Freesurfer

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30132 discussions

fsfast
by John Anderson 02 Aug '17

02 Aug '17

Dear Dr Greve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. I want to study the difference in functional connectivity between two groups My questions are regarding motion evaluation and the contrasts. 1. The attached figure is an output of "plot-twf-sess". Given the plotted data can we say that including run 003 is more reliable that all the other runs? 2. In the attached figure the command "plot-twf-sess" provides the maximum and minimum motion for every run on Y axes. I am wondering if there is any way to create a cutoff value of motion parameters for all the runs in the study were data can be included/excluded depending on lower/upper than this cutoff? 3. I used the following commands to study the differnc ein functional connectivity between two groups (each group has one run): ## preprocessing preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm -fsd bold -per-run -init-spm ### First-Level (Group) Analysis mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run #####Analyze First Level selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok Now for the next step I need to concatenate the sessions using isxconcat but this command needs a contrast which I didn't create it in the previous step. Given that I am looking for a differnce in the functional connectivity between two groups how can I create the contrast for this anlaysis. Thank you for any help and feedback!! John

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FreeSurfer is now available on OpenNeuro.org
by Chris Gorgolewski 02 Aug '17

02 Aug '17

Dear all, FreeSurfer BIDS App is now available on the OpenNeuro.org platform. This means that you can run recon-all on your datasets (with longitudinal pipeline and study specific template estimation) in the cloud for free (see example results here <https://openneuro.org/datasets/ds000108/versions/00001?app=FreeSurfer&versi…> ). You can learn more about OpenNeuro.org in the FAQ <https://openneuro.org/faq> and about the details of the FreeSurfer BIDS App here <https://github.com/BIDS-Apps/freesurfer>. Let us know if you have any questions! Best, The OpenNeuro Team PS If you are developing a neuroimaging pipeline and would like to host it on OpenNeuro.org please get in touch. We a non-profit project dedicated to enabling access to cutting edge neuroimaging methods and incentivizing data sharing.

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FSFAST (plot-twf-sess)
by John Anderson 02 Aug '17

02 Aug '17

Dear Dr Greeve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. My questions is regarding motion evaluation. The attached figure is an output of "plot-twf-sess". 1. Given the plotted data can we say that including run 003 is more reliable that all the other runs? 2. In the attached figure the command "plot-twf-sess" provide the maximum and minimum motion for every run on Y axes. I am wondering if there is any way to create a cutoff value of motion parameters for all the runs in the study were data can be included/excluded depending on lower/upper than this cutoff? Thank you for help John

2 1

Error: trac-all -prep "Segmentation fault (core dumped)"
by Walter Hugo Lopez Pinaya 02 Aug '17

02 Aug '17

Hello FreeSurfer Developers, I am attempting to compute the tracula preprocessing directive (-prep), but for all my subjects I get the following error when it computes the pathway priors from atlas to T1. ... WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels INFO: Length of center streamline is 9 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 1 INFO: Minimum allowable curvature at a dominant point is 0.070643 INFO: Points where local peeks in curvature occur are 121 129 57 (curv = 0.0819549) INFO: Intermediate dominant points are 123 130 49 123 130 51 123 129 54 122 129 56 120 130 58 *Segmentation fault (core dumped) * Linux hardleste 4.8.0-58-generic #63~16.04.1-Ubuntu SMP Mon Jun 26 18:08:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Qui Jul 27 21:23:25 BRT 2017 I have searched the list and no similar errors with reply have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the trac-all.log and trac-all.error in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.2 LTS xenial 3) trac-all.log and trac-all.error: see attached trac-all.error <https://drive.google.com/file/d/0Bz-56qlsQ1xDbjEzZ3NkUG1XVlk/view?usp=drive…> trac-all.log <https://drive.google.com/file/d/0Bz-56qlsQ1xDMk1FUHI2QlZkMGc/view?usp=drive…>

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using -make all with base
by Emily Grossnickle Peterson 02 Aug '17

02 Aug '17

Hello all, I made edits to the brainmask and wm of a base image (in the longitudinal stream) and am getting stuck when trying to re-process recon-all. Specifically, I can't seem to get the -make flag to work. I think it is probably either a silly error on my part or perhaps -make isn't designed for base edits? The command and error output are below. Thanks in advance, Emily *This is the command I ran on an HPC:* recon-all -base template_${SGE_TASK_ID} -tp T1_$SGE_TASK_ID -tp T2_$SGE_TASK_ID -make all *This is the error message:* Running on compute-0-0.local Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rm: cannot remove `/share/aeg58/Freesurfer/4047_both/template_4047/scripts/patchdir.txt': Permission denied cp: cannot create regular file `/share/aeg58/Freesurfer/4047_both/template_4047/scripts/lastcall.build-stamp.txt': Permission denied Subject 'template_4047': make all recon-all -s /share/aeg58/Freesurfer/4047_both/template_4047 -nuintensitycor ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base): template_4047 If you are trying to re-run a -base template you need to pass the -base and all -tp flags: \' -base <templateid> -tp <tpNid> ... -all \' (Instead of -all you can pass other flags, such as -autorecon2 -autorecon3 to run only parts.) make: *** [/share/aeg58/Freesurfer/4047_both/template_4047/mri/nu.mgz] Error 1

1 0

output with input matrix size and referential
by pierre deman 02 Aug '17

02 Aug '17

Hello, I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation. what is the best way to do it ? Cheers, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94

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white surface contour discontinued in 2D display in freeView
by Antonin Skoch 02 Aug '17

02 Aug '17

Dear experts, In one subject I found discontinued white surface contour in 2D display in freeView. See the screenshot. I have also uploaded the subject as discontinued_white_surf dir to your server so that you can take look and diagnose. RAS coordinates: -19.52,37.81,22.53. The discontinuity is only present in coronal view. Looking at the data in 3D display, I see nothing unusual except that the density of the vertices in that region is very low. Is it only an issue with freeView display? Regards, Antonin Skoch

1 0

Re: [Freesurfer] Brain editing for TRACULA?
by Yendiki, Anastasia 01 Aug '17

01 Aug '17

Hi Yuwen - TRACULA is pretty forgiving in terms of imperfections in the recon-all output. TRACULA uses only the aparc+aseg, after mapping it into the subject¹s diffusion space, which is typically lower-res than the structural. Also, TRACULA only uses the relative positions of white matter voxels to their neighboring aparc+aseg structures. So small errors in the boundaries of these structures will not make a difference for TRACULA. Of course, if there¹s a more catastrophic error, like a whole lobe missing from the aparc+aseg because of a brain mask error, that¹s going to affect TRACULA. a.y On 7/29/17, 1:31 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Yuwen Hung" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of yuwenh(a)mit.edu> wrote: >Dear DTI Expert: >I wonder I may get help with this quick question - Is the brain editing >necessary (or critical) for TRACULA processing? > >Thank you! >Yuwen > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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longitudinal TRACULA
by Lars M. Rimol 01 Aug '17

01 Aug '17

Hi, I've run cross-sectional TRACULA on one subject, three different timepoints. Now I'm trying to run a longitudinal analysis on the same subject's 3 timepoints. My understanding was that for TRACULA, unlike for morphometry, I don't need to first run cross sectional before longitudinal, the only requirement is that I have a longitudinal dmrirc file that specifies the timepoints with their corresponding files. It crashed with these error messages: #@# Inter-subject registration (base template) lø. 29. juli 14:25:45 +0200 2017 cp /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_base/dmri/xfms cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat': No such file or directory Linux compute-16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any idea what went wrong here? Thank you! Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's University Hospital 7006 Trondheim Norway

2 1

Postdoctoral Fellowship at Harvard Medical School
by Baran, Bengi 01 Aug '17

01 Aug '17

Dear members, Please feel free to distribute the job ad below as you see fit. Best, Bengi Baran, Ph.D. Instructor in Psychiatry, Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging 149 13th Street, Room 2626 Charlestown Navy Yard Charlestown, MA 02129 email: bbaran(a)mgh.harvard.edu<mailto:bbaran@mgh.harvard.edu> phone: 617-643-7964 fax: 617-726-4078 Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the Psychiatric Neuroimaging Division of the Psychiatry Department at Massachusetts General Hospital, Charlestown, MA and Harvard Medical School Position Description: Clinical/Cognitive Neuroscience Research Project: Multimodal neuroimaging studies of sleep and memory PI: Dara S. Manoach, Ph.D. The position will involve investigating the role of sleep in memory consolidation, how these processes go awry in schizophrenia and autism, and the effects of pharmacological and other interventions. Our work has linked cognitive deficits to specific heritable mechanisms (sleep spindles and other sleep oscillations) and we are seeking effective interventions. In collaboration with Dr. Robert Stickgold’s lab at Beth Israel Deaconess Medical Center, we are extending and expanding this basic and clinical research program using state-of-the art tools including high density EEG, MEG, DTI, functional connectivity MRI, fMRI, and behavioral studies. We are seeking someone to participate in these foundation and NIMH-funded investigations who is familiar with cognitive neuroscience, neuroimaging methodology including MEG and/or EEG and data analysis, and is interested in developing research questions and optimizing analysis streams tailored to the study aims and populations. New approaches and ideas are encouraged, as are independent projects that dovetail with current studies. The position requires working closely with the PI, as well as with Dr. Stickgold, other Martinos Center investigators, particularly Dr. Matti Hamalainen, Director of the MEG Core Lab, and lab mates to design studies, acquire data, and develop, explore, improve and apply data analytic techniques. Training in clinical research and in the acquisition, analysis, and interpretation of neuroimaging data will be provided. Requirements: PhD (or MD) in neuroscience, psychology, engineering or a related discipline and a strong research background are required. Ideal candidates would have extensive experience in data analysis, a background in computational neuroscience and/or signal processing, be proficient in Matlab/Python and be interested in methods development. The following are also beneficial: experience with MEG/EEG data analysis/methodology, background in cognitive neuroscience, experimental psychology and sleep; interest/experience with clinical populations; and experience in task design and analysis for cognitive experiments.

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