Freesurfer November 2021

freesurfer@nmr.mgh.harvard.edu

77 participants
118 discussions

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

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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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Converting .trk files in mini space to nifti using dorm_trk2trk
by Schaechter, Judith D. 23 Nov '21

23 Nov '21

Hi, I'd like to convert *trk files that are in mni space to nifti files using dmri_trk2trk. The *trk files are here: /autofs/vast/freesurfer/centos7_x86_64/7.2.0-beta/trctrain/hcp/mni Attempts so far (that have failed) are: dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_template_identity.mat with MGH35_HCP_FA_template_identity.mat generated by: flirt -in MGH35_HCP_FA_template.nii.gz -ref MGH35_HCP_FA_template.nii.gz -omat MGH35_HCP_FA_template_identity.mat dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat with MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat generated by: flirt -in MGH35_HCP_FA_template.nii.gz -ref MNI152_T1_2mm_brain.nii.gz -omat MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat Thanks in advance for your help! Judith ******************************************************* Judith D. Schaechter, Ph.D., M.S.P.T. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital, Harvard Medical School 13th Street, Building 149, Room 2301 Charlestown, MA 02129 Office 617-726-5622 | Cell 781-752-6247 | Fax 617-726-7422 Email jschaechter(a)mgh.harvard.edu

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Freeview grey matter, white matter and Tracula outputs
by Zeng, Qi 23 Nov '21

23 Nov '21

External Email - Use Caution Hi, If I want to freeview fully segmented grey matter, white matter, and Tracula outputs, are the following commands correct to the request? # to visualize the segmented cortical outputs freeview -v mri/aparc+aseg.mgz Question: why is one hemisphere brighter than the other? How can I adjust so that they are equally bright? # to visualize the segmented subcortical outputs freeview -v mri/aseg.mgz Question: why is only one hemisphere showing and how to add the other one? $ to visualize AD. RD, FA and color-coded each freeview -v dmri/dtifit_FA.nii Question: I cannot find the nifti outputs of AD and RD (however, the stats generated). where can I find it? Is there an example of how to color-code them for freeview? Thank you! Best, Jackie

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[WARNING: ATTACHMENT UNSCANNED]Using a Different Atlas for Anatomical ROI Analysis
by Flanagan, Shawn D 23 Nov '21

23 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/1w-f2b1Sv8FoWJqjWBtRI_gzdJ3kwmFPg5ehq75ANa6Is4a…>

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Freesurfer November 2021