Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

recon-all-clinical
by Andrew Dedinas Geoly 20 Jun '23

20 Jun '23

External Email - Use Caution Hello Freesurfer experts! I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days after intervention) and 1-month following the intervention. I have been working with the recon-all longitudinal pipeline stream (7.1.1) but have noticed pretty significant errors in terms of skull stripping and segmentation (participants are veterans with somewhat random lesion / atrophy patterns). I have tested your new recon-all-clinical program (7.4.0) on some of my worst cases and it is performing remarkably well. I am doing some more digging into the various synth segmentation packages available in FS newest versions and was wondering what the best course of action would be for integrating recon-all-clinical or synthseg into a longitudinal workflow. 1.Could I use the recon-all-clinical outputs as the "cross" for later base and long template construction? 2. SynthSeg and SCLimbic seem to have very good test-retest reliability-- would it be feasible to use the independent segmentation extractions from those and bypass the longitudinal stream entirely (not saying I would want to but I am curious)? Any and all help here would be greatly appreciated, and I thank you very much for your time. Warmest regards, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine

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FS 7.4.1, MiDeFace fix
by Douglas N. Greve 20 Jun '23

20 Jun '23

External Email - Use Caution FS 7.4.1 is now available here https://secure-web.cisco.com/17-PRJfqpn9BuagsDlTJ1iBDfnqh2fW4JB_SRTk0Nrzd56… The only change is a bug fix to MiDeFace. https://secure-web.cisco.com/1InRJsRxr1cJyXEd0j0nFXhSVxdktDhalS8LTSCvY-rSOK… A bug was found in the 7.4.0 version of MiDeFace when creating the head mask and true face surface. In a small number of cases, it was found that the thresholds were being set too high causing an undersegmentation of the head. The problem was worse in non-T1w contrasts. This likely does not compromise privacy; rather, it typically caused the defacing to be too aggressive. Release notes are here https://secure-web.cisco.com/1gJhtPWK_PcnfeYYEH5vaPwUgai85exNagU7tYLZl_yPeK… thanks and sorry for any inconvenience doug

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How are they using freesurfer in a big dataset?
by Michelle Diniz 20 Jun '23

20 Jun '23

External Email - Use Caution Hey guys. I'm using FMRIprep on the OASIS3 database and I've noticed that the processing time for each subject averages two days. 80% of that processing is due to the freesurfer. I will need to analyze many resonance images, more precisely the functional part. I tested SMRIprep and didn't get a significant improvement in processing time. How are you getting around this type of problem? How are they using freesurfer in a big dataset? -- Michelle Diniz Lopes

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Size of overlap between a label and a volume
by parsatad＠student.ubc.ca 20 Jun '23

20 Jun '23

External Email - Use Caution Hello, Hope you are doing well. I'm new to freesurfer so I was wondering if you could help me out with something please. I'm looking for a simple way to find the size (i.e. volume in mm3) of overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in an aparc+aseg file and a NIfTI volume file that can be overlayed on the aparc+aseg file. Please look at the attached file for a better visualization of what I'm describing. I'd really appreciate it if you could point me in the right direction. Thank you, Parsa

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aggregating outputs
by Nikolaidou, Sofia 20 Jun '23

20 Jun '23

External Email - Use Caution Good morning, I would like to aggregate the measurements for average cortical thickness across the two hemispheres. I read on the FAQ of the FreeSurferWiki that one way to do this is the following: bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea) Would you suggest any other alternatives to consider? Kindly, Sofia Sofia Nikolaidou | Clinical Research Coordinator MGH/HST Martinos Center for Biomedical Imaging 149 13th St, Charlestown, MA 02129 Phone: 617-417-4463 snikolaidou(a)mgh.harvard.edu

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Dimension mismatch MRIS PREPROC
by Akansha Mahesh Naraindas 20 Jun '23

20 Jun '23

External Email - Use Caution Hi I am attempting to create a group file using MRIS PREPROC My command is as follows mris_preproc --fsgd brainmorph.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --out mripreproc-rh-thickness.mgh But I am receiving the error ERROR: dimension mismatch between *first two subjects* Would you be able to advise the cause of this error as I am unsure what is causing it Thanks!

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Tksurfer tmp.tcl
by Robert Terziev 20 Jun '23

20 Jun '23

External Email - Use Caution Hello, I am trying to run an old script from the ENIGMA webpage, that was based on freesurfer 5.1 and uses tksurfer. Here is a code excerpt: tksurfer $sub lh pial -tcl tmp.tcl echo "labl_import_annotation \"aparc.annot\"" > tmp.tcl echo "scale_brain 1.35" >> tmp.tcl echo "redraw" >> tmp.tcl echo "save_tiff "$QCdir/$sub/"rh.lat.hr.tif" >> tmp.tcl I have found that I could try to use tksurferfv instead, but then I get the error message “Option 'tcl' not recognized. Run 'freeview -h' for more information.” Running 'freeview -h', I don’t find a solution. Is there a workaround for that problem? Thank you very much in advance. Kind regards Robert Freesurfer Version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Plattform: macOS Ventura v13.3.1

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Freeview: data not displayed
by Haley O Higginbotham 17 Jun '23

17 Jun '23

External Email - Use Caution Hi FreeSurfer Developers, I've just installed Freesurfer and am trying to view a sample subject's data in Freeview (bert T1.mgz) but nothing is displayed (blank black screen - see attached screenshot). Xming is running and I've confirmed graphics function with xeyes. The progress bar in Freeview also completes and zooming in/out hasn't helped. I've also tested other volumes, surfaces, and patients with the same results. I'm running freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 on Ubuntu 20.04.6 LTS via WSL2 Has anyone experienced something like this before or have any clue what might be going on? Sorry if it's a simple solution - I'm new here Thanks in advance, Haley [cid:71a16993-26fc-4e0c-b21c-e03609ba5b22]

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vol2subfield query when extracting stats from DTI images
by Anya Borissova 16 Jun '23

16 Jun '23

External Email - Use Caution Dear Freesurfer experts, We hope you are well. We are having problems with using vol2subfield when attempting to extract hippocampal subfield info from DTI images. Our T1 images have been co-registered to their matching DTI images in SPM prior to being run through the recon-all pipeline output files - this looks good. We have run segmentHA_T1.sh and the results look good. We created a register.lta between the DTI image and the orig.mgz: bbregister --s sub1/ --mov DTI.nii --reg register.lta --t2 The bbregister register.lta output looks good when checked with tkregister. We then run vol2subfield as recommended: vol2subfield --i DTI.nii --reg register.lta --sf sub1/mri/lh.hippoAmygLabels-T1-T2.v22.FS60.mgz --o dti.rh.FS60.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol avgwfvol.mgz When we look at the output image overlayed on the DTI.nii/orig.mgz, it looks like everything has been shifted down (on the output image - dti.rh.FS60.mgz) and it doesn’t line up with the anatomy (e.g. subfields are overlayed over the ventricles). However, when we overlay the hippocampal subfield segmentation on our original DTI image, this still looks fine. We can provide images of the various scans/registrations on request Are the stats files produced by vol2subfield related to the vol2subfield output image (and therefore look like they're sampling the wrong area), and could you help us figure out where we're going wrong if so, please? We are using Freesurfer version 7.3.2 with Linux (freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275, Linux login1.nan.kcl.ac.uk 4.18.0-425.19.2.el8_7.x86_64 #1 SMP Tue Apr 4 05:30:47 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux) Kind regards, Thank you Anya & Pete Anya Borissova (she/her) Academic Clinical Fellow, CT3 Psychiatry South London and Maudsley NHS Trust / King's College London Co-host The Thinking Mind podcast - https://secure-web.cisco.com/1_bQVYLS5BbWl03V1Zr9cgJ7t9uyj-JYZOohziGCJ-gD6I…<https://secure-web.cisco.com/1IRLk-P7rXb1Y1y9yU1Xvow2yPs6XwcJtMdZA62FbEy_9q…>

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place pial matter on top of the cortex using segmentation volume
by Malav Shah 16 Jun '23

16 Jun '23

External Email - Use Caution Dear freeesurfer team, Thank you for your support. I have cortical thickness measurements. I want to know if I can visualise it on top of the pial matter surface. I guess my mail missed the thread conversation, so asking as a new issue. At the moment, I can see only white matter surface in its appropriate form. Pial surface looks more like a blanket on top of the grey matter, rather than bedsheet as it should ideally look. I understand that's the issue because Iextract pial matter with mri_tesselate command from tissue segmentation (white-, pial- and grey-matter labels). I think I am looking for pial matter surface that the command 'mris_place_surface' generates in traditional recon-all pipeline, and want to measure its curvature and surface area). Can you please suggest how can use that command, or some other alternate to see pial mattter on top of the cortex? Thank you in advance. - malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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Freesurfer June 2023