Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

analyzing fmriprep data in fsfast
by Pedersen, Walker Scott 24 Jun '21

24 Jun '21

I am trying to use fsfast to analyze task-based functional data output by fmriprep. The subcorticals seem to be working, but I am having trouble with the surfaces. One thing I have noticed before running any fsfast code, when I load the surfaces output by fmriprep into freeview (overlaid onto the fsaverage ?h.inflated) both the *space-fsaverage_hemi-L_bold.func.gii and *space-fsaverage_hemi-R_bold.func.gii get overlaid onto the rh.inflated surface, instead of the L_bold.func.gii getting overlaid onto lh.inflated. I don't know if this points to some issue with my fmriprep output that may be causing dowstream problems. I have taken the func.gii in fsaverage space from fmriprep, converted them to nifiti and smoothed them using the following code adapted from code posted here: https://github.com/nipreps/fmriprep/issues/994 #*************************************************************** # convert surface files, smooth, and reinforce tr declare -a hemis=("l" "r") for hemi in "${hemis[@]}" do out_stem=fmcpr.sm${fwhm}.fsaverage.${hemi}h in_stem=${fmp_stem}_space-fsaverage_hemi-${hemi^}_bold.func mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage \ --sval ${fmriprepFunc_dir}/${in_stem}.gii \ --tval ${run_dir}/${out_stem}.nii.gz \ --fwhm-trg ${fwhm} --hemi ${hemi}h mri_convert ${run_dir}/${out_stem}.nii.gz ${run_dir}/${out_stem}.nii.gz -tr ${tr} done #*************************************************************** When running this, I get what appear to be warnings: ** DA[0] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) ** DA[1] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) ** DA[2] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) There are one of these for each TR in my data. Full output attached as convertAndSmoothOutput.txt Next I am running mkanalysis-sess with the following: #******************************************************************************* #!/bin/bash # Script for converting fmriprep outputs to fsfast structure for first levels # This converts files to fsaverage surface spaces and mni305 volume spaces conds="1,CX 2,eCS+1 3,eCS+2 4,eCS-atCS+1 5,eCS-atCS+2 6,lCS+1 7,lCS+2 8,lCS-atCS+1 9,lCS-atCS+2 10,NOShock_1 11,omittedSck_1 12,shock" fwhms="5" # source freesurfer source ${FREESURFER_HOME}/SetUpFreeSurfer.sh # set matlab path export MATLAB='/usr/local/bin/matlab' set MATLAB # full path to recons folder export SUBJECTS_DIR="/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/freesurfer" for fwhm in ${fwhms}; do for side in l r; do mkanalysis-sess \ -no-mask \ -paradigm events.txt \ -tpexclude tpef.txt \ -nuisreg MotConfounds.txt 12 \ -mni305 -analysis cond_fsavSurf_${side}_sm${fwhm} -per-run -polyfit 2 \ -event-related -TR 2.56 -fsd cond -refeventdur 6 \ -spmhrf 0 -nconditions 12 -force \ -funcstem fmcpr.sm${fwhm}.fsaverage.${side}h.nii.gz for i in ${conds} ; do condNum=${i%,*}; cond=${i#*,}; mkcontrast-sess -contrast ${cond} -analysis cond_fsavSurf_${side}_sm${fwhm} \ -a ${condNum} done #******************************************************************************* output attached in mkanalysisSurfOutput.txt When I then run selxavg3-sess on the data with: #******************************************************************************* #!/bin/bash fsfastD="/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast" regions="fsavSurf_l" fwhms="5" conds="cond" # source freesurfer source ${FREESURFER_HOME}/SetUpFreeSurfer.sh for fwhm in ${fwhms}; do for region in ${regions}; do for cond in ${conds}; do selxavg3-sess -no-preproc -s sub-101KI_ses-bld1 \ -d ${fsfastD} \ -analysis ${cond}_${region}_sm${fwhm} done done done #******************************************************************************* I get the following error: #******************************************************************************* Smoothing ACF /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/bin/mri_fwhm --mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz --i /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.nii.gz --o /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/bin/mri_fwhm --mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz --i /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.nii.gz --o /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only: Segmentation fault voxelvolume 1 mm3 Loading mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz Search region is 163842 voxels = 163842.000000 mm3 Smoothing input by fwhm=20.000000, gstd=8.493218 ERROR: /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/bin/mri_fwhm --mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/mask.nii.gz --i /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.nii.gz --o /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/sub-101KI_ses-bld1/cond/cond_fsavSurf_l_sm5/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only ans = 139 >> ------------------------------------------ ERROR: fast_selxavg3() failed\n #******************************************************************************* the full output is attached as selxavg3Output.txt Any idea on what is causing selxavg3 to crash? Thanks!

2 1

Extracting stats from surface overlay
by Gugger, James J 24 Jun '21

24 Jun '21

External Email - Use Caution Good morning, I am working with NODDI data and have created surface overlays in FreeSurfer space with NODDI values. I am interested in calculating vertex-wise asymmetry indexes utilizing fsaverage_sym similar to Greve et al Journal of Cognitive Neuroscience 25:9, pp. 1477–1492. I would ultimately like to extract average AIs for an ROI analysis. My question is how do I extract the overlay stats from the surface overlay mgh file to obtain average AI in each ROI? Thanks! Jim Gugger James Gugger, MD, PharmD Instructor of Neurology University of Pennsylvania

2 1

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)
by Douglas N. Greve 24 Jun '21

24 Jun '21

Don't use --grf with surfaces On 6/15/2021 7:24 PM, Paul, Jhelum wrote: > > External Email - Use Caution > > Hello, > > I also have the same error. I have been looking into all the tutorials > available for Freesurfer v7 and trying to search why, > > mri_glmfit-sim --glmdir lh.age_gender_volume.glmdir --grf 2 abs > --cwp 0.05 --2spaces > > is not working and throwing an error showing the following in the > screenshot: > > Is it possible to clarify which tutorial to follow for grf or > volume-based and surface-based group analysis in Freesurfer v7 and > what all multiple comparisons corrections can be done for volume and > surface analysis? > > Any suggestion is appreciated. > > Thank you. > > Regards, > > Jhelum Paul > > > ------------------------------------------------------------------------ > > UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any > attachments) is only intended for the use of the person or entity to > which it is addressed, and may contain information that is privileged > and confidential. You, the recipient, are obligated to maintain it in > a safe, secure and confidential manner. Unauthorized redisclosure or > failure to maintain confidentiality may subject you to federal and > state penalties. If you are not the intended recipient, please > immediately notify us by return email, and delete this message from > your computer.

1 0

nu correction
by Marina Fernández 24 Jun '21

24 Jun '21

External Email - Use Caution Dear experts, I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the T1w/T2 ratio? I applied nu correction to T1w images and worked fine but results were weird when nu correction was applied applied to T2w images. I am not sure if nu correction must only be applied to T1w images for this purpose, or if I have to modify some parameters to apply nu correction to T2w images. Thank you in advance for your help. Best, Marina

2 1

Hippocampus subfield segmentation
by Ishi Tandon 24 Jun '21

24 Jun '21

External Email - Use Caution Hello FS experts, I have performed hippocampus subfield segmentation on my T1 scans. I also gathered the volume from all my analyzed subjects through the following command - quantifyHippocampalSubfields.sh T1 hippotest.txt Now I want to perform statistics on these maps to find out the differences between groups. I am not sure if I should use mris_preproc and then follow the general GLM approach. Could you please give me some clarification on this? Thanks in advance. *Regards,* *Ishi Tandon (she/her)* *B.Tech + M.Tech - Cognitive Neuroscience* *Amity University, Rajasthan* *Contact- +918239259846* *Email - ishi.tandon(a)student.amity.edu <ishi.tandon(a)student.amity.edu>*

2 2

how to shrink WM surface in one region
by Lara Foland-Ross 23 Jun '21

23 Jun '21

External Email - Use Caution Hi everyone, Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all? Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3" Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points. Thank you in advance, Lara

2 2

Visualization of specific regions
by Jennifer James 23 Jun '21

23 Jun '21

External Email - Use Caution Hi FreeSurfer experts, We have used FreeSurfer version 6.0 to extract thickness values from MRI data of our subjects and then used SPSS for statistical modeling. We found significant results in the thickness of the following two regions: *lh_G&S_cingul-Mid-Ant_thickness* *lh_S_front_middle_thickness* We want to make a simple figure showing these two areas of the brain just for visualization purposes (similar to the attached figure from another paper). Could you tell us how we can make such an image in Freeview? We tried to use mri_extract_label but the figures we got are not really what we are looking for. Any help is highly appreciated! Best, Jennifer

1 0

Calculating group-wise Dice Similarity Coefficient and corresponding surface map
by Hye Min Shin 23 Jun '21

23 Jun '21

External Email - Use Caution Hello experts, I apologize if this has been asked before- but I couldn't find a question that was similar to what I wanted to know about so I decided to ask this question(s). I am trying to calculate dice similarity coefficient (DSC) for a group of subjects and I was wondering if it is possible to calculate this on FreeSurfer. I understand that FreeSurfer has mri_compute_overlap that can compute dice coefficient but I wasn't sure if this can be done on group-level. Do I have to first calculate dice for each subject and then calculate the average dice for the subjects? Also I was wondering if there is a way to visualize group-level dice coefficient map on inflated lh/rh surface. Best, Julia Shin

2 1

InfantFS witg segfile exiting with errors
by Fernanda Hansen P. de Moraes 22 Jun '21

22 Jun '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to process some newborn subjects including the segfile. In both situations, including the mask file and using the --forceskullstrip flag I get the following error (log file attached): *lta_convert successful./home/fernanda/Documentos/dHCP/freesurfer1 ERROR: Option --noverbose unknown* This is the exact command I am running: *infant_recon_all --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz --forceskulltrip --force* How can I overcome this? Thank you very much. Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

1 0

Re: [Freesurfer] bias field correction and intensity normalization
by Marina Fernández 22 Jun '21

22 Jun '21

External Email - Use Caution Hi Matt, We always really appreciate your help and advice. Thank you very much for your answer, now we understand much better why it is correct not to apply this correction. Best, Marina

1 0

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