Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

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

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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

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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

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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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fix topology issue
by miracle ozzoude 01 Aug '17

01 Aug '17

Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul

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negative header after preproc-sess
by Bai Haohao 01 Aug '17

01 Aug '17

Hello Freesurfer experts, I am running my data with preproc-sess to project my func data to individual anatomy file, and the command shows as below: preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run -force And the subjectname point to the subject dir that created after recon-all. After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info: >>> f.get_data() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in get_data return np.asanyarray(self._data) File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in asanyarray return array(a, dtype, copy=False, order=order, subok=True) File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in __array__ self._data = self._read_data() File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in _read_data data = self.header.data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in data_from_fileobj data = self.raw_data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in raw_data_from_fileobj return array_from_file(shape, dtype, fileobj, offset) File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in array_from_file raise IOError(msg) IOError: Expected -1804 bytes, got 264809160 bytes from file "fmcpr.vol2surf.lh.nii.gz" - could the file be damaged? Then I check the file header by nibabel, and I get this: >>> print(f.get_header()) <class 'nibabel.nifti1.Nifti1Header'> object, endian='<' sizeof_hdr : 348 data_type : db_name : extents : 0 session_error : 0 regular : dim_info : 0 dim : [ 4 -1 1 1 451 1 1 1] intent_p1 : 0.0 intent_p2 : 0.0 intent_p3 : 0.0 intent_code : none datatype : float32 bitpix : 32 slice_start : 0 pixdim : [-1. 1. 1. 1. 2.00000072 1. 1. 1. ] vox_offset : 352.0 scl_slope : 0.0 scl_inter : 0.0 slice_end : 0 slice_code : unknown xyzt_units : 10 cal_max : 0.0 cal_min : 0.0 slice_duration : 0.0 toffset : 0.0 glmax : 0 glmin : 146790 descrip : FreeSurfer May 13 2013 aux_file : qform_code : scanner sform_code : scanner quatern_b : -0.0115927606821 quatern_c : -0.996071338654 quatern_d : -0.0864994972944 qoffset_x : 73344.5546875 qoffset_y : -1492.14978027 qoffset_z : -2311.28955078 srow_x : [ -9.99280393e-01 2.56918129e-02 2.79041883e-02 7.33445547e+04] srow_y : [ 2.04970520e-02 9.84766901e-01 -1.72667429e-01 -1.49214978e+03] srow_z : [ 3.19152586e-02 1.71971247e-01 9.84584868e-01 -2.31128955e+03] intent_name : magic : n+1 Note that the dim has value -1, but when I use -surface fsaverage, the dim is correct(show as below): dim : [ 4 27307 1 6 451 1 1 1] And I read the source code, the difference between self and fsaverage is appeared when running rawfunc2surf-sess, and log files are attached. I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz, such as fslview, freeview, mri_convert, mri_surf2surf, ... and only tksurfer could read this file by -timecourse fmcpr.sm0.self.lh.nii.gz. I want to figure out how could I fix it, and any suggestion would be helpful. Thanks in advance, Bai Haohao Version info: System: ubuntu-16.04.1-server-amd64 Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP nibabel: python-nibabel 1.2.2-1

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Volume based ROI projected to surface
by Sadie Marvel 01 Aug '17

01 Aug '17

Hi Freesurfers, I am doing a surfaced based ROI analysis on each of my subjects functional data. Using information from other papers, the size of the ROI really matters when doing the analysis, and I want to take this information from these papers and apply them to my own data. However, these papers use volume based ROI analysis, by making spheres that have 6 mm radiuses around the location of peak activity. To translate what they did to a surface based approach, I thought I would try to approximate how large this sphere would be if it were projected onto the surface of the brain by creating cubes around a certain location in the volume and projecting them to the surface using mri_vol2surf. That way, I would have approximately the same amount of information in my surface ROI. This is more of a general question, but I was wondering how this command actually works and whether it takes just one face or slice of the volume I created and projects that to the surface, or if it would project all 6 faces of the cube to the surface. And how is this volume actually translated into vertices? And how does the location of the cube in the volume space of the brain determine how large it will be on the surface? Do you have any suggestions as to how I can approach this problem better? Thanks?!

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Freesurfer August 2017