Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

Surface-based smoothing of EPI data
by Mason Wells 28 Nov '21

28 Nov '21

External Email - Use Caution Hi Experts, This question may have been addressed elsewhere on the list, but I can’t find a response. I want to smooth BOLD data on the surface. First, I pre-processed the data in FEAT with no smoothing applied. Then I registered the filtered_func data to the anatomical using bbregister. I check the registration matrix looks good by running this command (using example_func as the reference): * tkregisterfv --mov example_func.nii.gz --reg junk.dat --lta reg/freesurfer/anat2exf.register.dat --surfs I then resampled my data with mri_vol2surf using the following command: * mri_vol2surf --src filtered_func_data.nii.gz --out lh_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat --hemi lh --projfrac 0.5 --out_type mgh I then want to smooth this data on the surface. I assume it would be best to run mri_surf2surf and set the target and source subject as the same? Such as this command: * mri_surf2surf --srcsubject sub-0006 --srcsurfreg lh.sphere.reg --trgsubject srcsubject --trgsurfreg sphere.reg --hemi lh --sval lh_func_native.mgh --tval lh_func_native_smoothed.mgz --mapmethod nnf --fwhm 5 --cortex Please can someone on this list give me some advice on this? Are my command suitible and/or am I missing anything? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1u6t7awlKd_1Wa1q3V5QSyioa1OcxttJUnTK7KvQfyTiKm…> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Can't load ROI labels
by Shapiro, Noah Lorenz 28 Nov '21

28 Nov '21

Hello, I am very new to FreeSurfer, and I was going through the tutorials and bumped into difficulties when loading ROI's. I can load volumes (e.g. orig.mgz) in Freeview; however, I can't load any ROIs. I can select a label (e.g. lh.BA45_exvivo.label) and hit "open", but then nothing happens. The label doesn't load at all. I don't get an error message either. I am using FS version 5.3, and I also tried on FS version 6. Quartz is updated. I am running on macOS Big Sur version 11.6. Do you have any ideas why I can't load ROI labels? Any help is highly appreciated. Best wishes, Noah Noah Shapiro Research Technician (II) Department of Neurology Alzheimer’s Clinical & Translational Research Unit Massachusetts General Hospital 149 13th Street Charlestown, Massachusetts 02129 E-mail: nlshapiro(a)mgh.harvard.edu

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FREESURFER Recon all not working
by Alison McDonnell 28 Nov '21

28 Nov '21

External Email - Use Caution When i run recon all the only thing created is in the mri folder. all the rest are left blank. i have attached all relevant screenshots including one that has the original data being used is in the right format and right place and the recon all log. any advice would be appreciated. this is being done via teamviewer from pc to mac but i cant see why that would cause any issues[image: Xquartz_screenshot.png][image: error_screenshot.png]

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Help
by Nilab Nasrullah 28 Nov '21

28 Nov '21

External Email - Use Caution Hi, I am editing subjects for a research project. After reconstruction, some parts of the brain are not included in the segmentation. Often, some parts of the temporal lobe and the cortex of the occipital lobe are not included. In some cases, the cortex of the frontal lobe is also affected. I have tried using controls points, but the results don't change. I have also reconstructed them again, running autorecon1 and autorecon2&3 separately. I have lowered the watershed parameters, used the gcut command and edited manually after autorecon1 but in the end, the results don't vary significantly compared to running recon-all -all. What can I do to include the missing parts? Thanks, Nilab När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1Ax2yPI22TBKL7RmNfE0byMHRpgXvbHg7XwE-k53PZw0hs…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1aWFKk6nAP5Da43ar-uO8SQFPaiCybDNs23oonfSVar3ls…>.

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28 Nov '21

External Email - Use Caution Hi Experts, My tracula completed with no error. So I was trying to view the fa.nii with the following command: freeview -v mri/brain.mgz mri/orig.mgz mri/wmparc.mgz:colormap=lut:opacity=0.2 dmri/dtifit_FA.nii:reg=touch/rusage.mri_ca_register.dat:colormap=heat:heatscale=.2,.2,1 -colorscale -viewport coronal. It returned with an error message saying: "reading registration failed". I have looked at the register.dat from the following link: RegisterDat - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1hv0bANzHoBn4ULec2TL4BHOCLGLVTqseZKeSEib8vKA0k…>. My register.dat is nothing like that (attached below). So where should the file locate? Best, Jackie

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Difficulty Running Single Subject Surfaced Based GLM
by Hiersche, Kelly J. 28 Nov '21

28 Nov '21

External Email - Use Caution Hello FreeSurfer Developers, First, I am new to using Freesurfer, so I apologize if any information is unclear. I am attempting to use the following tutorial https://secure-web.cisco.com/1KKgvfrXJGjQJ5zjq_uJgVI7FZF_1Yms747_s_N5YKZgNC… to do a surface based GLM in an individual subject (using my own data, not the tutorial data), but I am getting the following error: Error using MRIread (line 76) ERROR: cannot determine format of /subnum/bold/runnum/masks/fmcpr.brainmask.fsaverage.lh (MRIread) I am getting that error because the fmcpr.brainmask.fsaverage.lh does not exist. To fix this error, I re-ran preprocessing using the following tutorial: https://secure-web.cisco.com/1R3ca-_kZlKG6UMHW-K0XesdEmNb2A3RSqg26YdNzjZ-Rh… After preprocessing, I still got the same error. Here are the files that do exist in that path: subnum/bold/run-num/masks brain.e3.nii.gz brain.fsaverage.lh.pr.nii.gz brain.fsaverage.rh.pr.nii.gz brain.mni305.2mm.pr.nii.gz brain.nii.gz.mkbrainmask.log brain.fsaverage.lh.nii.gz brain.fsaverage.rh.nii.gz brain.mni305.2mm.nii.gz brain.nii.gz There are some fmcpr files in this folder: subnum/bold/run-num fmcpr.brainmask.norm.2x2x2.nii.gz fmcpr.mcdat fmcpr.norm.nii.gz fmcpr.sm5.fsaverage.rh.nii.gz fmcpr.brainmask.normtmp.2x2x2.nii.gz fmcpr.nii.gz fmcpr.sm0.norm.nii.gz fmcpr.sm5.mni305.2mm.nii.gz fmcpr.mat.aff12.1D fmcpr.nii.gz.mclog fmcpr.sm5.fsaverage.lh.nii.gz fmcpr.sm5.norm.nii.gz Here are the commands I am running: These commands work: mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions $nconditions -mask $func_stem.brainmask -gammafit 2.25 1.25 -nuisreg mcprextreg 6 -TR 1.0000 -polyfit 1 -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude $tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run mkcontrast-sess -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -contrast Con1-Con2 -a 1 -c 2 preproc-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage lhrh -mni305 -fwhm 5 -per-run This command errors mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions $nconditions -gammafit 2.25 1.25 -nuisreg mcprextreg 6 -TR 1.0000 -polyfit 1 -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude $tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run 1. I am running freesurfer through matlab on the Ohio Supercomputer; freesurfer/6.0.0 Thank you for all your troubleshooting help! Kelly

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interhemispheric registration: xhemi vs. mris_left_right_register
by Dr. Cornelius Kronlage 28 Nov '21

28 Nov '21

External Email - Use Caution Dear freesurfer community, concerning interhemispheric registration: What are differences between mris_left_right_register and the xhemi pipeline (including the fsaverage_sym subject)? I understand that xhemi/fsaverage_sym are meant to provide an unbiased reference as opposed to simply mapping all data to one hemisphere. I am trying to map a label from one hemisphere to the other on individual subjects. I noticed that mris_left_right_register results in output quite different from using fsaverage_sym via the xhemi process as an intermediate. As an example, see the figure file attached (original label on rh, mapped labels on lh). At the first glance, the output of mris_left_right_register seems to align with the curvature a lot better... For reference, the following code was used. Is that correct? surfreg --s ${subject} --t fsaverage_sym surfreg --s ${subject} --t fsaverage_sym --lh --xhemi mris_apply_reg \ --src-label rh.label --trg rh_on_lh.xhemi.label \ --streg ${SUBJECTS_DIR}/${subject}/xhemi/surf/lh.fsaverage_sym.sphere.reg ${SUBJECTS_DIR}/${subject}/surf/lh.fsaverage_sym.sphere.reg mris_left_right_register \ ${SUBJECTS_DIR}/${subject}/surf/lh.sphere \ ${SUBJECTS_DIR}/${subject}/surf/rh.sphere \ ${SUBJECTS_DIR}/${subject}/surf/lh.sphere.left_right \ ${SUBJECTS_DIR}/${subject}/surf/rh.sphere.left_right mris_apply_reg \ --src-label rh.label --trg rh_on_lh.left_right.label \ --streg ${SUBJECTS_DIR}/${subject}/surf/rh.sphere.left_right ${SUBJECTS_DIR}/${subject}/surf/lh.sphere.left_right Thank you and with best wishes Cornelius

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[WARNING: ATTACHMENT UNSCANNED]Help: Using a Different Atlas for Anatomical ROI Analysis
by Flanagan, Shawn D 28 Nov '21

28 Nov '21

External Email - Use Caution Hello, I would like to use the Brainnectome atlas for cortical thickness analysis parcellations. The T1 template volume (nifti file type) is attached if helpful. I have seen a couple of posts on this, but am not clear about the process. For example, the response to a similar comment was to "run recon-all on the AAL anatomical T1w volume template". At this point, I do not know what files, transformations, and/or code modifications are needed. For example, does the brainnectome template volume need to be preprocessed in any way, does it need to be saved in the MGH format? If so, how is this done? Does the process require any other files or subroutines? In summary, I am wondering if you can "walk me through" the process or provide a detailed example. Any help would be greatly appreciated! Thank you for your time. Best, Shawn --- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center 3860 South Water Street Pittsburgh, PA 15203 sdf29(a)pitt.edu<mailto:sdf29@pitt.edu> Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratory<http://secure-web.cisco.com/1xPYTwm1twYgyoLhqQPj3hQ3mM2mqTCUs_emm18SlHI78wP…>

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SynthSeg
by AJ 28 Nov '21

28 Nov '21

External Email - Use Caution Hi Thank you for your help. I ran SynthSeg successfully. How do you derive sbTIV value ? Could one use sbTIV from SAMSEG? Many thanks AJ

2 3

Freeview.app crashing
by ChristianBauer 26 Nov '21

26 Nov '21

External Email - Use Caution Dear Freesurfer experts, I am having issues with opening Freeview. I am currently using Freesurfer v.7.2.0 and I had no problems setting up Freeusurfer and Freeview on my Desktop computer. However, I have had issues with Freeview crashing on my Mac laptop every now and then and now I cannot open Freeview at all The error message I am getting is a s follows /Applications/freesurfer/7.2.0/bin/freeview: line 2: 3185 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ I have tried downloading and reinstalling Freesurfer several times as well as trying the stand-alone version. I have also changed the license file as was previously suggested by one of your team. Any advice would be greatly appreciated. Thanks in advance, Christian

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