Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Time course thalamic subregions
by stdp82＠virgilio.it 28 Aug '19

28 Aug '19

External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano

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An error during data processing
by Троицкий Антон Александрович 28 Aug '19

28 Aug '19

External Email - Use Caution Hello FreeSurfer Developers, I a beginner freesurfer user. It is my first patient that I try to process. The patient data was obtained on Philips MRI Achieva 3.0 T with dStream application. I performed /Applications/freesurfer/bin/recon-all -i /Users/anton.troitskii/Documents/FreeSurferData/Patients_input/2018-08-19/DICOM/IM_0001.dcm -subject Test1 -all The process started and an error occurred. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0 2) Platform: macOS Sierra 10.12.6 3) uname -a: Darwin mac-2ap023-2.fccho-moscow.ru<http://mac-2ap023-2.fccho-moscow.ru> 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached Best regards, Anton Troitskii.

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ERROR reading /<my data path>/fsaverage/label/lh.BA1_exvivo.label with recon-all.log
by liuxingze1993 28 Aug '19

28 Aug '19

External Email - Use Caution Hello，Dear FreeSurfer Developers, I’m a doctoral student from Xiangya 2nd Hospital of Central South University, and also a beginner to FreeSurfer. I'm attempting to follow the steps descripted on ‘Practice Working with Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own data, but I’ve met the same problem several times when I programing the command ‘recon-all -all -i 61492283 -s Sub219’: (**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack -src . -scanonly.log') SUBJECTS_DIR /media/dell/AA32E/Data_prac/219/20181211/19470000 (**PS: 19470000 is the folder where the T1 located) FREESURFER_HOME /usr/local/freesurfer Loading source label Invalid argument ERROR reading /media/dell/AA32E/Data_prac/219/20181211/19470000/fsaverage/label/lh.BA1_exvivo.label recon-all -s Sub219 exited with ERRORS at <local time here> I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such file here. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu14.04 LTS 3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank u for viewing, and I will be waiting here for your professional advice !

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Converting a binary overlay file to label
by Nillo, Ryan Michael R 28 Aug '19

28 Aug '19

External Email - Use Caution Hello FreeSurfer users/developers. I manually created a binary overlay file on the pial surface. I am interested in looking at regions outside of this overlay file, so I converted lh.cortex.label to a binary overlay file and took the difference between the two. I want to take this new file and create a label so that I can run mris_anatomical_stats on the new region. How might I do this? Sent from my iPhone

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Segmentation fail
by Giovana dos Santos Cover 28 Aug '19

28 Aug '19

External Email - Use Caution Dear Freesurfer experts, I am trying to segment the white and pial matter from my MR images but for some reason, the final segmentation always misses some brain areas. I attached here a nu and brainmask image with the segmentation as an example. The MR image I am using is a MEMPRAGE 0.5mm resolution acquisition from a 3T Siemens TrioTim scanner, possibly with a 64 coil channel. Can you please help me figure out how I could improve the segmentation? I am using the following command: recon-all -autorecon1 -autorecon2 -autorecon3 -s hires_test -hires -i high_res.nii On another note, the full recon-all command takes around four days to finish in an 8GB ram mem computer. I would appreciate if you happen to have any suggestions on how I could run it faster, if this is even possible. Thanks Gio.

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bug in freesurfer-dev (T2-specific parameters not passed to second call of mri_make_surfaces)
by Marco Aqil 28 Aug '19

28 Aug '19

External Email - Use Caution Hi, I would like to report a bug in freesurfer-dev. I have encountered this bug in a version downloaded on July 11th, 2019, and again in a version downloaded two days ago (August 20th). In short, it seems that parameters specified via an expert file relevant to T2-assisted pial segmentation, such as -T2_min, are not passed to the second call of mris_make_surfaces (the one actually using T2 data). In Freesurfer 6.0.0, this is not the case, and the T2_min parameter is indeed passed to the second call of mris_make_surfaces (although I note that in 6.0.0, when specifying -nsigma_below via the expert file, both the user-specified value and the standard value are passed to the second call of mris_make_surfaces). See below for more details on the specific freesurfer-dev behavior. Best, Marco Aqil Bug description: T2-specific parameters not passed to second call of mri_make_surfaces in freesurfer-dev Call: recon-all autorecon3? -subjid <subject id> -hires -T2pial -parallel -openmp 15 -expert <expert file path> Expert file content: mris_make_surfaces -T2_min 35 >From the recon-all log, the first call of mris_make_surfaces receives the -T2_min parameter: ---------------- #@# Make Pial Surf lh Mon Aug 19 13:43:02 CEST 2019 <scripts folder path> mris_make_surfaces -save-res -save-target -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs -T2_min 35 sub-006 lh ---------------- However, the second call of mris_make_surfaces, which relies on T2 data to refine the pial, does not receive the T2_min parameter, and looks as follows: --------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon Aug 19 14:02:23 CEST 2019 <other T2 pial steps> mris_make_surfaces -save-res -save-target -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-006 lh --------------- I observed the same behavior when specifying -nsigma_below via the expert file.

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Contrast of interaction between covariates in FSGD
by Zhi Li 28 Aug '19

28 Aug '19

External Email - Use Caution Dear Freesurfer experts, May I ask how to understand the contrast of interaction between covariates in the example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V? The interaction of group x age x weight is: [0 0 1 -1 0 0 0 0 0 0 1 -1] Why the interaction between group and weight should be put in the second row (what does each row mean in the F-contrast matrix)? If there are three levels in the factor one (three groups), I guess the interaction of group x age x weight should be: [0 0 0 1 -1 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 1 -1] Is this correct? If not how should I set this contrast? In addition, if I would like to know the interaction between age and weight without group, how should I set the contrast then? Looking forward to your kind suggestions. Thanks and best wishes, Lizhi

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freeview crash -- petsc error when opening volume
by TRISTAN J PAUTSCH 27 Aug '19

27 Aug '19

External Email - Use Caution Greetings all, I'll try to keep this succinct. I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview launches fine and stays open when launched alone, however attempting to open a volume (either through the GUI or directly via the CLI) causes a crash and the following error about 5-8 seconds after launching (brain images begin to populate, then crash): --- [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named xxxxxxx by xxxxxxx Tue Aug 20 13:44:15 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Segmentation fault (core dumped) --- I've seen a number of other posts on the mailing list about this, but all of them I could find either end abruptly without a solution or with an unanswered request for more info. Happy to provide any additional information or anything that may aid in the resolution of this issue. Thanks everyone, ~T

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Post-doctoral Fellowship in Human Perceptual Neuroscience at New York University
by Max Levinson 27 Aug '19

27 Aug '19

External Email - Use Caution The Perception and Brain Dynamics Laboratory (PI: Biyu J. He, Ph.D., http://www.med.nyu.edu/helab/) at New York University is currently recruiting for a post-doctoral fellow to conduct research to illuminate how prior knowledge shapes perception in the human brain. The position is funded by National Science Foundation (NSF) and is renewable yearly for up to 4 years. The planned research project involves a combination of cutting-edge human brain imaging technologies, including ultra-highfield (7 Tesla) fMRI and magnetoencephalography (MEG) in healthy subjects, electrocorticography (ECoG) in neurosurgical patients, along with psychophysics and neuropsychology. We are looking for a candidate with a passion for perceptual and cognitive neuroscience, independent critical thinking, strong analytical and quantitative skills, and good interpersonal skills. Experience with human brain imaging (such as fMRI, MEG, or ECoG) and excellent programming skills are highly desirable. Our laboratory is located on the medical campus of New York University in Manhattan, NY, and is affiliated with the Neuroscience Institute, Department of Neurology, and Department of Radiology. The position is expected to start in fall-winter of 2019, but early spring of 2020 is also possible. We provide competitive salary and benefits that adjust for cost of living in New York City. To apply, please send a CV, a cover letter, a statement of scientific and career goals, and names and contacts of three referees to Prof. Biyu Jade He (email: biyu.jade.he(a)gmail.com) with the subject line “post doctoral application 2019”. We strongly encourage interested candidates to apply as soon as possible, but no later than Oct 15.

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binary version of brainmask?
by Chris Adamson 26 Aug '19

26 Aug '19

External Email - Use Caution Freesurfer, Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz? Thank you, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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