Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

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

1 0

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

1 0

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

2 3

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.

4 12

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

1 0

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

2 3

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

1 0

Re: [Freesurfer] Noticeable artifacts running mri_synthsr
by Matias Grynberg Portnoy 21 Mar '23

21 Mar '23

External Email - Use Caution Hi, > I'm a student researcher at LIAA <https://secure-web.cisco.com/1pfeP0epsm_y7bnsj34ME3qFtKtcJHnsPc9xhFQXeP1DZj…> under Diego > Fernandez Slezak. I've been trying to run mri_synthsr under multiple > resolutions but seem to get very noticeable artifacts even at higher > resolutions. Here is an example output after running mri_synthsr: > [image: image.png] > > The input image used is 160x256x256 and is attached in this email. > The command used to generate this output is > mri_synthsr --i <input file> --o <output file> > Any guidance or explanation for these artifacts would be greatly > appreciated. > Thanks! > Matias Grynberg Portnoy >

1 0

mri_synthsr with CT images
by Gonzalo Rojas Costa 20 Mar '23

20 Mar '23

External Email - Use Caution Dear Juan: I tested mri_synthsr using three different CT images with the threshold (80 value) that you told me some days ago. The first works ok, but with the other 2, I got the following error: developer@developer-VirtualBox:~$ mri_synthseg --i /home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? 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

2 1

Error When Running Recon-all- "Segmentation Fault"
by Annie Cooper 17 Mar '23

17 Mar '23

External Email - Use Caution Hi there, I am currently trying to run recon-all using a supercomputer at my university and am running into more errors than usual. When trying to run recon-all from my terminal, I ran into this error message: [asurite@agave1:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/asurite/Desktop/subjects Actual FREESURFER_HOME /packages/freesurfer-5.0.0 Linux agave1.agave.rc.asu.edu 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux /home/asurite/Desktop/subjects/ATN001v1 mri_convert /home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz /home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz mri_convert /home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz /home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz Segmentation fault Linux agave1.agave.rc.asu.edu 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ATN001v1 exited with ERRORS at Fri Mar 17 10:44:47 MST 2023 Any tips on why I might be receiving a "Segmentation fault" when trying to run recon-all? I've tried utilizing the mail archive to find an answer and haven't found anything that helped. Thank you! Best, Annie

2 1

← Newer
1
...
4
5
6
7
8
9
10
...
16
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer March 2023