Freesurfer March 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
61 discussions

2 PhD positions in layer-fMRI of high-level cognition at the Max Planck Institute for Biological Cybernetics in Tübingen , Germany
by Romy Lorenz 05 Mar '24

05 Mar '24

External Email - Use Caution The newly established Cognitive Neuroscience & Neurotechnology group led by Dr. Romy Lorenz is looking for two enthusiastic PhD students (m/f/d) to join our growing team at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany. Our lab focuses on advancing our understanding of the frontoparietal brain network mechanisms that underpin high-level cognition and adaptive behaviour. For this, we pursue an interdisciplinary research programme that allows studying this brain system at multiple levels of granularity. Our methodology involves subject-specific brain-computer interface technology, fMRI at 3T and ultrahigh (i.e., 7T and 9.4T) magnetic field strengths (for resolving cortical layers), EEG, non-invasive brain stimulation as well as machine learning. You can find out more about our work at: https://secure-web.cisco.com/1DTFYMuBJpaThDmnsZx8BTzF2AVMPT_WTXTuNSPnfZdIr4… We are seeking two ambitious PhD students who will work on the exciting field of ultrahigh resolution fMRI that allows to investigate the human cortex at the scale of layers and columns. The ideal candidates should have a master’s degree in cognitive (neuro)science, psychology, computer science, biomedical or electrical engineering, physics, or related disciplines. A strong background in fMRI data analysis (e.g., FSL, Freesurfer, ANTS) and very good programming skills in Bash on Linux, Matlab and/or Python are required. Prior experience in MRI data acquisition and experience with ultrahigh resolution fMRI (e.g., at 7T) is desirable but not necessary. Equally, experience with machine learning-methods, code sharing platforms (e.g. GitHub) and high-performance computing clusters are highly desirable. The Max Planck Institute for Biological Cybernetics offers a world-leading research environment with access to the latest cutting-edge MRI hardware (including a Siemens 9.4T and Prisma 3T for humans as well as a 14.2T small animal system) and other excellent research facilities (EEG, eye-tracking, fMRI-TMS). The PhD student will receive generous support for professional travel and research needs (~2500€/year). Additionally, the student will have the opportunity to become part of the Graduate Training Centre of Neuroscience that provides training courses, summer schools and conferences to further educate doctoral students. Further, the Institute is part of the TübingenNeuroCampus (with more than 100 active groups), offering a vibrant community of international researchers and enriching environment of collaboration. The position is available from May 2024 on and remains open until filled. The salary is paid in accordance with the collective agreement for the public sector (65% TVL-E13, amounting to ~2000€ net per month). For more details about the two advertised PhD positions and how to apply, please see: https://secure-web.cisco.com/1HBQhEBJ4wZ9IS2zpkXMkuIwzjxkS5db6bDYMd0qWJKNhn… Dr. Romy Lorenz Max Planck Research Group Leader Research Group Cognitive Neuroscience & Neurotechnology Max Planck Institute for Biological Cybernetics Tübingen, Germany romy.lorenz(a)tuebingen.mpg.de http://secure-web.cisco.com/1-aUWpt7JdIbcqswpTsDWYsyChmNmUZeOBqxYreWQN848To…

1 0

Assistance Request: Issue with Merging .mgh Files in Ubuntu18
by Rosie 05 Mar '24

05 Mar '24

External Email - Use Caution Dear Support Team, I'm reaching out for assistance with merging two .mgh files. As I try to generate a surface mapping for all subjects, I merged all volume files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. But the value of each voxel seems to be thrown out. Because I found the max value of .mgh is not the same as .nii file. I guess I should merge files of all subject in mgh format to maintain the number of valid subjects, but it seems to be a volume encoded surface file format. So I don't know how to merge them. I'm working on Ubuntu18. I would be very grateful for your assistance. Best, Rosie

2 2

Re: [Freesurfer] recon-all-clinical synthseg error
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution  It could help to know what OS version and what Freesurfer version you are running.  From your path /usr/local/freesurfer it looks like you are running a Freesurfer release, e.g., 7.4.1. - R. On Feb 25, 2024, at 21:45, Agata Wolna <awolna(a)mit.edu> wrote:        External Email - Use Caution        Hi!I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message:the following problem occured with image [mypath]/mri/native.mgz :Traceback (most recent call last):  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in predict    image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i],  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in preprocess    im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in get_volume_info    im, aff, header = load_volume(path_volume, im_only=False)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in load_volume    x = nib.load(path_volume)  File "/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py", line 110, in load    img = image_klass.from_filename(filename, **kwargs)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py", line 503, in from_filename    return klass.from_file_map(file_map, mmap=mmap, keep_file_open=keep_file_open)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 526, in from_file_map    header = klass.header_class.from_fileobj(mghf)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 171, in from_fileobj    + int(klass._data_type_codes.bytespervox[tp]) * np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some problems occured for the following inputs (see corresponding errors above):[mypath]/mri/native.mgzError in SynthSegBest,Agata_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

mris_convert reading surf.gii files?
by Westin, Karin 04 Mar '24

04 Mar '24

External Email - Use Caution Hi I'm trying to create an .annot file from a label.gii file using an HCP fsavarage.surf.gii file (eg mris_convert --annot my_label.label.gii fsaverage_template.L.surf.gii lh.my_annot.annot). However I keep getting the error ** failed to open GIFTI XML file 'fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' mrisReadGIFTIdanum: gifti_read_image() returned NULL Is there a better way to read/open CIFTI files using mris_convert? Best and thanks Karin

2 9

Re: [Freesurfer] Subject does not have a bstampfile
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution   Let me add that it will not work to use shared mount point from the Windows filesystem as you list below, /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri - for your SUBJECTS_DIR when running a recon-all command.  The command will fail because the Windows file system does not support soft-links.   Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS image running freesurfer.  You could however copy the files from that mount point to create another SUBJECTS_DIR somewhere inside your Linux image, e.g., under your home directory in linux. .... in your linux terminal window ... $ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG . - R. On Jan 8, 2024, at 16:10, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:You need to specify the input files to process. Here is the wiki page for recon-all -  https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-----Original Message-----From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Joanna KidonSent: Monday, January 8, 2024 3:33 PMTo: freesurfer(a)nmr.mgh.harvard.eduSubject: [Freesurfer] Subject does not have a bstampfile       External Email - Use Caution        Hello FreeSurfer Developers,I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQR… I get the following error when I run the recon-all -all -s command:Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txtSubject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version DoneINFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux#--------------------------------------------#@# MotionCor Sun Jan  7 20:48:46 CET 2024ERROR: no run data found in/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.If you have a second run of data call it 002.mgz, etc.See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwu… LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan  7 20:48:46 CET 2024I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use.Best regards,Joanna------------------------------------------------------------------------------------dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w KatowicachPhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

Longitudinal Freesurfer in the presence of large tissue defects
by Philip P 04 Mar '24

04 Mar '24

External Email - Use Caution Dear Freesurfer Developers, I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5…) as well as related code on Github (https://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs…) I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version? Thanks already in advance! Best Philip

2 4

control points do not help with pial and white matter edits to frontal areas with atrophy
by Lydia Chung 03 Mar '24

03 Mar '24

External Email - Use Caution Hi Freesurfer Team, I have a pt with significant atrophy in the right orbitofrontal/rostral middle frontal area (see screenshots below). I have added several control points but this has not been successful, as there is not much white matter in that area to begin with. Do you have recommendations for dealing with this type of issue? Do you typically leave as is or discard the subject entirely? Thanks for your help, Lydia [image: image.png] [image: image.png] [image: image.png] [image: image.png] -- Lydia Wu-Chung, M.A. Doctoral candidate BMED Lab Department of Psychological Sciences Rice University 6500 Main St - MS201 Houston, TX 77030 Lab Phone: 713-348-8126 Email: lydia.wu(a)rice.edu <lw50(a)rice.edu> *Confidentiality Text:* The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

2 2

Re: [Freesurfer] Freesurfer white matter overestimated
by Douglas N. Greve 03 Mar '24

03 Mar '24

Can you include an image with and without the surfaces? Make sure to include slices where you think the white surface extends too far. On 2/28/2024 9:13 AM, Luisa Klahn wrote: > > External Email - Use Caution > > Dear Douglas, > Please find the nu.mgz screenshot attached. > Best, > Luisa > > > ------------------------------------------------------------------------ > *Von:* Luisa Klahn <luisa.klahn(a)gu.se> > *Gesendet:* Montag, 26. Februar 2024 08:53 > *An:* dgreve(a)mgh.harvard.edu <dgreve(a)mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Freesurfer white matter overestimated > Dear Douglas, > Please find attached the pictures for the following issue: > I am processing structural data from a 3T scanner using Freesurfer > version 7.3.2. For some subjects, the grey matter looks very thin, and > the white matter looks overestimated. I'll attach screenshots of the > brainmask, wm mask, and T1 including wm and pial surface lines. > I have tried to set control points into the wm but this did not change > the results. > Does anyone have an idea? Would it be possible to change the intensity > settings in the recon-all command? > > Thanks for helping! > Best, > Luisa

1 0

Is the slice delay of each slice needed for slice time correction with preprocess-sess?
by Maria Hakonen 03 Mar '24

03 Mar '24

External Email - Use Caution Dear all, Have I understood correctly that the slice delay of each slice is not needed when performing slice time correction with preprocess-sess? I am processing an open OASIS fMRI dataset. The dataset has fMRI data in nifti format and JSON files that contain information about the data. In the instructions they say: "Slice timing is included in the JSON when available. Some original DICOM files did not have slice timing info. When slice timing information is unavailable use the ratio TR/#slices." The data is collected with a Siemens scanner. If the slice timing is available it seems to be interleaved: "SliceTiming": [ 1.1025, 0, 1.165, 0.059999999999999998, 1.2250000000000001, 0.1225, 1.2875000000000001, 0.1825, 1.3474999999999999, 0.245, 1.4099999999999999, 0.30499999999999999, 1.47, 0.36749999999999999, 1.5325, 0.42749999999999999, 1.595, 0.48999999999999999, 1.655, 0.55000000000000004, 1.7175, Could I just run slice time correction with the siemens option? Best regards, Maria

2 1

Vertex / voxel lesion symptom mapping
by Martin Juneja 03 Mar '24

03 Mar '24

External Email - Use Caution Greetings FreeSurfer community, I was just wondering if it's possible to perform vertex/voxel lesion symptom mapping (VLSM) using FreeSurfer? In other words, I would like to assess the impact of lesion topography (of course, heterogenous locations across patients) on neurocognitive function in brain tumor patients. I would greatly appreciate any help/response. Thanks!

2 9

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 2024