Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

Demeaning for Longitudinal Analyses
by WON JONG CHWA 24 Jun '21

24 Jun '21

External Email - Use Caution Dear FreeSurfer experts, I am currently running longitudinal analyses using the paired analysis tutorial for two time points. There are two tests I am trying to run: 1. Calculating significant changes in volume between the two time points, controlling for age and gender. 2. Correlating BMI with change in volume between the two time points, controlling for age and gender. For (1), would it be necessary to demean age for a one-sample longitudinal analysis? And for (2), would I need to demean both BMI and age? Thank you for your help.

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mri_convert help w/ GE Genesis files
by Christopher Mcnorgan 24 Jun '21

24 Jun '21

External Email - Use Caution Hi all, I’ve been provided with some data collected on a 1.5T GE scanner from an old published study. The paper doesn’t indicate the scanner model (beyond that it’s a 1.5 GE scanner), but I believe they came from a GE Genesis, based on the .MR file extension. I have successfully used MRIcro to convert the series of .MR files from the anatomical scan to Analyze format, so there’s nothing wrong with the files. I would prefer to script mri_convert to convert the data, but I am having problems doing so, as each of my attempts results in a segmentation fault. Files were originally named <pattern>1.MR to <pattern>128.MR, and based on the program output prior to the core dump, I renamed them so that the file numbers were zero-padded, and I’ve tried it with and without the input filetype argument, but I get the segmentation fault/core dump either way. The command I’m trying is: mri_convert -i E11816S5I001.MR -it ge -o T1.nii.gz This gives me: reading from E11816S5I001.MR... fname_format : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%d.MR fname_format2 : /home/fruit/music/tmp/E11816/mri/S5/renumbered/E11816S5I%03d.MR Segmentation fault (core dumped) I was hoping someone could point out something that I’m missing. Thanks for your time. It’s much appreciated. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://secure-web.cisco.com/11HrmGviCIYIvUr8zM_GIo6mtULm1BjCwyqj-E9atrNMCWU… * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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T2 T1 registration with mri_robust_register
by Marina Fernández 24 Jun '21

24 Jun '21

External Email - Use Caution Dear experts, I would like to co-register T2 to T1 robustly, both images have a resolution of 0.65mm3. Firstly, I tried bbregister with the '--init-rr' flag, but this function doesn't allow to keep the native voxel resolution (i.e., 0.65mm3), changing it to 1 mm. As I wanted to maintain the native voxel resolution , I tried the mri_robust_register function (corresponding to the '--init-rr' flag) as explained in the help associated with this function, but this process took thirteen hours: EXAMPLE 4. Robust cross modal registration: mri_robust_register --mov movT2.mgz --dst dstT1.mgz --satit --iscale --mapmov T2_to_T1.mgz --lta T2_to_T1.lta --cost ROBENT --entradius 2 --entcorrection --weights T2_to_T1_weights.mgz I also tried the standard cross modal registration. The process didn't take as long, but the result was not as accurate as bbregister. EXAMPLE 5. Standard cross modal registration: mri_robust_register --mov movT2.mgz --dst dstT1.mgz --mapmov T2_to_ T1.mgz --lta T2_to_T1.lta --cost NMI Could you suggest me how to accurately register T2 to T1 images maintaining the native voxel resolution in a shorter time? Thank you very much in advance. Best, Marina

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The specific steps of the mri_surf2surf command
by 1248742467 24 Jun '21

24 Jun '21

External Email - Use Caution Hello, Fs I am not familiar with the exact steps of sampling a pre-segment file into the FSAVERAGE5 space. In other words, I am not very familiar with the exact steps of the mri_surf2surf command.

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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!

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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

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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.

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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

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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>*

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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

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Freesurfer June 2021