Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Special image protocol
by mustafa amin 28 Mar '19

28 Mar '19

External Email - Use Caution Dear member, I am really new with this freesurfer, just need to ask 1 question. Is there a special image protocol before running the MRI and then upload it to freesurfer? Please share your thoughts. Thank you for your kind attention and cooperation. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

5 19

Protocol for MRI
by mustafa amin 28 Mar '19

28 Mar '19

External Email - Use Caution Hi Bruce/ Doug, This is the picture I got from the MRI operator. She needed to know that she had done the right thing about the MP-RAGE sequence. Is this the right protocol? Please share some thoughts. Thank you for your kind attention and cooperation. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

2 1

tract all prep error mv: cannot stat ?/project/3015068.01/sub030/dmri/dwi_orig_las.nii.gz?: No such file or directory
by Camerino, .I.L. (Ileana) 28 Mar '19

28 Mar '19

External Email - Use Caution Hallo, I wrote to the mailing list last Monday because after running tract-all prep I got the following error: segmentation fault (core dumped). I tried to run tract-all prep with more gb (50 gb). Now, I do not get anymore the tract-all.e file containing the message: segmentation fault (core dumped) but I get another error (see attachment). The tract-all.e is empty and the tract-all.o and .log give a more clear error. It says: "mv: cannot stat ?/project/3015068.01/ilecam/RUNDMC_dwi_2015/subset_declined_constant/test_tracula/freesurfer/tracula_out/sub030/sub030/dmri/dwi_orig_las.nii.gz?: No such file or directory Linux dccn-c029.dccn.nl 4.4.121-1.el7.elrepo.x86_64 #1 SMP Sun Mar 11 14:33:50 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at wo mrt 27 18:26:20 CET 2019" A bit earlier in the tract-all o file, it seems looking for this file but it also says: "INFO: input image orientation is LAS INFO: input image determinant is -15.625 than it will try to tranform dwi_orig.nii in LAS" It seems odd to me that the program is trying to tranform the dwi.nii in LAS orientation when it says that the file is already in LAS orientation. Maybe the first issue was insufficient memory. Now it cannot find this dwi_orig_file. Please, do you have any idea/suggestion about how to solve this error? Thank you in advance Cheers Ileana

1 0

Symposium on Advances in High-Field MRI in Montreal, right after ISMRM (fwd)
by Bruce Fischl 27 Mar '19

27 Mar '19

FYI ---------- Forwarded message ---------- Date: Thu, 28 Mar 2019 01:53:47 +0000 From: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Symposium on Advances in High-Field MRI in Montreal, right after ISMRM External Email - Use Caution Hi Bruce, I’d appreciate it if you could forward this message to the Free-Surfer email list. Thanks! Amir. From: Amir Shmuel, Dr. Subject: Symposium on Advances in High-Field MRI in Montreal, right after ISMRM Symposium Advances in High-Field Brain Imaging – celebrating the arrival of McGill’s 7T MRI May 17, 2019 The Neuro (MNI), Montreal, QC, Canada Program Co-Chairs: Richard Hoge, Amir Shmuel, Julien Doyon The McConnell Brain Imaging Centre will host a one-day scientific symposium to celebrate the arrival of our 7T MRI scanner. This symposium follows the ISMRM meeting in Montreal. Speakers Julien Cohen-Adad, University of Montreal, Canada Laurentius Huber, Maastricht University, The Netherlands Seong-Gi Kim, Sungkyunkwan University, Korea Silvia Mangia, University of Minnesota, USA Ravi Menon, The University of Western Ontario, Canada Karla Miller, University of Oxford, UK Bruce Pike, University of Calgary, Canada Jonathan Polimeni, Massachusetts General Hospital and Harvard Medical School, USA Amir Shmuel, McGill University, Canada Christina Triantafyllou, Siemens, Canada Kamil Ugurbil, University of Minnesota, USA Larry Wald, Massachusetts General Hospital and Harvard Medical School, USA Nikolaus Weiskopf, Max Planck Institute for Human Cognitive and Brain Sciences, Germany For more information: https://www.mcgill.ca/neuro/events/advances-high-field-brain-imaging-sympos… Student promo code for registration: https://www.mcgill.ca/neuro/events/advances-high-field-brain-imaging-sympos… Contact: Deborah Rashcovsky, Events Officer, 514 398-6047 deborah.rashcovsky(a)mcgill.ca cid:image006.jpg@01D3A4D6.9D165740

1 0

Questions regarding Hippocampal Subfields And Nuclei Of Amygdala module
by Jessica Bourgin 27 Mar '19

27 Mar '19

External Email - Use Caution Hi, I am interested in the Hippocampal Subfields And Nuclei Of Amygdala module and have a few questions regarding its functionalities. Regarding the segmentation of amygdala nuclei, you say that currently, "volumes of the nuclei must be interpreted with caution". What does it mean exactly ? Can these volumes be used for comparison between patients and controls, or must we wait for further test ? I would like to create masks from this module and use these masks in functional connectivity analysis (Conn toolbox). Is it possible and if so, how can I do that ? You mention that the freesurfer command "recon-all" must be used before the segmentation of the nuclei is performed. I tried this and recon-all took about 7 hours to compute on one subject. I plan to use this module on 150 subjects, so do you know if there is a way to speed up data processing ? Thanks in advance for your help. Best regards, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

1 0

*.dcm to *.mgz
by Z Hessam 27 Mar '19

27 Mar '19

External Email - Use Caution Hello FreeSurfer Developers, I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?

3 7

mri_binarize --replace
by Song, Da-Yea 27 Mar '19

27 Mar '19

External Email - Use Caution Hello, I have a set of binary mask files that I'm trying to assign different values to. Currently I'm doing: mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2 mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace -128 2 The problem I'm having is that the values (V1) for each binary mask is not constant. For example, for one participant the values may be -117 whereas the values are -128 for another participant. Is there a way to set a range for the --replace option so that I can loop it through the subjects rather than having to do this command for each one separately? Any suggestions would be greatly appreciated! Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 1

exact time of data acquisition per run
by Nasiriavanaki, Zahra 27 Mar '19

27 Mar '19

Dear Freesurfer experts Hi I am trying to extract the time of data acquisition for each run from the functional data and compare it with my paradigm files. I thought the numbers in DICOM file names (ie, MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent with the date and time of data acquisition. But they don not exactly match with my paradigm files. Do these numbers represent the exact time of data collection for each run? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

2 2

Trouble making ROI labels from .mgz file that has been converted from .nii.gz
by JD Knotts 27 Mar '19

27 Mar '19

External Email - Use Caution Hello FreeSurfer Developers, I am having difficulty trying to convert mrVista-defined ROIs in matlab into FreeSurfer label files. I'm starting with an atlas.mgz file (containing subject-specific visual ROIs based on the Kastner FreeSurfer atlas), and I should note that I can successfully make ROI .label files in FreeSurfer from this .mgz file using successive calls to mri_vol2surf and mri_cor2label. For reference, when I do this for the first Kastner ROI, the resulting label correctly has 1591 label voxels. However, part of my pipeline involves intersecting these ROIs with a localizer ROI that was defined in mrVista. To do this, I first convert the atlas.mgz file to .nii.gz using mri_convert as follows: mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 After intersecting with the localizer in matlab, when I save a new .nii.gz file, convert back to .mgz, and run mri_vol2surf and mri_cor2label, I get the following error in mri_cor2label: ERROR: found no voxels matching id 1. To try to keep this short... as a sanity check I tried simply converting the lh.atlas.nii.gz file that pops out of the mri_convert step above directly back into .mgz (without modifying the .nii.gz file at all): mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 When I run mri_vol2surf and mri_cor2label on the resulting lh.atlas_reconverted.mgz file, I don't get an error, but the resulting label file for the first Kastner ROI incorrectly finds 111 label voxels, none of which overlap with the correct 1591 label voxels above. So it appears that I'm making at least one mistake in the mri_convert step from nii.gz to .mgz above, but I'm struggling to figure out what it is. Any guidance on this would be greatly appreciated! Thank you for your time, JD Knotts 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OSX 10.11.6 3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached for example subject

1 0

Conversion of thalamic nuclei labels
by Valentina Mancini 27 Mar '19

27 Mar '19

External Email - Use Caution Dear all, I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got nice results with a good delineation of all the nuclei. Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to perform functional connectivity with cortical regions in SPM. Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the command "mri_convert .mgz .nii". However, the resulting labels of the thalamus have a different resolution and I cannot visualize anymore the different thalamic subnuclei but only the entire thalamus. Do you have any suggestion to convert thalamic labels into nifti without losing the different subnuclei? Do you think that the thalamic segmentation is accurate enough to be used to perform functional connectivity? Thank you and best regards, Valentina Mancini

4 9

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