Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

Re: [Freesurfer] Freeview error: GLXBadContext
by fsbuild 12 Mar '20

12 Mar '20

External Email - Use Caution Hello Alek, When you say you are running Ubuntu 14 via a Windows 10 PC, do you mean you are running the add-on windows subsystem for linux (known as WSL) that allows you run an Ubuntu shell on Windows 10?    And then when you say you are remotely viewing things, does that mean you are remotely logging into that Windows machine? If you are in fact using WSL, then for X Window based GUI application like Freeview to run in WSL, you need to have an X server installed and running on the windows side, e.g., Xming.  Then WSL can send X windows based graphics from the Linux shell back to Xming on the Windows side for rendering..  But  Windows OS has to be able to handle rendering the graphics thru Xming using the drivers for whatever the graphics card/hardware is (which could include a GPU). If you look at this thread for the same error you posted, but on a pure linux desktop, https://stackoverflow.com/questions/9769613/x-error-badalloc-…, it reads to me like this may have been solved by updating the *mesa* libraries in linux which support displaying graphics (directly on the linux OS driving the graphics card).  Translating this to the Windows WSL environment however - it would seem the same error could be from the graphics received by the X-server on the Windows side not being compatible/supported by the graphics drivers/hardware there.  It might also have something to do with how the X-server is configured. I don’t have much experience with WSL, but I would think that in the Ubuntu linux shell you’d want to set display for the console,  $ export DISPLAY=:0 Then it sounds like that /usr/bin/xeyes or other *simple* X programs already get displayed correctly,  $ /usr/bin/xeyes Do you get the same error if you run a simple freeview command to open a single volume, e..g. $ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz I would try the above directly on the windows machine (not remotely logged in). - R. On Mar 11, 2020, at 10:46, Duvnjak, Aleksandar <aleksandar.duvnjak16(a)imperial.ac.uk> wrote:        External Email - Use Caution        Dear FreeSurfer experts,Version: Freesurfer version 6.0Platform: Ubuntu 14.04 (Via a Windows 10 PC) Upon completion of our first FreeSurfer job, in which we ran an array on ~50 subjects, we have tried to view the basic outputs (e.g. T1.mgz) using both freeview -v and FSLview. Upon running freeview -v, the app opens but shows no discernible image (see screengrab below). Upon exiting the viewing platform the command line reads: X Error: GLXBadContext 150  Extension:    143 (Uknown extension)  Minor opcode: 5 (Unknown request)  Resource id:  0x8000c8I have found reference to this error in the archives at: https://www.mail-archive..com/freesurfer@nmr.mgh.harvard.edu/msg30… much like with this original query, we are running freeview remotely via a high-performace-computing system, and when we type glxgears at the command line spinning gears do popup. Furthermore, (and although this does not relate directly to Freesurfer, it may provide additional useful information) upon trying to view the same T1.mgz file with FSLview rather than freeview we receive the message "missing header/image file" within the viewer but no error in the command line. We appreciate this may be a simple solution, however as it is our first time running FreeSurfer, it is difficult to know how to proceed. I have attached the recon-all report log for the subject attempting to be viewed in the screengrab below.<pastedImagebase640.png>Kind regards,Aleks Duvnjak<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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within-subject contrast between runs
by Milde, Christopher 11 Mar '20

11 Mar '20

External Email - Use Caution Dear Freesurfer Experts, I have a very basic questions about creating subject-wise contrasts between runs Background Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off). I performed the preprocessing and 1st levels stats in the native subjects space Questions * How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session? * Can I obtain this within-subject contrast by staying in the native subject space? * Do I have to concatenate both runs and create a new parradigm file? Thanks for your support Sincerely Chris

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Tracula Inquiry
by Ledesma, Jason 11 Mar '20

11 Mar '20

External Email - Use Caution Hi, I am seeing the following error: Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf Missing }. Missing }. }: Command not found. Missing }. red255green255blue255: Command not found. }: Command not found. Missing }. }: Command not found. margl1440margr1440vieww9460viewh8400viewkind0: Command not found. pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardirnaturalpartightenfactor0: Command not found. Badly placed (. ERROR: run list is longer than subject list Attached is my config file. Can you tell me what might be wrong? Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ___________________________________________________________________________________ LUNDQUIST Institute Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ___________________________________________________________________________________

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Converting ANTs nonlinear transform to .m3z
by Ardesch, D.J. 11 Mar '20

11 Mar '20

External Email - Use Caution Dear FreeSurfer experts, I am working on some monkey data and trying to get an accurate nonlinear transform to talairach space (talairach.m3z in the -careg stage). The problem is that the monkey brains look so different from the human brain that this registration ends up being very far off, even with an accurate talairach.lta. As an alternative, I did a two-stage nonlinear registration using ANTs (first from subject to a macaque template and then from macaque template to talairach), which gives an accurate nonlinear transform. However, I can’t seem to convert this nonlinear transform file correctly from .nii.gz to the .m3z format that FreeSurfer needs to continue down the pipeline. How would one go about converting the nonlinear transform from ANTs to a correct .m3z file? Some other things I tried: * I have tried a workaround in which I applied the inverse ANTs transform to the first frame of RB_all_2016-05-10.vc700.gca to get the talairach volume in subject space, and then ran mri_ca_register on that volume to obtain a talairach.m3z. That transform works but is still not accurate enough unfortunately. * The nonlinear transform itself seems correct because when I apply it to the movable volume using ANTs the results are similar to: mri_convert movable.mgz –apply_transform talairach.m3z -oc 0 0 0 movable_in_talairach.mgz where movable.mgz is the talairach volume in subject space and talairach.m3z is the transform made by mri_ca_register. The dimensions, orientation, and voxel size of movable_in_talairach.mgz and my own transformed volume are identical. Any help would be greatly appreciated! Platform: MacOS Mojave Version: FreeSurfer 6.0.0

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Freeview error: GLXBadContext
by Duvnjak, Aleksandar 11 Mar '20

11 Mar '20

External Email - Use Caution Dear FreeSurfer experts, Version: Freesurfer version 6.0 Platform: Ubuntu 14.04 (Via a Windows 10 PC) Upon completion of our first FreeSurfer job, in which we ran an array on ~50 subjects, we have tried to view the basic outputs (e.g. T1.mgz) using both freeview -v and FSLview. Upon running freeview -v, the app opens but shows no discernible image (see screengrab below). Upon exiting the viewing platform the command line reads: X Error: GLXBadContext 150 Extension: 143 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x8000c8 I have found reference to this error in the archives at: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30865.html and much like with this original query, we are running freeview remotely via a high-performace-computing system, and when we type glxgears at the command line spinning gears do popup. Furthermore, (and although this does not relate directly to Freesurfer, it may provide additional useful information) upon trying to view the same T1.mgz file with FSLview rather than freeview we receive the message "missing header/image file" within the viewer but no error in the command line. We appreciate this may be a simple solution, however as it is our first time running FreeSurfer, it is difficult to know how to proceed. I have attached the recon-all report log for the subject attempting to be viewed in the screengrab below. [cid:dc363bf5-90e3-4318-820f-38416df60417] Kind regards, Aleks Duvnjak

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Initializing FreeSurfer's recon-all with rigid registration
by Yeun Kim 11 Mar '20

11 Mar '20

External Email - Use Caution Hi, How do I concatenate the resulting recon-all transform with another rigid transform to produce a single transform? I have the aseg.nii.gz (generated from the T1w image in T1w space) output label in the atlas space and I would like to transform this label into the same subject's T2w space. I am aware there is a transform that moves the image from atlas to T1w native space (although I'm not quite sure of the specific file names of the transforms, only the command mri_label2vol). I have the transformation from the rigid registration between T1w and T2w (T1w moving to T2w space) and would like to concatenate the atlas-to-T1 transform with T1-to-T2 transform to reduce the amount of error caused by resampling (since the labels are in discrete integers). Thank you in advance, Yeun

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Problem with MP2RAGE data: correcting defects
by Abraham Y 11 Mar '20

11 Mar '20

External Email - Use Caution Dear FreeSurfer developers, I'm trying to apply Fujimoto's pipeline to reconstruct surfaces of MP2RAGE structural images. Citation: John R.Giudicessi, BA.Michael J.Ackerman., 2013. (2008). NIH Public Access. Bone, 23(1), 1–7. https://doi.org/10.1038/jid.2014.371 The MP2RAGE sequence generates several images: a UNI or flat image (T1w but with amplified noise outside the brain), a proton density image, and other images. To be able to run freesurfer on the flat image, Fujimoto invokes freesurfer two times and then stops them immediately after the brain masking step: the primary stream (input: the flat image) and the secondary stream (the multiplicative product of the flat image and the proton density, which removes the noise). Then, the brain mask generated during the primary stream is replace by the mask generated during the secondary stream, and the primary stream is resumed. I implemented this as follows: - run 'recon-all -s X -i Y -autorecon1' for the primary and secondary streams - copy the brainmask.mgz file of the secondary stream to the primary stream (and replace the file) - resume the primary stream with 'recon-all -s X -autorecon2 -autorecon3) The problem with this last step is that it gets stuck at correcting defects (eg: CORRECTING DEFECT 0). Sometimes it adds "Xl defect detected". Each of these corrections takes several days to run and this is not practical for our research. Any ideas on how I could fix this? I have attached a recon-all.log file (I stopped the process because it takes too long). FS version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c OS: Ubuntu 18.04.2 LTS

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Group analysis with qdec: qcache change this?
by Miguel Ángel Rivas Fernández 11 Mar '20

11 Mar '20

External Email - Use Caution Dear freesurfer experts, Before running group analysis in qdec is necessary run the qcache command over all subjects but, does this command change some segmentation file (eg. rh/lh Pial or white surface) or other importants file? We would also like to perform external analysis using the output metrics obtained with the recon-all. This is why we want to know if we can safely use this command without affecting any segmentation measure. Thanks in advance Best regards,

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question about sig.mgh
by 邓刊 11 Mar '20

11 Mar '20

External Email - Use Caution Dear freesurfer experts, I have analyzed intra-group differences in cortical thickness using QDEC. It generated the file sig.mgh. 1.I want to know what does the sig.mgh mean? Which p value and the cluster size this file present? 2.when I clicked the button Monte Carlo simulation (p<0,05) and listed in the qdec output file "mc-z.abs.th20.abs.sig.cluster.summary". However,there is no cluster in the file.Dose that mean there is no significant difference between two groups? I have attached the contents of the output file and a screenshot of the display window of QDEC. Thank you in advance for your help.

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aparc a2009s stats ROI names don't match ColorLUT for FS 6.0
by Don Hagler 10 Mar '20

10 Mar '20

External Email - Use Caution I have recently started using FreeSurfer 6.0 after previously working with 5.3 for several years. I found that the lh.aparc.a2009s.stats files use different ROI names (e.g., G&S_frontomargin) than they did in FS5.3 (G_and_S_frontomargin). However, the FreeSurferColorLUT.txt file still has the old names. What caused the ROI names to change for the a2009s.stats files? Was the ColorLUT supposed to have been updated but wasn’t? Where do those shorter names come from? Is there already a mapping file for the different versions of the names? Because some of the parcel names in the stats files no longer match the LUT, my existing code for compiling FreeSurfer results fails to load the results for those ROIs with new names. I think I can find a work-around for this, such as using a mapping file or a renaming rule applied to the a2009s stats ROI names, before matching to the LUT. But I thought I would email this list to raise the issue. I searched the archives and didn’t see something similar, so maybe no one else tries to match those names to the LUT.

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Freesurfer March 2020