Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Re: [Freesurfer] the virtual machine developer password RE: Password ubuntu password
by FS build 24 Mar '23

24 Mar '23

External Email - Use Caution Sent this again directly to your email. Please also check your spam/junk mail filters. - R. > On Mar 23, 2023, at 14:04, Zhao, Don <dzhao(a)messiah.edu> wrote: > > External Email - Use Caution > > The Freesurfer VirtualBox instructions state:“login as the user “developer” in the login menu. Get the password by sending an email request to the freesurfer help list.” > > Despite asking this question multiple times, I am still unsure of how to obtain the password. Can anyone provide assistance with this? > > Thank you in advance. > > Sincerely, > > Don > > From:Zhao, Don > Sent:Wednesday, March 22, 2023 2:00 PM > To:Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject:the virtual machine RE: Password ubuntu password > > “login as the user “developer” in the login menu. Get the password by sending an email request to the freesurfer help list.” > > Hi, freesurfer help list. > > May I have the password, please? > > Thanks, > > Don > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1-XqDz4WK1tf6mDhlS7ZpTZJj9SqZnaaQWC5dRd5x40Tn4…

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Password request for Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0 release installed
by Rato Mendes, Pedro Fernando 24 Mar '23

24 Mar '23

External Email - Use Caution Dear Sirs, Following the instructions on VM_67 FreeSurferWiki page, I kindly ask you to please send me a valid pass code for the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive. Thank you for your attention, best regards Pedro Rato-Mendes --*-- Pedro Rato-Mendes, PhD Technology Department CIEMAT - Ed.22 Avda. Complutense 40 28040 Madrid - Spain Tel: +34913466278 Fax: +34913466275

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Re: [Freesurfer] FreeSurfer Segmentation Fault
by FS build 23 Mar '23

23 Mar '23

External Email - Use Caution I setup the 7.3.2 release in an Ubuntu 20 VM by installing the .deb package available from under, https://secure-web.cisco.com/1Q2bcsIGqA45XXyvp1oUdk0FD9FaJp-NVNQeLjaHiqSpkZ… The tutorial data I tested is from 2020 (not 2019), but that might not matter for that file (whose date is from 2018). I also use some soft links from $HOME to point to the freesurfer distribution and the tutorial data subdirectory, but again don't see that should make a difference. But freeview does open that individual file in my VM setup. if you want to try the same copy of the tutorial data I used you can get it from https://secure-web.cisco.com/1p3t4GUS5V08DKAzGkEoAeSvD3K-WIb6nplLAYdQGXnfAh… You can see the terminal session in the attached screenshot, freeview_ub20,jpg If you did not use the .deb package for the install of 7.3.2, then I would try that. Otherwise there may be something going on with your shell environment. There may be more info listed about the crash in /var/log/messages if you look there just after the crash. - R.

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Re: [Freesurfer] Hippocampal subregions - FreeSurfer segmentation
by Iglesias Gonzalez, Juan E. 23 Mar '23

23 Mar '23

Dear Emily, These boundaries are mostly geometric and based on the atlas. For the atlas building: * the head/body boundary was place at the level of the uncal apex. * For the body/tail boundary, I’ll defer to Jean Augustinack (CCed) Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Merz,Emily" <Emily.Merz(a)colostate.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, March 23, 2023 at 12:18 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal subregions - FreeSurfer segmentation External Email - Use Caution What is the boundary FreeSurfer uses to distinguish between the hippocampal head and body? This may be for each subfield. In any case, if you could let me know the boundary, that would be great. Thanks, Emily Emily C. Merz, Ph.D. (she/her) Assistant Professor Department of Psychology Colorado State University 1876 Campus Delivery Fort Collins, CO 80523 (970) 491-2317

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mri_synthseg error...
by Gonzalo Rojas Costa 23 Mar '23

23 Mar '23

External Email - Use Caution Hi: I installed the 22 march freesurfer developer version. I test mri_synthseg with a CT image, but it shows me the following error: "mri_synthseg --i /home/developer/Documents/sub-0001/H2.nii.gz --o /home/developer/Documents/sub-0001 --cpu --ct Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/mri_synthseg", line 22, in <module> import tensorflow as tf File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/__init__.py", line 479, in <module> keras._load() File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/python/util/lazy_loader.py", line 45, in _load module = importlib.import_module(self.__name__) File "/usr/local/freesurfer/7-dev/python/lib/python3.8/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/__init__.py", line 25, in <module> from keras import models File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/models/__init__.py", line 18, in <module> from keras.engine.functional import Functional File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/engine/functional.py", line 25, in <module> from keras.engine import base_layer File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/engine/base_layer.py", line 43, in <module> from keras.mixed_precision import loss_scale_optimizer File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/mixed_precision/loss_scale_optimizer.py", line 20, in <module> from keras.optimizer_v2 import optimizer_v2 File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/keras/optimizer_v2/optimizer_v2.py", line 36, in <module> keras_optimizers_gauge = tf.__internal__.monitoring.BoolGauge( File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/python/eager/monitoring.py", line 360, in __init__ super(BoolGauge, self).__init__('BoolGauge', _bool_gauge_methods, File "/usr/local/freesurfer/7-dev/python/lib/python3.8/site-packages/tensorflow/python/eager/monitoring.py", line 135, in __init__ self._metric = self._metric_methods[self._label_length].create(*args) tensorflow.python.framework.errors_impl.AlreadyExistsError: Another metric with the same name already exists." Which could be the problem ? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

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mri_convert mosaic data
by John Anderson 23 Mar '23

23 Mar '23

External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D NIfTI file ,composed of all 64 dicoms, using the mri_convert. However, when I use the command mri_convert input_dicom output_nifti, the output does not seem right, as it only displays one slice in the sagittal and coronal views. Could you please provide guidance on how to properly convert these DICOM files using mri_convert? Thanks very much John

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FreeSurfer Segmentation Fault
by Bartlett, Rob 23 Mar '23

23 Mar '23

External Email - Use Caution Hi, I am using FreeSurfer 7.3.2 with Ubuntu 20.04.4 LTS. I have an issue where Freeview crashes with a segmentation fault when loading a .mgz volume file. The files I have been trying to open are part of the tutorial dataset. Build Stamp: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 Terminal Output: Segmentation fault Syslog Output: Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863337] ThreadIOWorker[390903]: segfault at ad0 ip 00005613a159eb5d sp 00007fb580f68d00 error 4 in freeview[5613a0ee8000+bc1000] Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863358] Code: ef c9 f2 0f 5c 14 24 66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 c9 48 8d 14 96 48 8d 0c 8e <f3> 0f 5a 09 f2 0f 58 4c > Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863380] ThreadIOWorker[390885]: segfault at fe1a641 ip 00005613a159eb5d sp 00007fb589f7ad00 error 4 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863393] Code: ef c9 f2 0f 5c 14 24 66 0f ef f6 85 d2 0f 48 d6 8d 75 ff 39 cd 0f 4e ce 48 8b 73 10 48 63 d2 48 63 c9 48 8d 14 96 48 8d 0c 8e <f3> 0f 5a 09 f2 0f 58 4c > Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863400] traps: ThreadIOWorker[390898] general protection fault ip:5613a159ebe0 sp:7fb58376dd00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863410] traps: ThreadIOWorker[390890] general protection fault ip:5613a159ebe0 sp:7fb587775d00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863450] traps: ThreadIOWorker[390901] general protection fault ip:5613a159eb5d sp:7fb581f6ad00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863478] traps: ThreadIOWorker[390875] general protection fault ip:5613a159eb5d sp:7fb58ef84d00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863499] traps: ThreadIOWorker[390905] general protection fault ip:5613a159eb5d sp:7fb57ff66d00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863542] traps: ThreadIOWorker[390884] general protection fault ip:5613a159eb5d sp:7fb58a77bd00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863566] traps: ThreadIOWorker[390886] general protection fault ip:5613a159ebe0 sp:7fb589779d00 error:0 Mar 21 10:29:12 mcrmgnc01 kernel: [11207764.863579] traps: ThreadIOWorker[390881] general protection fault ip:5613a159eb5d sp:7fb58bf7ed00 error:0 Kind regards, Rob Bartlett Research IT Officer University of Exeter http://secure-web.cisco.com/1ldWtsR_k8GujZ8y7If5rBkMRJurdJwyRqSfEIf5VZerYzR… Laver Building, North Park Road, Exeter, EX4 4QE [http://secure-web.cisco.com/119YVCp1hrsEYkFhq1AwKWgmIcpNnRFPYcQjZ0-xjjxoXAf…] This email and any attachment may contain information that is confidential, privileged, or subject to copyright, and which may be exempt from disclosure under applicable legislation. It is intended for the addressee only. If you received this message in error, please let me know and delete the email and any attachments immediately. The University will not accept responsibility for the accuracy/completeness of this email and its attachments.

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Hippocampal subregions - FreeSurfer segmentation
by Merz,Emily 23 Mar '23

23 Mar '23

External Email - Use Caution What is the boundary FreeSurfer uses to distinguish between the hippocampal head and body? This may be for each subfield. In any case, if you could let me know the boundary, that would be great. Thanks, Emily Emily C. Merz, Ph.D. (she/her) Assistant Professor Department of Psychology Colorado State University 1876 Campus Delivery Fort Collins, CO 80523 (970) 491-2317

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Flipping Thickness Matrices
by Anam Anzak 22 Mar '23

22 Mar '23

External Email - Use Caution Dear FreeSurfer Community, Has anyone had any success with solving the below problem: I am dealing with brain lesions which may present on the left or right hemisphere of the brain. 1. I wish to 'FLIP' RIGHT sided hemispheres (which contain lesions) to the LEFT side, so I ultimately can collate all my data and analyse brain hemispheres that are IPSILATERAL or CONTRALATERAL to the side of the brain lesion. 2. When I use the Flip function below, the matrix generated seems to be correct, HOWEVER the subsequent IMAGE generated from the matrix, appears incorrect (it is not at all a mirror image of the original image). 3. NOTE: My matrices include a Lesion Mask and a Medial Wall Mask (I am interested in examining Cortical Thickness values of all the cortex EXCEPT the lesion and medial wall (tentorium and ventricles etc). Here are the commands used, for eg. 'subject 1': %% 4b. Load the binary Lesion masks RIGHT right_lesion_filelist = strcat(P, '/Oedema_masks_bin/', Imaging_Code, '_rh_fsaverage5_bin.mgh'); % load RIGHT lesion masks into a matrix right_lesions = SurfStatReadData([right_lesion_filelist]); right_lesions = ~right_lesions; % create a left hemisphere matrix filled with 1s left_hemisphere = ones(17,10242) % concatenate horizontally lesions masks (L) with right hemisphere matrix fullbrain_with_right_lesions = horzcat(left_hemisphere, right_lesions) % create medial wall mask for all subjects r_whole_mask = repmat(mask, 17, 1) % add the medial wall mask on the lesion masks fullbrain_lesion_medialwall = fullbrain_with_right_lesions.*r_whole_mask % apply matrix with lesion & medial wall to the thickness values T_right = fullbrain_lesion_medialwall .* T_rightlesion %% Flip the Right sided images to the left % reverse the element in each row subject1 = T_right(1,:) SurfStatView(subject1, SP) SP = SurfStatAvSurf({[P '/fsaverage5/surf/rh.pial'],[P '/fsaverage5/surf/lh.pial']}) subject1_flipped = fliplr(subject1) SurfStatView(subject1_flipped, SP) mirror_image = fliplr(T_right) SurfStatView(mirror_image(1,:), SP) Any thoughts would be very much appreciated! Kind regards Anam Miss Anam Anzak MBBS PhD MRCS PGCCE NIHR Clinical Lecturer (Neurosurgery) Specialty Registrar in Neurosurgery, London deanery

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Open Postdoctoral Positions in the Neuroscience of Meditation at Harvard/MGH
by Eckman, Megan 22 Mar '23

22 Mar '23

Dear Colleagues, Research Fellow/postdoctoral positions are available in the Meditation Research Program at Harvard Medical School and Mass General in Boston, MA. The successful candidate(s) will develop the neuroscience of advanced meditation using cutting-edge neuroimaging/electrophysiology. Please see the full description and instructions for applying here<https://meditation.mgh.harvard.edu/people_subpages/HarvardMGH_MeditationRes…>. Please feel free to forward this announcement to anyone who may be interested. Kind regards, Megan Megan Eckman (she/her) Program Manager, Meditation Research Program, Massachusetts General Hospital Website: https://meditation.mgh.harvard.edu Email: meckman(a)mgh.harvard.edu<mailto:meckman@mgh.harvard.edu> Athinoula A. Martinos Center for Biomedical Imaging CNY Building #149 149 13th St., Charlestown, MA 02129-4522

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