Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

Two basic questions: brainmask file versions and qcache
by Harriott, Emily M 18 Jan '23

18 Jan '23

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all well. I have two relatively basic questions that I am hoping to get some help with. My basic planned processing pipeline is: Run initial recon-all with gcut and ws flags Edit white matter/pial voxels and add control points (as needed) Run second recon-all with autorecon2 and autorecon3 flags Run LGI I have two questions about this: When I run the initial recon-all, I end up with three versions of the brainmask within the /mri/ folder: brainmask.auto.mgz, brainmask.gcuts.mgz, brainmask.mgz. Which brainmask version do I edit, so that my edits are incorporated into the second recon-all run and thus the second attempt at wm/gm segmentation is better? When and with what command(s) do I use the qcache flag? I apologize that these are quite basic, but sincerely appreciate any input anyone might be able to provide. Thank you so very much in advance! All the best, Emily Harriott Doctoral student at Vanderbilt University

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Re: [Freesurfer] PetSurfer - MG coregister
by Marina Fernández 18 Jan '23

18 Jan '23

External Email - Use Caution Dear Rahul, I just used the wiki of the Freesurfer functions, the information is very complete. If you want to use Freesurfer, you can start by doing the cortical reconstruction process for each subject ( https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtmjwq2Q0VTCaZWdcX4QFapQPQO_Y7j…) and then prepare the maps to do the analysis that interests you. In the case of PET analysis, you can follow the steps explained on the PetSurfer wiki ( https://secure-web.cisco.com/1SUsUq0XwDtpjwx2dSpE1KOdwDPRl2MG5fyhegdBeDHaK3…) If you have any particular questions about feature options, you can search this list if other users have asked before. In case the question is not resolved, you can ask it here so that the experts can answer you. I hope it helps. Cheers, Marina.

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New Postdoc Position on Brain Connectivity at Karolinska Institute - Deadline 22/01/2023
by Joana Braga Pereira 17 Jan '23

17 Jan '23

External Email - Use Caution Dear all, We are looking for another new Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms and biofluid assays to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Associate Professor Joana B. Pereira and Assistant Professor/Neurologist Sara Garcia-Ptacek and it will involve analyzing the effects of different types of medication on brain connectivity in patients at different stages of Alzheimer's disease. The Postdoctoral fellow will work in the center of Stockholm together with 3 PhD students, 2 Postdocs and 4 affiliated members of Dr. Pereira's group. He/she will help collect data from patients at the local memory clinic using well-established and new imaging sequences as well as perform analyses using already acquired cross-sectional and longitudinal data. We work in a friendly and inclusive environment, where the future fellow will be involved in many projects, collaborate with group members on different studies, learn new skills, attend conferences, apply for grants and develop a wide network of international collaborations. The ideal candidate should have the following qualities: - A PhD in medicine, neuroimaging, computational science, physics, neuropsychology, statistics or a related field. - Experience in statistical techniques, programming, and scripting in MATLAB, STATA, Python, R or other softwares. - Experience with structural MRI, DTI, fMRI and/or EEG/MEG imaging analyses. - Experience with different softwares such as SPM, FSL, FreeSurfer, AFNI, etc. - Experience or interest in working with aging and/or neurodegenerative disorders, particularly Alzheimer’s and Parkinson’s diseases. - Good academic record with scientific publications in world-class journals. - Be independent and willing to supervise students. The Postdoctoral studies will be performed for 2 years, with possible extension for an additional year. To apply please go to: https://secure-web.cisco.com/1ck5sqkXIvnbFkdYGa5YGhpitAhn4cXIxrXSU25TPI75Bo… (Deadline: 22.Jan.2023) For further information or general inquiries, please contact Joana B. Pereira at joana.pereira(a)ki.se. Best wishes, Joana

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use specific tools from dev-version on cluster
by AmirHussein Abdolalizadeh 17 Jan '23

17 Jan '23

External Email - Use Caution Hi all, I am willing to use mri_synthseg and mri_easyreg which are available in the 7-dev version on a high-performance cluster. Is there a way to do it without installing the 7-dev version on it? I didn't have enough RAM space to do them on my local machine. Best, Amir

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VM file password
by Kern, Simon 17 Jan '23

17 Jan '23

External Email - Use Caution Dear Mailinglist, I would like to request the password for the vmware gz file. I was referred to this mailing list. Could you send me the password? I already have a license file. Best regards, Simon Kern -- [1570451663583] Simon Kern MSc Artificial Intelligence / BSc Cognitive Science PhD candidate Department of Clinical Psychology RG Psychology and Neurobiology of Sleep and Memory Central Institute of Mental Health J 5 · 68159 Mannheim, Germany Phone: + 49 17656774775 simon.kern(a)zi-mannheim.de<mailto:simon.kern@zi-mannheim.de> http://secure-web.cisco.com/1w78yI8LpZREd0df3OuMf1_mRT77p5wfwcmi6hOKVS__QLZ… <http://secure-web.cisco.com/1pn2Tt_MljUeP7ZoJC_PS4GMa9ssBkRA_00FpXOquRAeFk1…>Executive Board: Prof. Dr. Andreas Meyer-Lindenberg, Dr. Matthias Janta President of the Supervisory Board: Dr. Carsten Dose

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trac-all -prep early stage errors
by Simonas Jesmanas 14 Jan '23

14 Jan '23

External Email - Use Caution Hello everyone, I am having trouble getting past the very first stages of trac-all -prep. I am using FreeSurfer 7.3.2. I tried several workarounds based on previous answers to similar problems in this mailing list, but I am unsuccessful each time. First, when I try to run trac-all -prep without any configuration file, using only the defaults, it prints out an error: trac-all -prep -s sub-01 -i $SUBJECTS_DIR/raw/sub-01/dwi/1_0000.dcm ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction As I understand it, the default version of trac-all should assume default deb0=0, and not look for reverse-polarity images to do distortion correction for TOPUP. Then, I tried to perform the analysis using the configuration file and specify that I do not want to perform correction based on reverse-polarity images or phase maps (my data don't have these), by explicitly entering "set dob0 = 0". The problem persisted. I did what a previous user was told to do - set "pedir" and "epifactor" and "echospacing" manually. Then, I ran into the final error which I cannot overcome. No matter what I do, it ends in an error: mv: cannot stat '/home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz': No such file or directory It seems it cannot create this file. Earlier in the log there is also a previously mentioned error: INFO: input image orientation is LPS INFO: input image determinant is 6.49902 mri_convert -oni 128 -onj 128 -onk 60 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc 0 -21 7 -rt nearest /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig.1.nii.gz /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 128 -onj 128 -onk 60 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc 0 -21 7 -rt nearest /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig.1.nii.gz /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz mri_convert: directions must have non-zero magnitude; out_i_direction = (0, 0, 0) It appears to be a problem with converting into LAS. (Previously there was mention of there being a wrong "trac-preproc" file for runs with only 1 subject, but my problem remains when trying to run single and multiple subjects. I also tried to change my trac-preproc file to the versions from previous answers, with no luck). When I check the dmri folder the dwi_orig.1.bvals and dwi_orig.1.bvecs, and dwi_orig_las.1.bvals files contain correct values, but dwi_orig_las.1.bvecs contains only zeros. When I run mri_info on dwi_orig.1.nii.gz I get this: Volume information for sub-01/dmri/dwi_orig.1.nii.gz type: nii dimensions: 128 x 128 x 60 x 76 voxel sizes: 1.718750, 1.718750, 2.200000 type: SHORT (4) fov: 220.000 dof: 1 xstart: -110.0, xend: 110.0 ystart: -110.0, yend: 110.0 zstart: -66.0, zend: 66.0 TR: 7100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 76 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9959, y_r = -0.0243, z_r = -0.0868, c_r = -0.4050 : x_a = 0.0326, y_a = -0.9949, z_a = -0.0955, c_a = -21.6846 : x_s = -0.0841, y_s = -0.0979, z_s = 0.9916, c_s = 7.5075 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.7117 -0.0418 -0.1910 117.5550 0.0561 -1.7100 -0.2100 90.4641 -0.1445 -0.1683 2.1816 -37.9249 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 6.49902 ras to voxel transform: -0.5794 0.0190 -0.0489 64.5443 -0.0142 -0.5789 -0.0570 51.8698 -0.0395 -0.0434 0.4507 25.6592 0.0000 0.0000 0.0000 1.0000 "PhEncDir" shows UNKNOWN, but as I said, my config file contains "set pedir = (AP)". I also tried to do the analysis on FreeSurfer 7.2 and the develeopment version, but no luck. I would appreciate any input into how to solve this problem. Regards, SJ.

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Password for Virtual Box Installation
by Nathanial Osterhout 14 Jan '23

14 Jan '23

External Email - Use Caution Hello, I'm trying to install the Ubuntu image with Freesurfer preinstalled and it is asking for a password that I do not have. If I could get that passcode it would be greatly appreciated. Thanks

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DPABI V7.0 (together with DPABIFiber V1.0 and DPABISurf V2.0) were released!
by YAN Chao-Gan 13 Jan '23

13 Jan '23

External Email - Use Caution Dear Colleagues, We are pleased to announce the release of DPABI V7.0 (together with DPABIFiber V1.0 and DPABISurf V2.0)! New features of DPABI_V7.0_230110 (download at http://secure-web.cisco.com/1MWbt9_JkX0N-b69asiK-VJQRFqhpLp0G87vNiceDduCWos…, please also update the docker file by: docker pull cgyan/dpabi): 1. DPABIFiber 1.0. DPABIFiber is a fiber tractography analysis toolbox based on diffusion-weighted imaging (DWI), evolved from DPABI/DPABISurf/DPABINet/DPARSF, as easy-to-use as DPABI/DPABISurf/DPABINet/DPARSF. DPABIFiber is based on QSIPrep (Cieslak et al., 2021), MRtrix3 (Tournier et al., 2019), AFQ (Yeatman et al., 2012), fMRIPprep (Esteban et al., 2019), FreeSurfer (Tustison et al., 2014), ANTs (Avants et al., 2009), FSL (Jenkinson et al., 2012), SPM12 (Ashburner, 2012), dcm2niix (Li et al., 2016), PALM (Winkler et al., 2014), GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US), Docker (https://secure-web.cisco.com/17ehCqWSqC5O9OWmsiP3kcNkRtjCf5YhHTK1PkqFPhSBxX…) and DPABI (Yan et al., 2016). DPABIFiber provides a user-friendly graphical user interface (GUI) for pipeline DWI preprocessing, fiber tractography reconstruction, tract-based spatial statistics (TBSS) (Smith et al., 2006), automating fiber-tract quantification (AFQ) (Yeatman et al., 2012), structural connectome matrix analyses, seed-based structural connectivity analyses, and tract-weighted functional connectivity (TW-FC) (Calamante et al., 2013), while requires no programming/scripting skills from the users. Please see more details at: http://secure-web.cisco.com/191eSWJq5J2mXvcDTuor-octqxesBlW3Vt0UJRdwin_SJ5H… 2. DPABISurf 2.0. 2.1. Back engine updated to fMRIPrep V22.1.1, thus using FreeSurfer 7. 2.2. Added new mode: Calculate in Native Space. The processed results in native space also fits better to the TWFC analyses with DPABIFiber Pipeline. 2.3. Could segment subregions (Thalamus, Hippocampus, Amygdala and Brainstem) with FreeSurfer 7.3. 2.4. Could use FastSurfer instead of FreeSurfer to perform surface construction. 2.5. Could add wildcard strings in Defining ROIs. 2.6. Could select ROI Indices for specific ROI files. 2.7. Could delete first time points if start with BIDS. 2.8. Could detect TR if start with BIDS or fmriprep. 3. DPARSF 5.4. 3.1. Could add wildcard strings in Defining ROIs. 3.2. Could select ROI Indices for specific ROI files. 4. Statistical Analysis. Added option of TFCE2D for TBSS and surface-based statistical analysis. 5. y_ReadRPI. Fixed a bug in calculating new origin when flipping axes. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://secure-web.cisco.com/16hvP-ghq_sE1c4tXsx8w-XhbTldWtu6exnfeiytZLPgbhZ…>DPABI <http://secure-web.cisco.com/1jCKHgA8NXSGqW4lDQuwG8CucSBYRGBg2jcRHgYtoKEHArj…> <http://secure-web.cisco.com/16hvP-ghq_sE1c4tXsx8w-XhbTldWtu6exnfeiytZLPgbhZ…>, DPABISurf, <http://secure-web.cisco.com/1sJPlgiRblAVDfpXlj7NZDMfOf3mqEzR60JpsgQt-FoqFe6…>DPARSF <http://secure-web.cisco.com/16hvP-ghq_sE1c4tXsx8w-XhbTldWtu6exnfeiytZLPgbhZ…>, and The R-fMRI Network <http://secure-web.cisco.com/19iEX_xUFSFV7wxVEqtfm12UsAKuD8LolO8LKu_yHPci10T…> ( RFMRI.ORG <http://secure-web.cisco.com/18ZTBBg5lvUCnEvq1vFYhIXYA5uKoj5z3G0wX4UmLvcoPXz…>) http://secure-web.cisco.com/18FHUKDNlGFpvBUngijkF-Gpprt7iKKJGghh_O1hHHNTsq4… http://secure-web.cisco.com/1MsCgxu_df_Sr8z23NMTTFgBgNKsmGNX88SW38pZvgYuBzW…

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Hippocampal/Amygdala subfield segmentation error - Anterior Amygdala Area missing in FreeView
by Sarah Skinner 13 Jan '23

13 Jan '23

External Email - Use Caution Hi FreeSurfer Experts, I'm attempting to QC the hippocampal/amygdala segmentation in FreeView. When looking at ?h.hippoAmygLabels-T1.v21.FS60.mgz I can see that a few subjects are either missing a mask of the anterior amygdaloid area (AAA) for a single hemisphere or the AAA is extremely small. However, in both circumstances the volumetric value for the AAA in the output (?h.amygNucVolumes-T1.v21.txt) looks normal. In the cases where no AAA mask is visible, if you check the box "Show existing labels only", the label "7010 Anterior-amygdaloid-area" does not even appear for that hemisphere. AAA is the only structure where this is occurring. There are other structures (such as the medial nucleus) that appear small in FreeView, but still have a normal volumetric value. However, no other structure is completely missing. Note: In all of these cases aseg looks fine. And T1s were processed using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but we used freesurfer-darwin-macOS-7.1.0-20200511-813297b to run with hippocampal/amygdala segmentation (segmentHA_T1.sh). Thank you for you time and help, Sarah Skinner Research Specialist University of Wisconsin - Madison

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NIH-Sponsored Advanced Stats Course in Neuroimaging and Genetics, April 3-14, 2023, Salt Lake City, Utah
by ROBERT CARY WELSH 13 Jan '23

13 Jan '23

External Email - Use Caution Hi, Our NIH-funded course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”, will be held in-person in Salt Lake City, UT, from April 3 – April 14, 2023. This is a course geared to advanced undergraduate students graduate students, postdocs, and junior faculty. Topics include: Bayesian methods of functional connectivity and activation, longitudinal modeling, network neuroscience, polygenic risk scores, multimodal modeling and predictive modeling. The course is a mix of lectures and hands-on computer labs. Our main lecturers include: Martin Lindquist, Johns Hopkins University Mandy Mejia, Indiana University Rick Betzel, Indiana University Anna Docherty, University of Utah To read more about the course and to apply please see: https://secure-web.cisco.com/1tb13yIDDieGruGkIUgpXHZCMqfiUm2RO-w9TGq_7uZ51z… Due to a previously unrecognized issue with the web, we are keeping the application portal open till Jan 27th. For more information please email : advancedstatisticscourse(a)utah.edu<mailto:advancedstatisticscourse@utah.edu> Best, Robert Welsh and Anna Docherty

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