Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30060 discussions

Questions about the different ways in which metrics such as the cortical surface area can be extracted in Freesurfer
by 1500787798 28 Aug '23

28 Aug '23

External Email - Use Caution Dear FreeSurfer developers,       When I extract the surface area of the brain regions corresponding to the DK atlas in fsaverage space with the following command, the corresponding DK atlas brain regions calculated after summation or averaging, whether using lh.area or lh.area.pial, do not match the values of the surface areas directly extracted from the lh.aparc.stats file. I'm curious to know why this is the cause?  mri_surf2surf --srcsubject $subject --sval area.pial --src_type curv \   --trgsubject fsaverage --trgsurfval $SUBJECTS_DIR/$subject/lh.area.pial.fsaverage.mgh --trg_type curv --hemi lh Best, Jinfeng Hou

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Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged
by Douglas N. Greve 28 Aug '23

28 Aug '23

External Email - Use Caution Sorry, I don't have your previous email so I don't know what the context is. Can you resend this email with the previous exchanges included at the bottom? Also, please remember to send to the FS list instead of us personally. thanks! doug On 8/24/2023 6:01 PM, Proulx, Jean Sebastien wrote: > Thanks for the suggestion! The two fov indeed don't align in freeview. > I played a little with the --no-resample option but did not acheive > what I wanted. > > Here I simplified the problem to two single-slice images (run1.nii.gz > and run2.nii.gz attached) acquired the same way (same resolution) but > in two different positions in scanner space. In freeview it looks like > this: > freeview anat.nii.gz run1.nii.gz run4.nii.gz > > > I need the fov to align, but the data to not change at all (because > the fov moved with the patient's head during the experiment). > > To get the transformation, I ran > tkregister2 --mov run4.nii.gz --targ run1.nii.gz --regheader --reg run4to1 > and clicked "save reg" without touching anything. It spits out the > following matrix > 0.99988 -0.01117 0.01053 -0.63259; > 0.01065 0.99879 0.04792 -0.70029; > -0.01105 -0.04780 0.99880 -3.93196; > 0.00000 0.00000 0.00000 1.00000; > Is this indeed the run4 to run1 transformation matrix? Do you know of > a way to get that transformation without user information? > > Then I thought > mri_vol2vol --mov run4.nii.gz --targ run1.nii.gz --reg run4to1 > --no-resample --o run4to1.nii.gz > would do the trick but no, the run1.nii.gz and run4to1.nii.gz don't > align, just like in the image above, as if the transformation is not > actually applied. > > Allowing resample > mri_vol2vol --mov run4.nii.gz --targ run1.nii.gz --reg run4to1 --o > run4to1.nii.gz > makes the two field of view align in freeview but the data is altered. > > It looks like the transformation is not actually applied so that only > the intersecting voxels are effectively resampled. > > There is no error message. > > I tried the dev environment and stable711. > > I tried renaming the run4to1 registration file to run4to1.lta and I > get the folloing error from mri_vol2vol: > regio_read_register: loading lta > error: Cannot allocate memory > error: LTAalloc(675792816): could not allocate xforms > > I tried renaming the run4to1 registration file to run4to1.xfm and > nothing changes (no error but the registration still does not seem to > be applied). > > Any idea what's going on? > > Thanks a lot for your help and > Good evening! > Sebastien

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Import Matlab SynthSeg labels to FS
by Haley O Higginbotham 28 Aug '23

28 Aug '23

External Email - Use Caution Hi, I experienced issues with segmentation (exclusion of large portion of cerebellum) and so used SynthSeg in Matlab (as the built-in mri_synthseg in freesurfer wasn’t working on my computer) to create the segmentation. Does anyone know how to import the resultant 3D categorical array containing the labels back into freesurfer (for the sake of further manipulating it in freeview and replacing the aseg file)? Best, Haley

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mri_watershed Error while running recon-all
by Iman Kianian 27 Aug '23

27 Aug '23

External Email - Use Caution Hi there, I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 samples as it is mentioned in the documentation (" https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2A…"). when I was trying to use the recon-all command, after almost 1 hour of processing I encountered this error: """ mri_watershed Error: GLOBAL region of the brain empty ! Command exited with non-zero status 1 """ I appreciate your time for helping me. Note that I attached the recon-all.log for your review if it is needed.

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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

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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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