' > > ^ > > SyntaxError: invalid syntax > > > > I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any > arguments gives: > > File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119 > > print '\nERROR: Specify --qedc' > > ^ > > SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')? > > > > Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04? > > > > Best, > > Falk > > ............................................... > > > > <image001.gif> > > Universit?tsklinik f?r Neurologie > > > > Otto-von-Guericke-Universit?t Magdeburg > Medizinische Fakult?t > Leipziger Str. 44 > 39120 Magdeburg > > > > Telefon: +49-391-6117-512 > > falk.luesebrink(a)med.ovgu.de > http://www.kneu.ovgu.de/kneu.html > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ Message: 2 Date: Fri, 25 Jan 2019 16:34:14 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST poor registration To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <367a8e86-05d2-f02b-d19b-94401864c91d(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Yes, that file is the only thing linking the functional to the anatomical. It's too bad you messed up the files, but I'm relieved it was not my software:). On 1/25/19 5:09 AM, Keri Woods wrote: External Email - Use Caution Hi Douglas Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem subjects individually, and the registration worked well. So the problem is that the anatomical and functional images come from different subjects. But I've checked and the subjectname files are correct. That's the only thing linking the anatomical and functional images? Thanks very much, you've helped me a lot. Now I just have to go and see where I mixed up the files! Thanks again, Keri On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote: Can you tar up the anatomical and functional analyses and send them to me through our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2/ when it asks for an email of the recipient, use greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> On 1/23/19 5:57 AM, Keri Woods wrote: > > External Email - Use Caution > > I meant some are nearly perfect. > > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods(a)gmail.com<mailto:keri.woods@gmail.com> > <mailto:keri.woods@gmail.com<mailto:keri.woods@gmail.com>>> wrote: > > Hi Douglas > > Thanks for the response. > > No, some of the registrations are fine. Some are close, but not > perfect, while others are very bad. > > I've checked the subjectname file for some subjects with poor > registration (eg 20_101), and they are correct. > > Thanks, > Keri > > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. > <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote: > > Are you saying that all of them have bad registrations? Some > of them > (eg, 20_1, 20_10) look like they should be good. Others (eg, > 20_101) > look like they could be bad. For the bad ones, are you totally > sure that > the subjetname file has the correct name of the subject? > > On 1/21/19 3:19 AM, Keri Woods wrote: > > > > External Email - Use Caution > > > > Hi Douglas > > > > Thank you for your reply. > > > > I'm using > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a > > > > I am using whole brain data. The functional and structural > images were > > acquired in different sessions on the same day, I don't know > if that > > complicated things? Each subject has 2 runs of the same task. > > > > This is what I get after running the command in the format of > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold > -per-run -bbr-sum > > > > 20_1 013 0.5155 > > 20_1 014 0.5090 > > 20_10 013 0.5247 > > 20_10 014 0.5229 > > 20_100 038 0.8420 > > 20_100 040 0.8443 > > 20_101 008 0.9052 > > 20_101 010 0.9289 > > 20_102 058 0.6924 > > 20_102 059 0.6902 > > 20_103 045 0.9778 > > 20_103 046 0.9931 > > 20_104 010 0.9324 > > 20_104 012 0.9413 > > 20_105 013 0.8754 > > 20_105 014 0.8937 > > 20_106 047 0.4433 > > 20_106 048 0.4377 > > 20_107 008 0.9178 > > 20_107 010 0.9238 > > 20_11 013 0.7631 > > 20_11 014 0.7615 > > 20_110 048 0.7687 > > 20_110 049 0.7549 > > 20_112 013 0.8821 > > 20_112 014 0.9161 > > 20_113 052 0.7689 > > 20_113 053 0.7757 > > 20_116 046 1.0072 > > 20_116 047 1.0256 > > 20_117 008 0.7742 > > 20_117 010 0.7826 > > 20_119 013 0.7929 > > 20_119 014 0.7854 > > 20_120 048 0.5090 > > 20_120 049 0.4973 > > 20_126 047 0.8285 > > 20_126 048 0.8281 > > 20_128 046 0.9580 > > 20_128 047 0.9314 > > 20_130 047 0.9439 > > 20_130 048 0.9425 > > 20_132 047 0.8550 > > 20_132 048 0.8558 > > 20_134_1 013 0.5716 > > 20_134_1 015 0.5744 > > 20_135 011 0.8357 > > 20_135 012 0.8401 > > 20_136 044 0.9995 > > 20_136 045 0.9604 > > 20_137 047 0.7922 > > 20_137 048 0.7990 > > 20_142 047 0.5282 > > 20_142 048 0.5278 > > 20_144 013 0.8755 > > 20_144 014 0.8838 > > 20_146 047 0.7997 > > 20_146 048 0.7895 > > 20_149 049 0.9251 > > 20_149 050 0.9408 > > 20_151 048 0.5905 > > 20_151 049 0.5519 > > 20_152 048 0.9024 > > 20_152 049 0.9021 > > 20_155 048 0.5285 > > 20_155 049 0.5324 > > 20_156 048 0.8883 > > 20_156 049 0.9267 > > 20_158 048 0.5404 > > 20_158 049 0.5297 > > 20_159 048 0.8021 > > 20_160 013 0.5002 > > 20_160 014 0.4942 > > 20_162 047 0.5401 > > 20_162 048 0.5401 > > 20_164 047 0.8944 > > 20_164 048 0.8940 > > 20_165 047 0.9163 > > 20_165 048 0.9077 > > 20_166 045 0.8787 > > 20_166 046 0.8848 > > 20_167 050 0.8428 > > 20_167 051 0.8442 > > 20_169 049 0.9407 > > 20_169 050 0.9462 > > 20_170 047 0.8921 > > 20_170 048 0.9113 > > 20_171 013 0.9060 > > 20_171 014 0.9060 > > 20_173 048 0.9193 > > 20_173 049 0.9141 > > 20_177 048 0.8695 > > 20_177 049 0.8600 > > 20_178 048 1.0327 > > 20_178 049 0.8979 > > 20_180 045 0.7999 > > 20_180 046 0.8002 > > 20_182 047 0.9135 > > 20_182 048 0.9130 > > 20_184 048 0.9842 > > 20_184 049 0.9960 > > 20_185 046 0.9640 > > 20_185 047 0.9514 > > 20_187 048 0.8134 > > 20_187 049 0.8082 > > 20_189 047 1.0063 > > 20_189 048 0.9701 > > 20_19 013 0.8485 > > 20_19 014 0.8534 > > 20_190 047 0.9279 > > 20_190 048 0.9169 > > 20_191 046 0.9586 > > 20_191 047 0.9751 > > 20_192 049 0.8544 > > 20_193 013 0.9084 > > 20_193 014 0.9110 > > 20_194 047 0.9220 > > 20_194 048 0.9166 > > 20_195 048 0.9552 > > 20_195 049 0.9508 > > 20_196 047 0.9098 > > 20_196 048 0.9011 > > 20_199 048 0.8569 > > 20_199 049 0.8567 > > 20_20 013 0.8750 > > 20_20 014 0.8749 > > 20_201 048 0.8864 > > 20_201 049 1.0040 > > 20_202 048 0.8542 > > 20_202 049 0.8516 > > 20_203 048 1.0267 > > 20_203 049 1.0060 > > 20_204 048 0.8513 > > 20_204 049 0.8588 > > 20_208 014 0.9130 > > 20_208 015 0.9329 > > 20_209 047 1.0020 > > 20_209 048 1.0120 > > 20_21 027 0.9747 > > 20_21 028 1.0081 > > 20_210 048 0.8607 > > 20_210 049 0.8564 > > 20_220 047 0.8888 > > 20_220 048 0.8903 > > 20_222 047 0.9998 > > 20_222 048 0.8597 > > 20_224 013 0.8122 > > 20_224 014 0.8107 > > 20_226 013 0.7855 > > 20_226 014 0.7845 > > 20_227 013 0.9372 > > 20_227 014 0.9818 > > 20_231 047 0.8355 > > 20_231 048 0.8506 > > 20_232 048 0.9730 > > 20_232 049 0.9591 > > 20_234 048 0.9357 > > 20_234 049 0.9429 > > 20_235 048 0.7528 > > 20_235 049 0.7483 > > 20_236 047 0.8997 > > 20_236 048 0.8922 > > 20_239 049 0.8920 > > 20_239 050 0.8817 > > 20_24 013 0.8197 > > 20_24 014 0.8280 > > 20_240 047 0.9109 > > 20_240 048 0.9231 > > 20_243 013 0.8227 > > 20_243 014 0.8333 > > 20_245 045 0.8620 > > 20_245 046 0.8635 > > 20_246 047 0.8236 > > 20_246 048 0.8269 > > 20_248 053 0.6015 > > 20_248 054 0.6091 > > 20_25 013 0.8676 > > 20_25 014 0.8658 > > 20_250 048 0.9124 > > 20_250 050 0.9090 > > 20_251 048 0.9061 > > 20_251 049 0.9078 > > 20_277 008 0.7923 > > 20_277 010 0.7970 > > 20_278 048 0.4834 > > 20_278 049 0.4845 > > 20_279 008 0.4363 > > 20_279 010 0.4370 > > 20_281 013 0.8672 > > 20_281 014 0.8647 > > 20_282 043 0.8884 > > 20_282 044 0.8886 > > 20_284 052 0.9152 > > 20_284 053 0.9118 > > 20_285 047 0.9546 > > 20_285 048 0.9517 > > 20_286 008 0.9607 > > 20_286 010 0.9596 > > 20_287 055 0.8976 > > 20_287 056 0.8756 > > 20_288 047 1.0127 > > 20_288 048 1.0307 > > 20_290 048 1.0089 > > 20_290 049 1.0391 > > 20_293 052 0.7792 > > 20_293 053 0.7772 > > 20_3 017 0.8530 > > 20_3 018 0.8501 > > 20_40 013 0.9392 > > 20_40 014 0.9787 > > 20_41 013 0.9562 > > 20_41 014 0.9547 > > 20_44 013 0.8725 > > 20_44 014 0.8872 > > 20_51 013 0.9420 > > 20_51 014 0.9417 > > 20_55 013 0.9796 > > 20_55 014 0.9837 > > 20_58 013 0.9677 > > 20_58 014 0.9506 > > 20_59 013 0.9180 > > 20_59 014 0.9157 > > 20_69 013 0.9265 > > 20_69 014 0.9283 > > 20_74 014 0.9476 > > 20_74 015 0.9201 > > 20_78 012 0.9822 > > 20_78 013 0.9501 > > 20_81 013 0.8664 > > 20_81 014 0.8693 > > 20_84 013 0.8827 > > 20_84 014 0.9196 > > 20_86 016 0.9138 > > 20_86 017 0.9152 > > 20_88 039 0.9905 > > 20_88 041 1.0168 > > 20_90 049 0.8263 > > 20_90 050 1.0208 > > 20_95 008 0.8892 > > 20_95 010 0.9359 > > 20_96 013 0.9191 > > 20_96 014 0.9326 > > 20_97 008 0.9569 > > 20_97 010 0.9731 > > 20_98 008 0.9317 > > 20_98 012 0.9409 > > 20_PHRU 047 0.7797 > > 20_PHRU 048 0.7894 > > > > So the registration is really poor. I've visually checked the > > registration for many of the subjects, and the functional > data isn't > > left-right reversed, I've also checked some of the > subjectname files > > (which I created by running a script) and they are correct. > > > > I'm new to Freesurfer, so maybe I've made a mistake > somewhere? I'm > > been following these instructions: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial > > > > Thanks, > > Keri > > > > > > On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D. > > <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>>> wrote: > > > > What version of FS are you using? version 6 initializes with > > mri_coreg (the FS equivalent of spm_coreg). On > whole-brain data, > > I've found this to be very robust. Is your data whole-brain? > > > > On 1/18/19 5:10 AM, Keri Woods wrote: > >> > >> External Email - Use Caution > >> > >> Hi > >> > >> I have a problem very similar to this one: > >> > >> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html > >> > >> I've tried the suggestions given there, but it didn't > fix my problem. > >> > >> I'm running the FSFAST preproc-sess stream and the > quality of the > >> registration is very poor for most of the subjects. > >> > >> I've tried initializing the registration differently, using > >> bbregister with --init-fsl, --init-spm and init-header, > which > >> didn't improve the results at all. > >> > >> I've also tried register-sess with --init-fsl, > --init-spm and > >> init-header, as well as spmregister-sess and > fslregister-sess. > >> > >> Is there anything else I could try? > >> > >> Using the SPM GUI, the registration was fine, so I > thought that > >> spmregister-sess would have been an improvement, but it > wasn't. > >> Is there anyway I can import the registration obtained > using the > >> SPM GUI? > >> > >> Thanks for your help. > >> > >> Thanks, > >> Keri > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
by Yi Leng Fung 02 Feb '19

02 Feb '19

External Email - Use Caution Dear FreeSurfer Developers, I ran -recon-all -all on my subjects with the aim of examining the gray volumes of the ex vivo entorhinal and perirhinal cortex. Prior to extracting the gray volume numbers of the entorhinal and perirhinal cortex from ?h.BA_exvivo.thresh.stats file, I was examining the entorhinal and perirhinal cortex on the ?h.BA.thresh.annot on Freeview. However, I noted that their locations on the annot file did not correspond to the locations indicated by ?h.entorhinal.thresh.label and ?h.perirhinal.thresh.label. I have also loaded the annot files and label files from the fully recon-ed subject named "bert" on Freeview and observed the same mismatch in the labeling. I am curious why this might be the case. For your reference, I have uploaded a few screenshots from Freeview, on "bert", to demonstrate the label names in the annot file, both with and without the outline of the label files. I have searched the archive and have not been able to find any similar queries on this, hence it would be of tremendous help if someone could clarify this observation. If it is of interest, I am running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu 16.04. Thank you for your assistance and I look forward to hearing from you. Best regards, *Yi-Leng*

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