Freesurfer

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30132 discussions

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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Re: [Freesurfer] PetSurfer questions
by Soo-Jong Kim 31 Jan '20

31 Jan '20

External Email - Use Caution I ran gtmseg for my partial volume correction 1. but I have a question. What regions are for the detail?? in this option. mri_gtmpvc --default-seg-merge. I searched mri_gtmpvc --help but it is default schema for merging ROIs. So I wanna know what regions you use as default. for example, in FreeSurferLUT. 1000, 1010, etc.. Can you tell me what regions freesurfer uses. 2. In general, After PVC (i.e.MG or RBV), Does some smoothing kernel apply to pv-corrected images from rbv as rbv.nii.gz? If then, how large smoothing kernel? Best, Soo

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orig2rawavg transformation matrix
by Sam W 31 Jan '20

31 Jan '20

External Email - Use Caution Hello! How can I get a transformation matrix that maps orig.mgz to rawavg.mgz? I only see examples bringing freesurfer results into original anatomical space with mri_vol2vol, but I really just want the transformation matrix. Thanks! Best regards, Sam

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Re: [Freesurfer] medial wall metric file
by Alexopoulos, Dimitrios 31 Jan '20

31 Jan '20

External Email - Use Caution Having difficulty with how to use label2label for this purpose. Just need a binary mask of medial wall (vertex number and 0 or 1s) on native surface. What's would this command be? On Jan 28, 2020 5:42 PM, "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> wrote: Attention: This email originated from outside the university. Do you mean you want a binary mask of the medial wall? You can create a mask of the cortical label (?h.cortex.label) with mri_label2label You can then invert that with something like fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below). I’d like to be able to export the medial wall metric into Worbench. Thanks. Jim [cid:part1.330140F5.A370F13A@mgh.harvard.edu] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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