Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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.

1 0

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

1 0

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…

1 0

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

2 2

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

1 0

mris_convert to gifti
by Lauri Tuominen 13 Jan '23

13 Jan '23

External Email - Use Caution Dear Freesurfer experts, A quick question. I am trying to convert my cortical thickness analysis results into a gifti file preferably combining left and right, like so: mris_convert --combinesurfs lh.gamma.mgh rh.gamma.mgh both.gamma.gii I get this error: error: ERROR: MRISread: file 'lh.gamma.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! It then try to convert a single hemi: mris_convert lh.gamma.mgh test.gii but I get the same error. The gamma file looks fine to me, so I am not sure what the issue is. I am running this version of freesurfer: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Could someone provide an example how this is done? Thank you so much! Lauri Tuominen

2 1

WG: Problem with recon-all --> nii.gz file not found
by Livia Ruehr 13 Jan '23

13 Jan '23

External Email - Use Caution ________________________________ Von: Rühr, Livia Gesendet: Donnerstag, 12. Januar 2023 17:25 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Problem with recon-all --> nii.gz file not found Dear Sir or Madame, for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. I use Freesurfer 7.0 on a Linux Mint 21"Vanessa". I am using the following layout: recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all This worked for me in december, whereby all my subjects were processed successfully and freesurfer created the directories. However, today I wanted to continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist not found (error message): ERROR: cannot find sub-03-ses-01_T1w.nii.gz Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023 For more details, see the log file To report a problem, see http://secure-web.cisco.com/1z5XiLDbECZb1gv8wAZoV7fS7G_v-k4oqEkA6DCAbe1thCc… This applies not only to one file, but for all of them. I have also tried to rerun recon-all of another file that had been successful in december, I have also copied and renamed it to not overwrite it.. but none of the data sets were found! For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the source (SetUpFreeSurfer.sh). After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh ... I can now clearly see, that I am in the correct SUBJECTS_DIR -------- freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /freesurfer FSFAST_HOME /freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/lirh717c/Desktop/V5LGN MNI_DIR /freesurfer/mni After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my files. Additionally, I can open freesurfer now and open the scans within freeview, so that the following appears to me: - my data are okay and I can open them - freesurfer is generally running (only thing is one warning: (process:3965): Gtk-WARNING **: 17:07:37.677: Locale not supported by C library. Using the fallback 'C' locale.) - even if setting subjects directory to another directory, it is not working, the problem is neither the data nor the directory - the subjects directory has correctly been set and I can access it --> my files are seen here To this reason, I have no ideas anymore. I am looking forward to your reply! Kind regards Livia Rühr

3 10

correlation analysis two groups (paired analysis)
by Agurne Sampedro Calvete 13 Jan '23

13 Jan '23

External Email - Use Caution Dear FreeSurfer experts, I have two groups and two time points and I would like to do a correlation analysis between a variable (cognition) and the change score in cortical thickness between the two time points (time2 minus time1). I would like to see if the *correlation *is *different *among each group, if there is an interaction with the group. I have followed the paired t test instructions ( https://secure-web.cisco.com/11YHUupGYyGBe5w6QAQb3OOLcNluK0Tqv4VUmAmDx5wuog…) but I am not sure about the contrast(s) I have to use. The paired-diff.fsgd file (second fsgd file) is the following: GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables cognition Input subject1pair Group1 0.546 Input subject1pair Group2 -0.243 ... How should it be the contrasts files to see the *correlation *of the variable cognition with the change score in thickness taking into account the groups? And should I use DODS or DOSS? Using DODS: 0 0 0.5 0.5 or 0 0 1 -1 I don't understand the difference between both contrasts. I think I should use the one of "0 0 1 -1" to see whether the cognition variable correlates with change in thickness differently according to the group. Is this correct? Using DOSS: 0 0 1 Thank you very much in advance. Kind regards, Agurne

2 2

VM freesurfer pass code
by mirus.jindrova＠seznam.cz 13 Jan '23

13 Jan '23

External Email - Use Caution Hello, can I get the passcode for the FS_7_2_0_Ubuntu_18_04_06.ova.7z file? Thanks in advance! Kind regards, Miroslava Jindrova

1 0

Gray to White Matter Signal Ratio (GWR)
by Xiao Da 12 Jan '23

12 Jan '23

External Email - Use Caution Dear FreeSurfer team, I am currently using to Gray to White Matter Signal Ratio (GWR) to analyze our longitudinal AD/MCI MRI data. I feel a little confused about the interpretation after reading some recent papers like Putcha et al, 2022 or Jefferson et al, 2015 and some early papers like Salat et al, 2011 and I hope Freesurfer team could help me confirm if my understanding is correct. 1, Freesurfer "recon-all" generates the GWR map by default using "pctsurfcon" and the T1 image. The formula is 100*(W-G) GWR = --------- 0.5*(W+G) The white matter is sampled 1mm below the white surface. The gray matter is sampled 30% the thickness into the cortex. 2, Gray to White Matter Signal Ratio (GWR) generated by "recon-all" is the same as Gray and White Matter tissue contrast. So Gray to white matter signal intensity ratio (GWR) declines across the lifespan? AD patients have smaller GWR than cognitively normal elders? Decrease of GWR is observed with increasing AD disease severity? Thank you so much and best regards, Xiao Da Senior Data Scientist Cognito Therapeutics, Inc. 1218 Massachusetts Ave, Cambridge, MA 02138 xda(a)cognitotx.com<mailto:xda@cognitotx.com> [A picture containing text, sign Description automatically generated]

2 3

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