Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30067 discussions

T2 FLAIR images
by Alan Francis 11 Aug '23

11 Aug '23

External Email - Use Caution Good evening all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 #-------------------------------------------- #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.* Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023 -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Installation tensorflow: protobuf requires Python '>=3.7' but the running Python is 3.6.8
by Jong, J.J.A. (Joost) de 11 Aug '23

11 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I would like to run samseg with the lesion module, hence samseg is asking to install Tensorflow using the following command: fspython -m pip install tensorflow==1.13.1 However, when execute the command, I get the following error: protobuf requires Python '>=3.7' but the running Python is 3.6.8 The problem persists when create a conda environment and try to install tensorflow there. I cannot seem to work around this problem, as fspython version seems to be 3.6.8. Why does FreeSurfer come with a Python version that conflicts with a protobuf version required to install tensorflow 1.13.1? Looking forward to your ideas/suggestions! Best regards, Joost de Jong Maastricht UMC+, The Netherlands FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Platform: CentOS Stream release 8 uname -a Linux radstation27.prd.corp 4.18.0-408.el8.x86_64 #1 SMP Mon Jul 18 17:42:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux ___________________________________________ Dr. Ir. Joost de Jong Senior Researcher Department of Radiology and Nuclear Medicine Visiting address: P. Debyelaan 25 | 6229 HX Maastricht Location: 4th floor, Room 4.H1.002 Postal address: Postbus 5800 | 6202 AZ Maastricht Maastricht UMC+ is a commercial name of azM, Chamber of Commerce no.:14124959 E e-mail address: j.dejong(a)mumc.nl | T +31 (0)43 38 74871 I http://secure-web.cisco.com/1TpM-pyj3jiJroVpfVeteQX14SCBG38j6yjGHU417S98I6E…<http://secure-web.cisco.com/1QKGqMChi0EuhQOKcM2h6MgZEowPxfNXfjZnF63KheUmVyX…> | http://secure-web.cisco.com/1OWWDYyMq9U6pHTPuxlmvarkGZroDverVyUC-msNiVy-hy6…<http://secure-web.cisco.com/1M1zOL-XvgT6vJF2ypQQAMXmM6wb82kiy6zYURLqTj3Gpad…> Follow us on Twitter<https://secure-web.cisco.com/1_xhiCTMlQOowUfDjYP14RRMxfPgUPnZOckHkdvvZtSD3l…>, Facebook<https://secure-web.cisco.com/1iZHQnMegyxXeanDho81aAKRFgmFeaf4vvT2rMQKdMjvAR…> and LinkedIn<http://secure-web.cisco.com/1YweY1DY29HflopcYocSi02MCLHl2sA6mPcIrSXx-EbYH1p…> ________________________________ This email and any attachments may contain confidential or privileged information and is intended for the addressee only. If you are not the intended recipient, please immediately notify us by email or telephone and delete the original email and attachments without using, disseminating or reproducing its contents to anyone other than the intended recipient. The Maastricht UMC+ shall not be liable for the incorrect or incomplete transmission of this email or any attachments, nor for unauthorized use by its employees. ________________________________

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Question about glmfit results and visualization by using Freeview
by inbal paran 11 Aug '23

11 Aug '23

External Email - Use Caution Dear FreeSurfer developers, Thank you for your response to my previous questions, I have a few more (I'm inexperienced with both Freesurfer and Linux): 1. Can I visualize my results after running mri_glmfit by using Freeview, such that the image shows cortical brain regions as well as subcortical brain regions on both hemispheres? If yes - how can I do that? 2. Is there a text file of the glmfit results that includes the correlation parameters, cluster size, significance/p-values? If yes - where can I find it? If not - how can I generate one? Thank you very much Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1YZJEd4xAGXQnv0pIXxLgi_JVIUWn7hQJs_Lvjrak6I2_f9…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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RA Position for Human Intracranial EEG Lab
by Winfield, Jalen 11 Aug '23

11 Aug '23

External Email - Use Caution Dear all, The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research - Hofstra Northwell School of Medicine in New York is looking for a research assistant with earliest start date in October 2023. The successful candidate will help with the lab's research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macro-scale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The responsibilities will include assisting with the collection and analysis of the aforementioned data, project management, assistance with grant applications and progress reports, help with analysis of neural and imaging data using existing scripts (Matlab, Python), further development of those scripts (depending on coding and signal processing proficiency), and helping to present lab findings at conferences and in journals. The relative weighting of responsibilities can be adjusted depending on the interest of the applicant. If there is interest, the RA will have a scientific project with dedicated time to work on. Past research assistants have presented their work at clinical and basic research conferences, co-authored publications, and are working on first-author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: - B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) - 2-year commitment - Experience with at least one programming language (MATLAB, R, or Python) Desirable: - Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data - Previous experience working with patients - Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation For more information about the position please send your CV along with your questions to Dr. Stephan Bickel (sbickel(a)northwell.edu<mailto:sbickel@northwell.edu>). Looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Fundi of Sulci
by Bluye Demessie 11 Aug '23

11 Aug '23

External Email - Use Caution Dear FreeSurfers, I am hoping to do an analysis of DTI metrics within the WM at the fundi of sulci. I am working with FreeSurfer v7.4.1 and want to use the ?h.curv to isolate the bottom of the sulcus based on the most positive curvature. Since ?h.curv is not a surface but rather a scalar field, is it possible to map ?h.curv to a volume in NIfTI format that can be overlayed on the original input NIFTI file with T1-weighted images used to produce the curvature map? Sincerely, Bluye

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mri_segstats --avgwf output question
by Lara Foland-Ross 11 Aug '23

11 Aug '23

External Email - Use Caution Hi there, I'm running mri_segstats on a collection of clusters resulting from a statistical analysis. My command line usage is as follows: mri_segstats --i lh.fwhm10.thickness.mgh --avgwf clusterAverages.txt --seg cache.th13abs.sig.ocn.mgh The results from my statistical analysis in the case of left hemisphere thickness shows 4 clusters that are significant in total, but the clusterAverages.txt contains a total of 5 mean thickness values per subject. This extra value is also reflected in other analyses in my dataset (for other hemisphere and for thickness, area and volume). Is the extra value listed per subject a global mean of some sort? If so, is it the first column of values or the last? Thank you, Lara

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Freesurfer Virtual Machine Password Request
by Gabriel Varga 11 Aug '23

11 Aug '23

External Email - Use Caution Hi, I'm looking to get the virtual machine password as I have been trying to get freesurfer to run on my windows computer. Please let me know if you need more information from me before sending, I'd be happy to provide it. Thank you! Regards, Gabriel Varga

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Password Required for Freesurfer
by Ameiy Acharya 11 Aug '23

11 Aug '23

External Email - Use Caution Respected Manager, I am Ameiy Acharya, an undergrad at VIT Chennai. I need to use the Freesurfer software for an academic project. I am using the Virtual Box Ubuntu implementation of Freesurfer on Windows. There is a password required to extract the Ubuntu image with Fressurfer pre-installed zip file. Additionally please provide the Password to open the image once loaded into the virtual box as well. User : developer Kindly provide both passwords at the earliest Thank You Regards Ameiy

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recon-all-clinical out of memory error
by Matthew Lynch 10 Aug '23

10 Aug '23

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 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 the 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

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Re: [Freesurfer] Setup Error with Freesurfer
by fsbuild 10 Aug '23

10 Aug '23

External Email - Use Caution  Please send along the link to the video you were using so we can check the instructions. The license is just a single file you obtain by filling out the web form, https://secure-web.cisco.com/1hH-N_TseC854TUMeRYHcee_7ls4Btyl5Nn0kU16Lq7t0_…  If the form submission is accepted, the screen will be refreshed and you will see a new page saying your license has been sent to the email address you specified. Assuming you are on a Mac reading your email, the default location for downloads is your Downloads folder.  When you receive that email, you can save the license.txt file attached to the email to the default location.  It will be saved to $HOME/Downloads which you can see in the Finder Window when you open your Downloads folder - or from the terminal. Open a new terminal window and check/setup the license.txt file, $ cd$ pwd/Users/<your userid> $ ls -l Downloads/license.txt-rw-r—r--@ 1 userid  group  71 Aug 10 12:53 Downloads/license..txt    <— your userid, group, date, etc. will differ Copy that to your home directory with this command (that is a space followed by a period at the end of the line).  Or you could move it in the Finder. $ cp -p -f  Downloads/license.txt .$ ls -l  license.txt-rw-r—r--@ 1 userid  group  71 Aug 10 12:53 license..txt    <—— your date, etc. output will differ The above only needs to be done once.  To tell freesurfer where to find the license file, you can use the environment variable FS_LICENSE.  You set that in your terminal session with the following (using the default zsh = bash compatible shell). $ export FS_LICENSE=$HOME/license.txt I’ll assume you used one to the .pkg installers we provide for the Mac releases, which you can download from https://secure-web.cisco.com/1W8vsqGghiuM0oaEbdbdwmxzEGH9qLKdqIXh…  If you downloaded the latest 7..4.1 installer, https://secure-web.cisco.com/1hOOmlU9howzc7Jw9g6LR2G-cR50ze… then freesurfer was installed under /Applications/freesurfer/7.4.1 You can navigate to /Applications/freesurfer in the Finder and see what your directory is there under Applications/freesurfer.  You will need to add what you find under /Applications/freesurfer to substitute for 7.4.1 in the example below if you did not install the 7.4.1 .pkg. Check our setup script is there in the installation$ ls  -l  /Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh-rwxr-xr-x  1 root  wheel  1350 Jun 14 00:09 /Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh Once you have verified the above path to the freesurfer installation, then setup the freesurfer environment with, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1     <— change 7.4.1 etc. to be what you installed if different$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni Try running freeview with no arguments and verify that it opens an empty window.  It should not crash given FS_LICENSE is set above. … check freeview is there ..$ which freeview/Applications/freesurfer/7.4.1/bin/freeview $ freeview… should open an empty window … then manually quit freeview … Try opening one of the example subject volume files $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz … and you should see freeview display some images. - R. On Aug 10, 2023, at 12:03, Aqeel Mohamed <aqeel.t.md(a)gmail.com> wrote:        External Email - Use Caution        Hello,I am a new Freesurfer user and am currently struggling to run the freeview software on my MacBook Pro Ventura 13.5 OSX.I was following the step-by-step guide video on the Freesurfer wiki, but when it came to opening the 'bert' file, freeview would immediately crash (details of the report below). I unfortunately am a bit inexperienced with computers so I am unsure what the report means so would greatly appreciate any insight you can provide! I am also struggling to create a .license folder via terminal for my license key. I had hunted through the archives of the mailing list and managed to find a pico command but it is not letting me save the folder so would appreciate some help with this too!Apologies for such trivial questions - greatly appreciate any help you can provide!Aqeel

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