Freesurfer

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Re: [Freesurfer] recon-all-clinical out of memory error
by fsbuild 25 Aug '23

25 Aug '23

External Email - Use Caution  Thanks for the updates.  Not that it will likely help with the memory underrun, but it should be straightforward to update Freesurfer from 7.2.0 to 7.4.1 in the VM from the command line. You can use the Firefox browser in the VM to download the 7.4.1 installer with the link,https://secure-web.cisco.com/1NY_o7fEYkraJG0kPriDNOoRkAxLu_PnGwgYcRK1s… In a terminal window, remove the existing freesurfer 7.2.0 installation,$ sudo apt remove freesurfer Then go to where the 7.4.1 installer was downloaded and run,$ sudo apt install ./freesurfer_ubuntu18-7.4.1_amd64.deb There was likely a soft link to the previous freesurfer distribution in developer's home directory, so to update that, $ cd $HOME$ rm -f  freesurfer$ ln -s  /usr/local/freesurfer/7.4.1  freesurfer$ ls freesurfer<output deleted) .... check you have 7.4.1 ... $ cat  freesurfer/build-stamp.txtfreesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 - R. On Aug 19, 2023, at 08:00, Matthew Lynch <matthewl077(a)gmail.com> wrote:        External Email - Use Caution        Thank you fsbuild for the suggestions.  Unfortunately it still does not work.  I did not try the virtual machine, because I could only find version 7.2.0 ova file on the freesurfer website.  It appears the 7.4.0 version does not yet have a virtual machine?  I am trying to use recon-all-clinical, which did not appear until 7.4.0.  The standard recon-all works fine on 1mm scans on my 16 Gb machine under WSL.  But I am trying to explore use of recon-all-clinical.It appeared as if WSL was not using any of the available swap space, so I tried a few different swap and memory configurations in .wslconfig.  Then I tried to create a cgroup that would limit physical memory and force freesurfer to use swap.  This did cause freesurfer to use swap space, but it still crashed with out of memory error when the combined swap and physical memory got to about 23 Gb (out of a total of 100 Gb virtual memory).I then created a total Linux version using Porteus Linux live USB and unpacking the freesurfer 7.4.0 tar.gz and finding a few minor dependencies.  This is a fairly lightweight Linux distro that runs from USB so I didn't have to create a dual boot..  The base memory usage was about 1.3 Gb before running recon-all-clinical.  I also activated a 16 Gb swap file with swapon.  It didn't work either, even in a pure Linux environment.  At maximum memory usage, it used only about 7-9% of the 16 Gb swap space and I think it also crashed at the same place around 21 Gb total memory usage with an OOM error.So it appears to be complaining of out of memory even when there is ample memory available in the form of swap space.  I have tried various options for vm.overcommit and vm.swappiness.This seems to occur only for a few selected scans.  For most of them it works.  There is a long error chain but this seems to be the relevant line:OOM when allocating tensor with shape[1,288,288,192,72] and type float on /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu[[{{node model_5/unet_parc_merge_8/concat}}]]It fails there every time. I bit the bullet and bought an additional 16 Gb physical RAM for a total of 32 Gb.  I'll let you know if that works.On Sun, Aug 13, 2023 at 10:11 PM fsbuild <fsbuild(a)contbay.com> wrote:You might be better off with swapping inside the Linux VM instead of on the windows host.  Or I don’t see anything preventing the Windows host from trying to swap out the entire VM process - which I would not expect to be efficient.  You only need the application running *inside*the*Linux*VM* to be swapped out if necessary (using the Linux OS to do that).This should be straightforward to setup using VirtualBox to run the Ubuntu Linux VM we provide with Freesurfer already installed, i.e., download fromMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oFOJz1tXGspfsKNscw0jmPq8nuxBXOxbqTB1n… the screenshot below, the FreeSurfer VM starts with 4G allocated to it.  So correspondingly, inside the VM the “free” command reports there is ~4G available of which only 1G is being used since nothing consequential is running.  If you stopped the VM, increased the allocated memory in the VirtualBox application, and re-started the VM, you would see the total available memory scale up accordingly.For available swap space, you would look at the boot image on /dev/sda1.  That image is made on purpose as small as possible so it can grow and/or space can otherwise be used.  The “df” commands shows that out of the box, the VM takes up 22G of the max allowed size of 170G.  That leaves potentially 170-22=148G to be used for other purposes.  You certainly would not want to allocate all that for swap space, but there is space to use for a good chunk of swap space apart from space you will consume doing work that adds files into the VM.   Here is 1 of many articles about setting up swapping in VirtualBox (which we do not setup by default),MailScanner has detected a possible fraud attempt from "secure-web.cisco..com" claiming to be https://secure-web.cisco.com/1Zqb8y3NbSCxfL4B31cjKDD_lN8KL6yjtwEypw… efficiency of swapping will be limited by your system, e.g.., how fast the disks are, their bus interface, etc.  There’s no guarantee even the most efficient swap configuration won’t cause the machine to slow down to a crawl depending upon what you are processing.  It’s not a substitute for having RAM to allocate to the VM.   We have discussed increasing the published memory system requirements for Freesurfer.- R.On Aug 13, 2023, at 06:39, Matthew Lynch <matthewl077(a)gmail.com> wrote:        External Email - Use Caution        The method I mentioned before does not always work.  It worked for all but about 3 scans out of approximately 30.  There are some scans for which the "committed memory" caps at about 23 Gb in the task manager and then either the out of memory error occurs or the WSL session is killed.  Increasing the .wslconfig swap and memory beyond 32 Gb didn't work.  Increasing the Windows pagefile size to 8 Gb didn't work.  The output of free -h during the synthseg run was 0Gb used, 40Gb free, which seems to suggest it is not using the swap.  I suspect this is a matter of somehow getting WSL to properly use large amounts of swap space.On Thu, Aug 10, 2023 at 5:52 PM fsbuild <fsbuild(a)contbay.com> wrote: Hello Matthew,Thanks for this info.If it is not too much work, just wondering if you could make a rough estimate or compute an average for the *total*memory* in use = (size of physical RAM in use by synthseg + size of all swap files resident on disk used by synthseg).- R.On Aug 10, 2023, at 16:08, Matthew Lynch <matthewl077(a)gmail.com> wrote:        External Email - Use Caution        Here is some additional follow up.  I was able to get recon-all-clinical working in Ubuntu in WSL on a 16 Gb machine by increasing the swap and memory allowed in WSL..  This is done through the .wslconfig file which is located in the %USERPROFILE% folder (e.g. C:\Users\username\).  I had to specify a swap size of 32 Gb and also specify that WSL is allowed to use 32 Gb (even though the system only has 16 Gb -- it will use swap space).Here is the .wslconfig file I used:-----[wsl2]# Limits VM memory to use no more than x GB, this can be set as whole numbers using GB or MB# This must be set to 32 Gb or so to accomodate recon-all-clinical# If you set a 32 Gb swap but not 32 Gb memory allowance, WSL will stop at the memory limit and not use swapmemory=32GB # Sets amount of swap storage space to 8GB, default is 25% of available RAMswap=32GB# Sets swapfile path location, default is %USERPROFILE%\AppData\Local\Temp\swap.vhdx# I believe the double backslash is necessaryswapfile=P:\\Users\\username\\WSL\\wsl-swap.vhdx------For information on the .wslconfig file, see: MailScanner has detected a possible fraud attempt from "secure-web..cisco.com" claiming to be https://secure-web.cisco.com/19DCKWC0AnWOY-AFXDoqJLBE2tTUpB9JfKhrDV… Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch <matthewl077(a)gmail.com> wrote:I was able to get recon-all-clinical working with 16 Gb computer.I thought the problem might be Windows hogging memory, so I created a live persistent USB install of lubuntu, using lubuntu 22 as a low resource distro in order to minimize memory usage, and installed freesurfer 7.4.0.  Even with initial memory usage on 1Gb on lubuntu, synthseg still failed with out of memory error with 8 Gb swap file.  I watched the swap memory fill up and then process was killed.I added 16Gb swap using the following instructions, for a total swap space of 24 Gb + 16 Gb memory:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1kRX3xVbTiZ9JT54ixRH2s2lX2HsDjAcrgZSns… worked.On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch <matthewl077(a)gmail.com> wrote:I do not have access to a computer with more RAM.  I can run recon-all with 1mm T1 images without any problems.  How much RAM would recon-all-clinical be expected to need?  Does it require less RAM if it uses the GPU instead of CPU?  On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Can you try it on a computer with more ram?  From: freesurfer-bounces@nmr..mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Matthew LynchSent: Thursday, July 13, 2023 1:55 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all-clinical out of memory error         External Email - Use Caution        I am having trouble running the new recon-all-clinical module.  I input 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be an out of memory error.  I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a computer with 16 Gb RAM.   Can anyone provide any thoughts on how to correct this?  Thanks in advance!  Here is the command: recon-all-clinical.sh ./T1AX5MM/119 fsclin 1  here is the error output: SynthSeg-robust 2.0using CPU, hiding all CUDA_VISIBLE_DEVICESusing 1 threadpredicting 1/1the following problem occured with image /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :Traceback (most recent call last):  File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in predict    post_patch_segmentation, post_patch_parcellation, qc_score = net.predict([image, shape_input])  File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 70, in error_handler    raise e.with_traceback(filtered_tb) from None  File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/tensorflow/python/eager/execute.py", line 52, in quick_execute    tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name,tensorflow.python.framework.errors_impl.ResourceExhaustedError: Graph execution error:Detected at node 'model_5/unet_parc_merge_8/concat' defined at (most recent call last):    File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 2642, in <module>      main()    File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 162, in main      predict(    File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in predict      post_patch_segmentation, post_patch_parcellation, qc_score = net.predict([image, shape_input])    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler      return fn(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2382, in predict      tmp_batch_outputs = self.predict_function(iterator)    File "/usr/local/freesurfer/7.4.0/python/lib/python3..8/site-packages/keras/engine/training.py", line 2169, in predict_function      return step_function(self, iterator)    File "/usr/local/freesurfer/7.4..0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2155, in step_function      outputs = model.distribute_strategy..run(run_step, args=(data,))    File "/usr/local/freesurfer/7.4..0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2143, in run_step      outputs = model.predict_step(data)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 2111, in predict_step      return self(x, training=False)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler      return fn(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py", line 558, in __call__      return super().__call__(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler      return fn(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__      outputs = call_fn(inputs, *args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler      return fn(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3..8/site-packages/keras/engine/functional..py", line 512, in call      return self._run_internal_graph(inputs, training=training, mask=mask)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py", line 669, in _run_internal_graph      outputs = node.layer(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler      return fn(*args, **kwargs)    File "/usr/local/freesurfer/7.4..0/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 1145, in __call__      outputs = call_fn(inputs, *args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler      return fn(*args, **kwargs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/layers/merging/base_merge.py", line 196, in call      return self._merge_function(inputs)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/layers/merging/concatenate.py", line 134, in _merge_function      return backend.concatenate(inputs, axis=self..axis)    File "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/backend.py", line 3581, in concatenate      return tf.concat([to_dense(x) for x in tensors], axis)Node: 'model_5/unet_parc_merge_8/concat'OOM when allocating tensor with shape[1,256,256,160,72] and type float on /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu         [[{{node model_5/unet_parc_merge_8/concat}}]]Hint: If you want to see a list of allocated tensors when OOM happens, add report_tensor_allocations_upon_oom to RunOptions for current allocation info.. This isn't available when running in Eager mode. [Op:__inference_predict_function_10473]resuming program execution _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/19kJTXmqHxdv9FUBUNscNtwPP-oousx8-y3qBf… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1d3qoA8jkiEujxcb_3JFzMd8QkU88j8PgCllAB… has detected a possible fraud attempt from "secure-web..cisco.com" claiming to be https://secure-web.cisco.com/1vjDVAlnQcZSScJlFw_X3CoNDMlcbgzI5NuM-L…; ._______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BbIXKRtCoHVre8VbJJhEr8xJ7iyvoJdAeHrQy… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Postdoctoral Research Fellow position - Boston University
by Wen Wen 25 Aug '23

25 Aug '23

External Email - Use Caution A Postdoctoral Research Fellow position is available in the laboratory of Associate Professor Rob Reinhart, in the Department of Psychological & Brain Sciences, Boston University. This position is funded by an NIH R01 grant from the National Institute of Aging. The project focuses on using electrophysiology and noninvasive neuromodulation to investigate (and potentially rectify) the neural oscillatory mechanisms of various memory systems in people with Mild Cognitive Impairment and Alzheimer's Disease. Representative papers Grover S, Wen W, Viswanathan V, Gill CT, Reinhart RMG (2022). Long-lasting, dissociable improvements in working memory and long-term memory in older adults with repetitive neuromodulation. *Nature Neuroscience* 25(9):1237-1246. Reinhart RMG and Nguyen JA (2019). Working memory revived in older adults by synchronizing rhythmic brain circuits. *Nature Neuroscience* 22(5):820-827. Candidates should have a PhD with expertise in one or more of the following areas: memory, EEG, computational modeling, fMRI, brain stimulation. Candidates should be fluent and versatile at coding in MATLAB and/or Python. We seek individuals who enjoy working on challenging problems with enthusiasm and creative rigor in a collaborative team-based environment. The postdoctoral fellow will also have opportunities to pursue collaborative projects involving reward processing, decision-making, OCD, schizophrenia, and consciousness. This position is open to both US citizens and foreign nationals. Start date is flexible. For more information about the lab, see: https://secure-web.cisco.com/1yqENug4Ez6bVfjha-o7k7n2lWfBus_qH-TPnnmUYSI_xC… Neuro Science Labs | Reinhart Labs | Boston, MA <https://secure-web.cisco.com/1yqENug4Ez6bVfjha-o7k7n2lWfBus_qH-TPnnmUYSI_xC…> Reinhart Labs is a cutting-edge neuro science research facility that employs the top neuroscientists in the world. reinhartlab.org Applicants should send a short cover letter, CV, and names of three references to rmgr(a)bu.edu. Thanks!

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Thalamus Anatomy and Connectomics Conference (October 30 – 31 in Tübingen)
by vin 25 Aug '23

25 Aug '23

External Email - Use Caution Dear Esteemed Researchers, Greetings! We are thrilled to invite you to the upcoming Thalamus Anatomy and Connectomics Conference, funded by the SPP-2041. The conference aims to dive deep into the fascinating and intricate thalamus. This event promises to be an enriching experience, fostering discussions and collaborations. 📅 Date: October 30 – 31, 2023 📍 Location: Max Planck Campus Tübingen, Germany *Registration:* The conference is free of charge. The onsite-registration is limited to approx. 50 participants. Please apply. *https://secure-web.cisco.com/1853qzKEycyxgei1Y43JRjDcZ5DToj6Mtlldfz3vMRmwBXnVAM6zrHW0ibdr-HX-psI3qbmQdD4ZlCRhxetLx8Sm9RNT1139z-GK4j8IuEk-kImJ_g1klArfhi8pyACkxR-hC2fboI1zJCH18btzC0BxAq2PxbYjsGlZqNNZF7MxmksC9G-gLCjppNanWfZgj3msAqMShQdb1tZphRujpYAVQHTGbEWGl5lvHZDsvdgAaYcicR8H7Vn0-eDYDwoXmhYPjw7mq8RUBl1NMeAI7iyMjDvUUv84-Tp4fg1CRIZwLO7hGfmbQ9OSm7hb_JcjDWHyVzrooFE_cF6jBeUZzrQ/https%3A%2F%2Fwww.tuebingen.mpg.de%2Fthalamus <https://secure-web.cisco.com/1853qzKEycyxgei1Y43JRjDcZ5DToj6Mtlldfz3vMRmwBX…>* We look forward to welcoming you to an intellectually stimulating and inspiring conference. Kindest regards, Organizing Team Thalamus Anatomy and Connectomics Conference Vinod Kumar Max Planck Institute for Biological Cybernetics Tuebingen, Germany.

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Request for pass code
by Anna-Liisa Iive Sepp 24 Aug '23

24 Aug '23

External Email - Use Caution Dear Free Surfer expert, Would you please send me the pass code for opening the .ova Ubuntu VM image with FS 7.2.0? The 7z file cannot be extracted without it. Appreciate the help, Anna -- Dept. Biomedical Engineering at Columbia University

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Easyreg > cortical parcels missing after SynthSeg with --parc option ?
by Eric BARDINET 24 Aug '23

24 Aug '23

External Email - Use Caution Hello Freesurfer Developpers, I attempted to run mri_easyreg (Freesurfer 7.4) between two MP2RAGE UNI images (acquired on a SIEMENS PRISMA 3T). First, I did not include segmentations, as I understood that EasyReg would run it for me. But it didn't. I don't know why. Then I first ran mri_synthseg with the --parc option on the two images. I checked the results, and saw cortical labels on both hemispheres. But when I ran again mri-easyreg adding these images (--ref_seg --flo_reg), I get again the > no cortical parcels. What did I do wong? Any hints? Thanks in advance for your help. Best, Eric

2 5

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

3 2

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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