Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

selxavg3-sess design ill-conditioned
by Marco Ninghetto 17 Jan '20

17 Jan '20

External Email - Use Caution Hello, I'm analyzing retinotopy data. I used expanding ring and rotating wedge. For my pilot, unfortunately, we used only 2 cycles for each stimulus and 1 cycle lasted 200 seconds (for sure I will change to more cycles lasting less). TR = 2.5. Retinotopy paradigm files are as follow: -for expanding ring (pos direction since it expands): stimtype eccen direction pos -for rotating wedge (neg direction since is counter-clockwise): stimtype polar direction neg To compute analyses, I ran the following pipeline: 1) recon-all 2) preproc-sess 3) mkanalysis-sess 4) selxavg3-sess Having only two cycles for each stimulus, in mkanalysis-sess, I used the option -hpf and lowered the filter to 0.5. In the last level (selxavg3-sess), I get the error. Basically this step runs up to when MATLAB starts to calculate. Here I get the following error: MATLAB is selecting SOFTWARE OPENGL rendering. > < M A T L A B (R) > > Copyright 1984-2019 The MathWorks, Inc. > R2019b Update 3 (9.7.0.1261785) 64-bit (glnxa64) > November 27, 2019 > > To get started, type doc. > For product information, visit www.mathworks.com. > > >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > >> /usr/local/freesurfer/matlab/MRIread.m > >> >> >> starting fast_selxavg3b > > #@# SUBJ02 ############################### > /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02 > ------------------------- > $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ > ------------------------- > outtop = /media/sf_w_Desktop/w_pRF/retinotopy > Extension format = nii.gz > INFO: key nSliceGroups unrecognized, line 11, skipping > nruns = 2 > autostimdur = > > > outanadir = /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh > Found 118266/125623 (94.1) voxels in mask 1 > Creating Design Matrix > ... creation time = 0.008 sec > DoMCFit = 1 > ntptot = 260, nX = 158, DOF = 102 > Saving X matrix to > /media/sf_w_Desktop/w_pRF/retinotopy/SUBJ02/bold/retinotopy.lh/Xtmp.mat > XCond = 6.85663e+16 (normalized) > ERROR: design is ill-conditioned > ans = > 1 > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n I'm stuck with analyses and I cannot proceed further. Could you provide some insight on what to do? Having only two long lasting cycles, do I have to use further optional flags in my commands? Thank you for your time, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Calculate thickness in a ROI volume
by Karel Mauricio Lopez Vilaret 17 Jan '20

17 Jan '20

External Email - Use Caution Dear Freesurfer team, I would like to get the thickness values of a specific ROI (volume mask). Could you provide to me a function to calculate that? Thanks in advance, Karel

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cannot find Matlab 2012b runtime in location
by Benjamin Ineichen 17 Jan '20

17 Jan '20

External Email - Use Caution Dear Freesurfer Experts, I ran the following command in FS: recon-all -i /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/SW1-1875_M12/Brain/DICOM/0000D7EA/AACF54F0/AAA4DDA4/000037CC/EE021428 -subject 000037CC -qcache -hippocampal-subfields-T1 -brainstem-structures -cw256 -3T -all The command exited with error. Attached the log file. Additionally, this message shows up in the terminal output: ERROR: cannot find Matlab 2012b runtime in location: /Applications/freesurfer/MCRv80 It is looking for either: bin/glnxa64/libdctprocess.so (Linux 64b) or bin/maci64/libdctprocess.jnilib (Mac 64b) You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b. To do so, please run the following commands (you might need root permissions): LINUX: cd /Applications/freesurfer curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do…" -o "runtime2012b.tar.gz" tar xvf runtime2012b.tar.gz MAC: cd /Applications/freesurfer curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do…" -o "runtime2012b.tar.gz" tar xvf runtime2012b.tar.gz I did now download the runtime2012b according to the suggestion. The untaring created a folder called MCRv80. I moved this folder to the Freesurfer_Home. Before I run everything again: 1.) Is the correct procedure to download the Matlab runtime? 2.) Did the recon-all run everything just without hippocampal subfields and brainstem? If yes, can I just re-run these two commands or do I need to re-run everything? Many thanks for the support! /Ben ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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Postdoctoral Fellowship
by Didenur Sahin 17 Jan '20

17 Jan '20

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Postdoctoral Fellowship
by Didenur Sahin 17 Jan '20

17 Jan '20

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin -- Didenur Şahin Graduate Student Neuroscience Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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Re: [Freesurfer] `GLIBCXX_3.4.19' not found error
by fsbuild 16 Jan '20

16 Jan '20

External Email - Use Caution Hello Pascale, Yes, that kind of symbol error has been posted before, and it can from the version of the standard C++ (or C) libraries being too different on the machine the binaries are running on - compared to the machine they were built on.  Generally speaking, newer versions of the OS try to be backwards compatible, e.g., such that binaries built on CentOS 6 could run on CentOS7.  However, forward compatibility may not to work, e.g., CentOS 7 binaries may not run on CentOS 5 or 6. You could let us know something more about the binaries you are using and the version of the OS you are running on in order to match them up, but using different version of the standard C libraries to run only some binaries is not recommended. - R. On Jan 16, 2020, at 12:33, Pascale Patenaude <pascalepatenaude(a)hotmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I'm attempting to produce an automated segmentation of the hippocampal substructures and the nuclei of the amygdala (see hippocampal module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) When I try to run the segmentHA_T1.sh bert  [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: /freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found /freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found It was suggested in the archives that this is a library problem but does anyone have any suggestions on how this can be fixed? Thank you in advance,Pascale _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Edit surface in Freeview
by Davide Momi 16 Jan '20

16 Jan '20

External Email - Use Caution Dear Freesurfer expert, I am working with bem model and I have created the outer and the inner skull. Unfortunately, for few subjects the two surfaces intersect each other (see attached). I've tried to edit it manually but I had hard time in figuring it out. Could you please help me with this? thanks Dave

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Segmentation Fault during recon-all using FLAIR Image
by Swanson,Clayton 16 Jan '20

16 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform a recon-all using a T2-FLAIR image. I have already run this particular participant through recon-all with their T1 image without error. While running the recon-all using the T2 the process exited with error stating a segmentation fault. Is there any way to run fix this problem on my end or better understand why this would be occurring? I have uploaded the recon-all.log for your convenience. Thank you, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu>

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Flag for recon-all to output aparc2005 labels (freesurfer 6.0)
by Grodin, Erica 16 Jan '20

16 Jan '20

External Email - Use Caution Hello, I am running recon-all on my data using freesurfer 6.0 which is working correctly. However, I need to create some VOIs which labels are only outputted from the aparc2005 set and do not appear in the aparc2009 set; specifically: 9001, 9501 ctx-lh-primary-motor, ctx-rh-primary-motor 9005, 9505 ctx-lh-prim-sec-somatosensory, ctx-rh- prim-sec-somatosensory 9002, 9502 ctx-lh-premotor, ctx-rh-premotor 9004, 9504 ctx-lh-posterior-parietal, ctx-rh-posterior-parietal Is there a flag or some other option to output the 2005 set in addition to the 2009? Thank you for your help, Erica Grodin ---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry

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Re: [Freesurfer] Oval shape in average subject inflated
by Marina Fernández 16 Jan '20

16 Jan '20

External Email - Use Caution Is there something wrong? > Dear Freesurfer team, > > I created the FS average subject of the same dataset with 5th and 6th order icosahedron tesselation using the following commands: > make_average_subject --fsgd fsgd.txt --ico 5 --out avg_subject_ico5 > make_average_subject --fsgd fsgd.txt --ico 6 --out avg_subject_ico6 > > When I load the inflated surface of the avg_subject_ico5 with tksurfer , it has a oval shape while > when I load the avg_subject_ico6 it seems to be a normal shape. > Please, see attached image. > > Thank you in advance. > > Best wishes, > Marina.

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Freesurfer January 2020