Freesurfer November 2021

freesurfer@nmr.mgh.harvard.edu

77 participants
118 discussions

Fieldmap Echospacing Error
by Kaplan, Elizabeth 29 Nov '21

29 Nov '21

External Email - Use Caution Hi All, I am working on processing diffusion data with Tracula and can't seem to resolve an error I encounter attempting to run the "trac-all -prep -c" command on my data. The error message that I get arises due to the line of code where I specify the echospacing in fieldmap images. It reads that the "flag is not recognized". I am able to run the command smoothly and obtain diffusion metrics when specifying dob0 = 0. I have included my trac-all.log and configuration file for reference. Can anyone offer guidance in navigating this issue? It is greatly appreciated! -- [image: Brown logo] *Liz Kaplan '22* *She / Her / Hers* Sc.B. Candidate Cognitive Neuroscience B.A. Candidate Contemplative Studies 69 Brown St Mail #4391 Providence, RI 02912

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Smoothing and ROI averages from .stats output
by Daniel Westfall 29 Nov '21

29 Nov '21

External Email - Use Caution Good afternoon, It is my understanding that if I am only interested in the already averaged region ROIs that are output in the .stats files that I should not use a smoothing kernel as they are already averaged across all vertices, correct? My specific question has to do with calculating the average cortical thickness and total surface area of the Yeo networks using this command: mri_surf2surf \ --srcsubject fsaverage \ --trgsubject $dir \ --hemi lh \ --sval-annot /$SUBJECTS_DIR/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval /$SUBJECTS_DIR/$dir/label/lh.Yeo2011_7Networks_N1000.annot In this case, if I want to use the output from the lh.Yeo2011_7Networks_N1000.stats then I would NOT want to use the --fwhm 10 flag, as they are already averaged and this could cause bleeding between the different regions, correct? Thank you!

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Visualization error in freeview from recon-all
by achille.teillac＠chu-lyon.fr 29 Nov '21

29 Nov '21

External Email - Use Caution Dear experts, We are working with a large MRI dataset (FLAIR, T1) and we are performing recon-all based on the 3D T1. At the end, no error is detected but the visualization of the pial, white and inflated surfaces in freeview is somehow bad as you can see on the picture attached (lh.pial_freeview, lh.white_freeview, lh.inflated_freeview). Can it be an error that I missed and is there a way to correct it ? Or could it be a 3D rendering issue that can be fixed with visualization options ? Oddly, when I zoom really close for all surfaces, it seems perfectly smoothed... I thought first it could be linked to the topological defect correction (which I didn't do) but when I display the surfaces with paraview it works fine as you can also see on the picture attached (lh.pial_paraview, lh.white_paraview, lh.inflated_paraview). Everything works fine otherwise. Thanks in advance for any help you may provide and I can send you some screenshots highlightening the issue or the recon-all log. Best, Achille Teillac

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Re: [Freesurfer] Help
by Douglas N. Greve 29 Nov '21

29 Nov '21

Can you send them in plain, unzipped format? On 11/29/2021 4:07 AM, Nilab Nasrullah wrote: > > External Email - Use Caution > > I am attaching a few screenshots of the segmented brain as zip-files. > Hopefully, you can see the results. If not, let me know so I can send > it to you in a different format. > > Thanks, > Nilab > ------------------------------------------------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgreve(a)MGH.HARVARD.EDU> > *Sent:* 29 November 2021 04:01 > *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Help > Can you send some pictures? > > On 11/23/2021 4:02 AM, Nilab Nasrullah wrote: >> >> 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/1j67IzVGn-rPDxWTuNJ7rL_6odYOWCRBu23QS17cACnRyi…>. >> >> >> /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/1Kc7a3pEbtZ_tk8Amzoyyo0glZd7MCe1sLIURpc1mdQ8wc…>. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1-E1yjOjKQ9KDEXvwYBVr3bbOq2bacLh1h8cbFg8HZIRk9…> > > > > /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/1AbbExkRRcd9A1GsUXiwxmB8hzvltggGn77dypaT3DX51u…>. > > > /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/1AwEFqqXcjoj26oT8N6wol9bYPT2t48T1NQwZruliDsSsz…>. >

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SynthSR
by AJ 28 Nov '21

28 Nov '21

External Email - Use Caution Hi, Could synthetic MRIs generated by the SynthSR script be potentially used to harmonize T1w weighted images acquired on different scanners? Then used harmonized images for volumetric analyses? Many thanks AJ

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FREESURFER Recon all problem
by Alison McDonnell 28 Nov '21

28 Nov '21

External Email - Use Caution Hi I tried to running recon all on a large amount of data and got the below error message. the listed files that say the tag image orientation can't be found aer in the folder but seem to be blank. i was wondering is there a way to run recon all and skip/ignore those seemingly blank files or should i delete them from the folder? Thanks [image: error_message.png]

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fsaverage_sym lobes parcellation mri_annotation2label
by Dr. Cornelius Kronlage 28 Nov '21

28 Nov '21

External Email - Use Caution Dear freesurfer community, when trying to obtain lobe labels for fsaverage_sym, mri_annotation2label segfaults - see terminal output below. It works smoothly for fsaverage and any other subjects. Is there any workaround? >mri_annotation2label --subject fsaverage_sym --hemi lh --lobes fsaverage_sym_lh.lobes.annot subject = fsaverage_sym annotation = aparc hemi = lh surface = white Reading surface /home/ckronlage/epi/DATA/tmp4_working//fsaverage_sym/surf/lh.white Loading annotations from /home/ckronlage/epi/DATA/tmp4_working//fsaverage_sym/label/lh.aparc.annot reading colortable from annotation file... colortable with 1036 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) Seg base 1000 MRISmergeAnnotations: parcCount=10, newparcname=frontal mri_annotation2 supposed to be reproducible but seed not set Segmentation fault (core dumped) > Thank you and best wishes Cornelius

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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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Freesurfer November 2021