Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

surface label generation from vertex?
by Jason Tourville 24 Aug '23

24 Aug '23

External Email - Use Caution Hi Freesurfers, I would like to generate a label that extends some distance from a chosen vertex on the surface. Is this possible in the freeview gui? Otherwise? Many thanks for you feedback. Best, Jason

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How to register single voxel spectroscopy VOI to FreeSurfer processed brain
by Lauren Stephens 24 Aug '23

24 Aug '23

External Email - Use Caution Dear FreeSurfer, I am trying to extract tissue composition of %GM, %WM, and %CSF from a Freesurfer processed brain. I have the coordinates for the voxel but do not know how to place a voxel on the brain in FreeSurfer before running mri_compute_volume_fractions. Can anyone provide direction on how to do this in FreeSurfer using a Mac running Ventura 13.4.1? Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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The Affective Neuroscience Project of the national, longitudinal Midlife in the U.S. (MIDUS) study is recruiting a research associate
by STACEY M SCHAEFER 23 Aug '23

23 Aug '23

External Email - Use Caution The Midlife in the US (MIDUS) Affective Neuroscience Project is recruiting a research specialist to help collect and process multimodal neuroimaging and psychophysiological measures of brain structure, function, connectivity, and affective responses in our longitudinal participants to learn more about the emotional determinants of health, wellbeing, and brain aging. More information about the position and how to apply is here: https://secure-web.cisco.com/1D8SX5dQgGEwfUjzhDc4Wrvmv0IzxMZOFGbHvNNuIMgLRD… Learn all about MIDUS here: https://secure-web.cisco.com/1nlARnnEnUJzHScP-Bj6VyZYjzGKgJfYtRyT3yCNI1prm9… and about the Affective Neuroscience Project in particular here: https://secure-web.cisco.com/1oepRN7crMjDdZgRLnDk__6XioHk4fEbdw_Oubx43ag7K9… Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core Institute on Aging 2245C Medical Sciences Center University of Wisconsin-Madison 1300 University Ave Madison, WI 53706 USA

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FreeSurfer 7Zip archive passcode
by Byripudi Naveen Kumar ed20d402 23 Aug '23

23 Aug '23

External Email - Use Caution Dear experts, I am trying to install Freesurfer on the VitualBox. However I do not have access to unzip the ova.7z file. Can you kindly provide me with the passcode of FS_7_2_0_ubuntu_18_04_06.ova.7z? Sincerely Naveen

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Re: [Freesurfer] Freeview output viewing error
by fsbuild 23 Aug '23

23 Aug '23

External Email - Use Caution  If you search the freesurfer mail archives for WSL you should find postings about how to setup an  X-server on the windows host in order for Linux applications to run in WSL and use X-Windows to display images.   We provide some documentation, however we cannot guarantee these settings work with the current version of the 2nd iteration of WSL, i.e., WSL2, which you are running.  See,https://secure-web.cisco.com/11H-L4FbGidKmZY-de-JntjYeQLAeVrQ1XgpdUHaMqg8CCouWlZ-csPc_4IeioBAVAqHhk45el9cRUZPv7wIb0Fa33nZc9N4PkjKI0dF1RPJVN-he9XBt1Ua6a4QSVeD_w5bZnfOLabOM5n15lkCAJOV069NjUvo7wvfKDC7ihp4tfFZRlqy04d4Ulv8M3XzFbXzHa3_X6PzLyLptMRW0DpSEH15MxILMfCaw2aXqyXv8WbtHT_dWkB1oPK8nKUInT_c31S6utPE9VzRLR2IkzwjB7r2AqOCZO1vkEd_sd-w--NZS1-g316PnttbIo3N5Ia8In0FQw1pQlYDew151jQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl Some people have found Moba X-term to be easier to setup and use compared to Xming for the X-server.https://secure-web.cisco.com/1wbbTwhirUX48Lj_j7Zcog0e6ACmMB4oLvaYM… Before trying to run freeview, check that simple X-windows programs like “xclock” or “glxgears” run directly from the terminal window inside linux, i.e., you should see a clock displayed,$ xclock… and spinning gears ...$ glxgears An alternative to WSL is to run the VirtualBox VM we provide with freesurfer 7.2.0 pre-installed running on Ubuntu 18,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-s… You can upgrade the VM from Ubuntu 18, to 20, etc….  Similarly you can uninstall freesurfer 7.2.0 and install the latest 7.4.1 rpm matching the Ubuntu OS you are running from the Freesurfer downloads page,https://secure-web.cisco.com/1m70yw-FWa8H1WUCpyYEQ2AgIFTjm9W5pcTX0Peja… Advantages to the VM are it will run (thru Virtualbox) on most Linux, Mac, or Windows hosts and since the X-server is built into the VM, there is no need to install and configure a 3rd party X-server on a Windows host.  Some users have switched to VirtualBox because they found it easier to use.  See,https://secure-web.cisco.com/1vK-WU9hm5IesyZObbEUx1tWoPmNR_OvT3eg0YDwj-sSQIXzdhv-YwluzAWgB4gG9phXhLQcVB_o2cNHMOGnK9Gp9XWPjB8FgTqezBrM26yU2u5N756v_OP8sEXvbixcSFk6pTTTGbu3wEJMe_5kxVgYIInMdlJVcY40F7nAa8KOLYdDPEcKUtp7gnSXtBSNLE4rpSwwlEQr2t1r_26eI3pnjxD9fv1Z2pFrryslOZVdLTsNVxs6jZcYOZZYcGKMTjoPot6uYkAjYPe0eKi-U441Xz0011uiNKcTTbbhPOQ4bs6_q6eY9BWkFuxm6JBvP1WaMMtWPal2bAZD488thEA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67 - R.

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Freeview output viewing error
by Byripudi Naveen Kumar ed20d402 23 Aug '23

23 Aug '23

External Email - Use Caution Dear experts, I'm trying to use freeview to analyse the freeview outputs. I am able to load all the surfaces and volumes onto freeview but I can't see anything on the viewing planes in all 3 slices and 3d views. I have tried to install freesurfer on a completely new device and still the problem persists. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the screenshot of freeview window for reference Hope you could help me resolve this. 1. FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Ubuntu 22.04.2 LTS (code name jammy) 3. uname -a Linux Navi 5.15.90.1-microsoft-standard-WSL2 #1 SMP Fri Jan 27 02:56:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4. Freeview window screenshot attached Thank you Naveen Kumar IIT Madras [image: image.png]

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Spurious BOLD activations along the edge of an oblique partial volume
by Itzik Norman 22 Aug '23

22 Aug '23

External Email - Use Caution Dear FreeSurfer team, I'm using fsfast to analyze 1.2mm^3 7T BOLD data collected with a partial coverage over the hippocampus and superior temporal lobe. I ran preprocessing with the following flags: preproc-sess -d /functional-data -s SUB01 -fsd bold -surface SUB01 lhrh -fwhm 2 -init-header -bbr-int /functional-data/SUB04/bold mT2_WB -per-session And then I ran the GLM analysis (stimulus-vs-baseline) using selxavg3-sess, keeping the data in the subject's native space (using the '-native' flag combined with '-per-session'). The resulting t-map shows a diagonal line of spurious activation along the edge of the functional volume. Is there a way to eliminate this artifact? (see figures attached) Moreover, is there a way to use the -native flag together with -per-run? I want to simultaneously measure the hippocampal activation (in native space) and cortical activity smoothed on the surface; but I want all the data to be processed the same way (-per-run), and currently the volume analysis forces me to use -per-session. I haven't encountered any previously documented issues similar to this one. Please let me know if you have any thoughts. 1) FreeSurfer build stamp: freesurfer-darwin-macOS-7.3.2-20220804-6354275 2) Platform: Mac Studio M1 (macOS) 3) selxavg3-sess log: attached 4) analysis config file: attached Thanks, Itzik [image: image2.png][image: image3.png][image: image1.png]

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Job Position: Postdoc Research Associate at the Center for Healthy Minds
by Center for Healthy Minds Human Resources 22 Aug '23

22 Aug '23

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin–Madison<https://secure-web.cisco.com/1alZdwyt9ShUTl9SUEacJ-4HTHzY4BrOzC7GyTMTJZ7g0n…> is seeking multiple highly motivated postdoctoral researchers to work on intervention studies in U.S. adults to promote wellbeing and prevent suicide. Areas of research include the evaluation and mechanistic examination of behavioral and physiological interventions in healthy and distressed adults using multiple types of MRI, passive measures of behavior and physiology, and survey measurements. The postdoctoral research associates will have opportunities to participate in activities related to neuroimaging methods development and evaluation, study data collection and analyses, research publications, grant writing and are expected to make positive scholarly contributions to this interdisciplinary and highly collaborative research program. Qualifications: Required Ph.D. in medical physics, psychology, neuroscience, and/or a related field Prior experience with brain imaging techniques (e.g. MRI, DTI, and/or fMRI) and/or behavioral data Strong communication and organization skills are a must. Preferred Experience with brain image analysis software tools, MATLAB, Python, C++ and/or other computer programming (e.g., R, Mplus) Experience with large and complex research studies and/or clinical trials Emerging track record of publishing in academic journals, strong analytic skills, and excel at working in a collaborative environment. We are an equal opportunity/affirmative action employer. We promote excellence through diversity and encourage all qualified individuals to apply. To view the full posting with application instructions please go to https://secure-web.cisco.com/1VdOrlXBZlLhFv9xXJTvkxUg9UcYvjBez8PJM194TBa2Rz…

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Password for unzipping Virtual Box Image file
by mkassinopoulos＠barcelonabeta.org 22 Aug '23

22 Aug '23

External Email - Use Caution Hi, I would like to request the passcode for unzipping the Virtual Box Image file (i.e. FS_7_2_0_ubuntu_18_04_06.ova.7z). Best regards, Michalis

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[FreeSurfer] ValueError axes don't match array
by Krystal Xiwing Yau 22 Aug '23

22 Aug '23

External Email - Use Caution Dear FreeSurfer experts, I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: writing template transform to /home/admin1/freesurfer/subjects/103_samsegOutput/template.lta writing talairach transform to /home/admin1/freesurfer/subjects/103_samsegOutput/samseg.talairach.lta atlas registration complete: 0:00:17.614971 /home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray return array(a, dtype, copy=False, order=order) Traceback (most recent call last): File "/home/admin1/freesurfer/python/scripts/run_samseg", line 190, in <module> _, _, _, optimizationSummary = samseg.segment( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 255, in segment self.preProcess() File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 318, in preProcess self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/SamsegUtility.py", line 139, in readCroppedImages croppedImageBuffers = np.transpose(croppedImageBuffers, axes=[1, 2, 3, 0]) File "<__array_function__ internals>", line 5, in transpose File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 653, in transpose return _wrapfunc(a, 'transpose', axes) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc return _wrapit(obj, method, *args, **kwds) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit result = getattr(asarray(obj), method)(*args, **kwds) ValueError: axes don't match array Would somebody be kindly advise? Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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