Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

Error in segmentSubjectT1_autoEstimateAlveusML
by Pascale Patenaude 05 Feb '20

05 Feb '20

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 SUBJECT_ID [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: Open file failed because file '/tmp/MCR_1572363005/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' Attempt to execute SCRIPT kvlWriteImage as a function: /tmp/MCR_1572363005/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m Error in segmentSubjectT1_autoEstimateAlveusML (line 1547) MATLAB:scriptNotAFunction Does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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Cannot load overlay through GUI
by Fengdan Ye 04 Feb '20

04 Feb '20

External Email - Use Caution Dear FreeSurfer experts: I encountered a weird problem when trying to load overlay through the Freeview GUI. I opened a surface file through terminal command “freeview -f lh.pial”, and then in the GUI I clicked Overlay -> load generic -> Select overlay file. After I selected the overlay file Freeview stopped responding. The following messages showed up in terminal: 2020-01-29 16:13:31.469 Freeview[1067:24667] warning: <NSRemoteView: 0x7fee5240bf70 com.apple.appkit.xpc.openAndSavePanelService ((null)) NSServiceViewControllerForTouchBarItem> determined it was necessary to configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy 2020-01-29 16:13:31.491 Freeview[1067:24667] warning: <NSRemoteView: 0x7fee5240ddd0 com.apple.appkit.xpc.openAndSavePanelService ((null)) NSServiceViewControllerForTouchBarItem> determined it was necessary to configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy The first message showed up when I clicked on the folder icon to select overlay file, and the second message showed up when I clicked “Open” after I selected overlay file. However, if I just ran “freeview -f rh.pial:overlay=<some_overlay_file>”, the viewer could open the overlay file without problem. Is there any fix for this GUI problem? I am on macOS Catalina Version 10.15.2. Thank you, Fengdan

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activation timeseries
by Nasiriavanaki, Zahra 04 Feb '20

04 Feb '20

Dear Freesurfer experts I want to extract "activation timeseries (BOLD signal changes in each time point) " from a predefined ROI in a single subject task fMRI data. Previously, I extracted these values from fmcpr.sm0.self.lh.nii.gz by using mri_segstats, but the data seems to be too noisy. I searched the forum and found this solution (mri_glmfit --y fmc.nii --qa --glmdir qa.glm --save-yhat This will detrend the time series (removing mean, linear, and quadratic trends). With --save-yhat, one of the outputs will be yhat.mgh (the detrended time series). If you have a task, the task will still be in there.https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18901.… I ran this command: mri_glmfit --y fmcpr.nii.gz --qa --glmdir qa.glm --save-yhat and then this command to extract the timeseries: mri_segstats --i yhat.mgh --slabel arap_7T_all lh $SUBJECTS_DIR/arap_7T_all/lh.label --id 1 --avgwf-remove-mean --avgwf ./lh.01.txt I got this error: ERROR: dimension mismatch between input volume and seg input 174 174 51 seg 148565 1 1 I would like to know if this is the right way to extract timeseries from a task data. and if yes, how can I fix the error. Thanks a lot Mona Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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mri_deface error: could not find wm peak
by Tim Schäfer 04 Feb '20

04 Feb '20

External Email - Use Caution Dear FreeSurfer experts, I am running mri_deface for all relevant volume files of more than 700 subjects (~3500 MGZ files in total). For roughly 10% of the files, the command fails, i.e., it stops with non-zero exit code and does not produce a result file. The relevant part of the mri_deface output is: after smoothing, mri peak at 0, scaling input intensities by inf GCAhistoScaleImageIntensities: could not find wm peak The full command line, an example file and the full output can be found in the footer of this email. Is there anything I can try to fix this? Some more information/observations: I noticed that for the subjects with errors, there are almost *always* the same 3 files affected: * mri/orig.mgz * mri/rawavg.mgz * mri/orig/001.mgz The file mri/T1.mgz is never affected. The file mri/orig_nu.mgz is only affected 2 times in total, and in these cases the image quality is extremely bad, so they can be ignored. Therefore, I suspect that the problems with the orig/rawavg/001 files are related to intensity inhomogeneity, which may lead to issues with the registration to the skull/face templates. Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany * Demo file: rawavg.mgz uploaded via FTP to /transfer/incoming/rawavg.mgz on surfer.nmr.mgh.harvard.edu * System info: FreeSurfer v6 stable, MacOS * Full mri_deface command and output for the demo file: $ SKULL_TEMPLATE="${FREESURFER_HOME}/average/talairach_mixed_with_skull.gca" $ FACE_TEMPLATE="${FREESURFER_HOME}/average/face.gca" $ mri_deface /path/to/subject/mri/rawavg.mgz "${SKULL_TEMPLATE}" "${FACE_TEMPLATE}" ~/defaced.mgz logging results to defaced.log reading '/Applications/freesurfer/average/talairach_mixed_with_skull.gca'... reading '/path/to/subject/mri/rawavg.mgz'... changing type of input volume to 8 bits/voxel... MRIchangeType: Building histogram bounding unknown intensity as < 10.3 or > 1461.6 total sample mean = 111.8 (0 zeros) spacing=8, using 2055 sample points, tol=1.00e-03... resetting wm mean[0]: 143 --> 144 resetting gm mean[0]: 89 --> 89 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (40, 39, 17) --> (213, 255, 225) using (98, 111, 121) as brain centroid... mean wm in atlas = 144, using box (77,84,95) --> (119, 137,146) to find MRI wm before smoothing, mri peak at 89 robust fit to distribution - 89 +- 6.7 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=109, mri_peak=141 after smoothing, mri peak at 0, scaling input intensities by inf GCAhistoScaleImageIntensities: could not find wm peak

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Post Doctoral Position: Neuroimaging
by Keedy, Sarah [PSY] 03 Feb '20

03 Feb '20

External Email - Use Caution Post Doctoral Position: Neuroimaging The Human Behavioral Pharmacology Laboratory in the Department of Psychiatry and Behavioral Neuroscience at the University of Chicago is seeking a post-doctoral fellow with expertise in fMRI study design and analysis, as well as human behavioral research. Join an active and collaborative lab http://hbpl.uchicago.edu/ to investigate behavioral and brain effects of psychoactive drugs (stimulants and other drugs) in healthy volunteers. Requirements: PhD and experience with fMRI design and analysis (e.g., SPM, AFNI); experience with programming or script-driven data analyses; experience with human subjects behavioral testing preferred. Publications and good writing skills essential. Send cv and letter to H. de Wit hdew(a)uchicago.edu<mailto:hdew@uchicago.edu>

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surfaceRAS to vertex coordinates
by Noah Markowitz 03 Feb '20

03 Feb '20

External Email - Use Caution Hi all, I’m trying to get the coordinates for specifice vertices of an inflated surface. I noticed there’s a difference between surfaceRAS and vertex coordinates (though I don’t understand it much). After getting the index of the specific vertex of interest I load the inflated surface through matlab with `vert = read_surf(‘lh.inflated’);` but notice that the coordinates it outputs is in surfaceRAS. ex: For fsaverage vertex 34686 SurfaceRAS = -17.53, -15.27, 48.87 Vertex = -46.54,-28.5,56.26 Is there a way I can get the vertex coordinates from those surfaceRAS coordinates? Please let me know when you get the chance. Have a good day, Noah

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New UCSF Cross-Sectional FreeSurfer (6.0) data
by Hasan Al Marzouqi 03 Feb '20

03 Feb '20

External Email - Use Caution I'm trying to access the ADNI/FreeSurfer dataset mentioned in the link below. How can I download it the directions are not clear. How can I get to the DOWNLOAD | Imaging | MR Image Analysis section of the ADNI archive? http://adni.loni.usc.edu/new-ucsf-cross-sectional-freesurfer-6-0-data-avail… Hasan Al Marzouqi Assistant Professor Electrical and Computer Engineering [cid:image001_5b9d5da2-5226-498c-8efe-a7084a62646b.png] P O Box 127788, , UAE T +971 2 6075090 F +971 2 447 2442 hasan.almarzouqi(a)ku.ac.ae ku.ac.ae<http://www.ku.ac.ae/> [cid:social_logos_bc6725d5-148a-4909-ae81-760d8b1c3dc4.png] [cid:MBZIRC_4cc4c5e3-e83d-4eb1-a48f-3e36e61af982.jpg]<http://bit.ly/mbzirc> <http://bit.ly/KUranking16> <http://bit.ly/KUranking16>

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Re: [Freesurfer] Tuning WM threshold
by Wright, Paul 02 Feb '20

02 Feb '20

External Email - Use Caution Dear Bruce Thanks for the explanation. Is there a way of turning off the -mprage flag from the recon-all command? If not I think I can figure out how to run the first stage taking individual commands from recon-all.cmd. Paul Hi Paul yes, the -mprage flag could definitely cause what you are seeing. It assume higher CNR and lower SNR in the images (hence bigger class separation between gray and white), and if used on SPGR it could definitely erode boundaries like this. cheers Bruce On Fri, 31 Jan 2020, Wright, Paul wrote: External Email - Use Caution Dear FreeSurfer experts I am a relative novice with FreeSurfer. I am reprocessing some older images with v6.0 that were previously processed with v5.3. In the newer batch, the GM-WM boundary is wider and the pial boundary is pushed out, but the newer version does a better job in the hippocampus. I am trying to figure out what parameters might differ between versions so I can get a cortical reconstruction as well as hippocampal segmentation. Both batches used plain vanilla recon-all -all. The attached figure shows v5.3 on top and v6.0 below, with aseg.mgz over T1.mgz. I used an example that as well as thin cortex in the new version, shows a hippocampal error in the older version. (The slices are aligned at the hippocampus, but the pitch is slightly different so they don't line up more superiorly.) >From the T1, it looks like the step that sets white matter to 110 is more aggressive in 6.0. I looked through recon-all.cmd and noticed both normalization steps include the -mprage flag in 6.0 not 5.3.Could this be the why the results differ? (The images are SPGR not MPRAGE.) Looking at help for mri_normalize it doesn't mention this flag or how to switch it off, so I'm stuck here. Of course, it might be something else, not the -mprage flag. I'd much appreciate any guidance from the list. Best wishes Paul Paul Wright, PhD Postdoctoral Researcher, Department of Neuroimaging King's College London Maurice Wohl Clinical Neuroscience Institute 125 Coldharbour Lane London SE5 8NU Desk: +44 20 7848 8579 Mobile: +44 7491 905754 Email: p.wri...(a)kcl.ac.uk _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Cortical segmentation error
by Monica Bondy 02 Feb '20

02 Feb '20

External Email - Use Caution Hello FreeSurfer experts, I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions. I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this? I have attached an image of what the problem looks like below. Please let me know if you need anything else. Thank you! 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 2. Platform: macOS Mojave (version 10.14.6) 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64 [image: Screen Shot 2019-12-13 at 9.56.46 AM.png]

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make_average_surface with unique surface
by Gabrielle-Ann Torre 31 Jan '20

31 Jan '20

External Email - Use Caution Hello developers, I'm attempting to compute a group average of a surface generated using mris_vol2surf. The generated surface is a ratio of T1-T2, as described in Glasser and Van Essen, 2011. Such a surface exists as a symbolic link in each subjects' /surf folder. When I apply make_average_surface to a set of subjects, I get the following error: $Id: make_average_surface,v 1.62 2016/02/16 17:17:20 zkaufman Exp $ Wed Jan 29 19:14:37 EST 2020 /projectnb/perlab/projects/DNAP/brains/alex4 output ddir is /projectnb/perlab/projects/DNAP/brains uid=323856(gat) gid=275709(perpwm) groups=275709(perpwm),275954(perlab) ==================== make_average_surface ==================== Wed Jan 29 19:14:37 EST 2020 /projectnb/perlab/projects/DNAP/brains/alex4 /share/pkg.7/freesurfer/6.0/install/bin/make_average_surface --out alex4 --subjects p0110 p0246 --surf-reg surf.t1t2.ratio input subjects: p0110 p0246 output subject: alex4 mri_add_xform_to_header -c auto /projectnb/perlab/projects/DNAP/brains/alex4/mri/mni305.cor.mgz /projectnb/perlab/projects/DNAP/brains/alex4/mri/mni305.cor.mgz INFO: extension is mgz #@# Making lh registration template --------- /projectnb/perlab/projects/DNAP/brains/alex4 mris_make_template -norot -annot aparc lh surf.t1t2.ratio p0110 p0246 lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject p0110 (1 of 2) reading spherical surface /projectnb/perlab/projects/DNAP/brains/p0110/surf/lh.surf.t1t2.ratio... MRISread(/projectnb/perlab/projects/DNAP/brains/p0110/surf/lh.surf.t1t2.ratio): could not open file No such file or directory mris_make_template: could not read surface file /projectnb/perlab/projects/DNAP/brains/p0110/surf/lh.surf.t1t2.ratio No such file or directory I have tried this using both "lh.surf.t1t2.ratio" and "surf.t1t2.ratio" as the name of the surface but neither works. I have also tried it with and without the .mgz file extension. Not sure what the error is or why my surface is unreadable. Does mris_vol2surf not generate surfaces that can be used as alternate surfaces using the --surf-reg flag? Any help would be appreciated! Best, Gabrielle -- Gabrielle-Ann Torre, Ph.D. Center for the Study of Learning Georgetown University Medical Center Building D, Suite 150 W: *202-687-2823* C: *520-393-9252 *

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Freesurfer February 2020