Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

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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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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mri_glmfit with flag -pvr
by Vicky Shi 31 Jan '20

31 Jan '20

External Email - Use Caution Dear Freesurfer team, I am running the glm analysis on CBF maps. I have two class and I want to see the group difference regressing out the cortex thickness. I know that I can add the average cortical thickness as one covariable in FSDG file. However, I think it might worth trying to do this with GLM by using a per vertex regressor (thickness). My fsgd file is like below: Class Patient Class CTL INPUT subj1 Patient INPUT subj2 CTL .... My command is below: mri_glmfit --y lh.fsaverage.cbf.sm10.mgz --fsgd fsgd.txt --C contrast.mtx --glmdir lh.output.glmdir --surf fsaverage lh --pvr lh.thickness.sm10.mgz My contrast matrix is -1 1 0. I am wondering if what I do is correct or not. Does it make sense or I should use the mean thickness as regressor? Thank you for your time! Best regards, Vicky

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Question longitudinal study about treatment effect with change of scanner and head coil?
by Markus Gschwind 31 Jan '20

31 Jan '20

External Email - Use Caution Dear experts, I am reviewing a study that proposes a longitudinal study in patients across several years on the effect of medical treatment in terms of fcMRI and DTI-connectivity measures. However, in several but not all patients, the scanner was upgraded from Trio to Prisma and the head coil was changed from a 12 to a 20-channel. Every patient had the upgrade at another time point. I would like to hear your opinion on this. In my experience, the scanner upgrade and especially the head coil upgrade heavily affected the images. So I have fundamental doubts about the feasibility. What would be the conditions under which it could be acceptable? Thank you in advance! Best, Markus

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Software support
by Ricardo J Rodriguez Colon 31 Jan '20

31 Jan '20

External Email - Use Caution Hi, I was wondering if there is a version available for Windows OS or is this available for Mac and Linux only? Thank you, - Ricardo J. Rodríguez

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recon-all errors - mri_segstats and mri_relabel_hypointensities
by Laurel Quinlan 31 Jan '20

31 Jan '20

External Email - Use Caution Hi FS Support, I have two brains for which recon-all exited with errors after I edited the wm.mgz volume. It seems that the problem occurs during the mri_segstats and mri_relabel_hypointensities steps (if I'm reading the output of the command "tail scripts/recon-all.log" correctly). I attached one of the recon-all.log files as a zipped txt file. Please let me know if you have troubleshooting suggestions. Thank you for your help! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Freesurfer January 2020