Freesurfer

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19 participants
30132 discussions

Infant FreeSurfer - some questions re. inputs and outputs
by Fleur Warton 05 Oct '20

05 Oct '20

External Email - Use Caution Hi FreeSurfer experts, I have a few questions regarding the infant freesurfer tool, which I'm currently trying to get up and running on my neonatal data. Question 1: I've run the command infant_recon_all --s SUBJ --age 0, but I was wondering if there are specific additional flags that you would recommend. The main thing we're wanting to look at right now is total cortical gray and cerebral white matter volumes (L and R hemispheres separate). Should I be including --gmwm2 and --force (or any others)? Questions 2,3: After running that command (without the extra flags) I couldn't find any aseg.stats. I was wondering if there's something I've either done wrong, or should be including. Also, which of brainvol.stats, lh.aparc.stats and rh.aparc.stats should I use for the most accurate measure of cortical gray volume and cerebral white volume? Question 4: I saw on this mailing list a thread about quality-checking/ manual editing of the outputs, and that this is currently not available for the infant tool. Is that still the case, i.e. we can check the outputs visually but not make corrections. If so, would we then just run the infant_recon_all command and use those outputs as is? Sorry for the load of questions. I've attached the infant_recon_all log file in case that's needed. Thanks very much, -- Fleur Warton Postdoctoral Research Fellow Division of Biomedical Engineering Faculty of Health Sciences University of Cape Town

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postdoc opening with Thomas Yeo
by Fischl, Bruce 05 Oct '20

05 Oct '20

Thomas Yeo is looking for a postdoc with a PhD in neuroscience, psychology or related field. Start date is any time in 2021. Topics are quite flexible. More details can be found here: https://sites.google.com/view/yeolab/jobs Contact Thomas if you are interested. Cheers Bruce

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mri_vol2surf MRISread error
by KN Qiao 05 Oct '20

05 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, mri_vol2surf --mov $mask_dir/rest_brainmask.nii.gz --reg $reg_dir/rest2t1.dat --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi ${hemi} --o ${mask_dir}/mask.fsaverage.${hemi}.nii.gz --noreshape --cortex --surfreg sphere.reg Error: Loading label /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /Applications/freesurfer/subjects/freesurfer/surf/lh.white MRISread(/Applications/freesurfer/subjects/freesurfer/surf/lh.white): could not open file No such file or directory This problem happens again when I try to use this command on a server in my lab. I didn’t get why it attempted to get surface from /Applications/freesurfer/subjects/freesurfer Should it try /Applications/freesurfer/subjects/fsaverage as well? It can load label properly. Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Darwin-OSX and CentOS6_x86_64

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Re: [Freesurfer] Right-side bias in thalamic segmentation pipeline?
by Iglesias Gonzalez, Juan E. 05 Oct '20

05 Oct '20

Dear Evan, The atlas is designed to be symmetric. Is it possible that the asymmetry is in your data? Another FS user (Chris Vriend, CCed) reported a similar effect (you can find his massage in the archive). Doug: any further ideas? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Gallagher, Evan (NGG)" <Evan.Gallagher2(a)pennmedicine.upenn.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 30, 2020 at 14:18 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Right-side bias in thalamic segmentation pipeline? External Email - Use Caution Hi all, I’ve been working on a project that involves the thalamic segmentation pipeline published by Iglesias et al. in 2018 in NeuroImage (“segmentThalamicNueclei.sh”). While the pipeline itself works great, we have noticed that the right hemisphere VOIs tend to have slightly larger volumes than the left hemisphere VOIs. This has been true in two separate datasets (n=24 and n=25), neither of which has an obvious physiological trait that would lead us to expect these sorts of hemisphere differences. This is my first time posting a question on this list, so I’m not sure if images are OK. If yes, there are a couple posted at the bottom of this message that should visualize what I’m talking about. If not, I can say that the volume differences are most pronounced in the largest VOIs (PuM, VPL, VLp, etc); in these regions, the right side is ~200-300 cmm larger than the left side. Additionally, the average volumes on both sides are reasonable based on Figure 8 of Iglesias et al (in the sense that our average volumes are well within the violin plots in that figure). I’m wondering if anyone has encountered this trend before, and/or if there’s a correction I might implement to equalize the volumes. We want to be understand—to the extent possible—the extent to which these differences are driven by biology vs image processing. Thanks so much, Evan Images follow: [cid:image001.png@01D69736.EDCFE020] [cid:image002.png@01D69736.EDCFE020] [cid:image003.png@01D69736.EDCFE020]

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Error in selxavg3-sess and Xtmp.mat file
by Erica Israel 05 Oct '20

05 Oct '20

External Email - Use Caution Hi there, I am having trouble running the selxavg3-sess command, in which I am receiving the error: Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3b (line 394) XCond = cond(XtX); I assume it has something to do with my paradigm file, but was not able to figure out the main issue as I keep getting the same error after changing possible problems in the file (extra characters, changing to plain txt etc.) Looking into the Xtmp.mat file, I saw that only the 7th and 8th rows and columns consisted of NaN but am not sure how to interpret this. Below is what my paradigm file looks like and my Xtmp file is attached. 0.0000 0 20.00 1.0 rest 20.000 1 20.00 1.0 thumbab 40.000 0 20.00 1.0 rest 60.000 2 20.00 1.0 thumbflex 80.0000 0 20.00 1.0 rest 100.000 3 20.00 1.0 thumbrot 120.000 0 20.00 1.0 rest 140.000 4 20.00 1.0 index 160.000 0 20.00 1.0 rest 180.000 5 20.00 1.0 digits 200.000 0 20.00 1.0 rest 220.000 6 20.00 1.0 wristProSup 240.000 0 20.00 1.0 rest 260.000 7 20.00 1.0 elbowFlex 280.000 0 20.00 1.0 rest 300.000 8 20.00 1.0 wristFlex Additionally, here is an example of what I ran to make one of the analysis sessions: mkanalysis-sess -fsd left -stc up -surface self lh -fwhm 5 -event-related -paradigm ParadigmFile -nconditions 8 -spmhrf 0 -TR 1.08 -refeventdur 20 -nskip 4 -polyfit 2 -analysis left_arm.lh -per-session -force Thank you for the help! -- Erica Israel Senior Research Support Associate MIT Media Lab - Biomechatronics Group

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Extraction of subject-wise values after permutation test !
by Martin Juneja 05 Oct '20

05 Oct '20

External Email - Use Caution Hello everyone, I have significant group differences in volume (controls > patients) for one of the clusters (say C1) - calculated after permutation test using PALM, which gives me following outputs: *_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of voxels = 1105) *_clustere_tstat.mgz *_dpv_tstat_fwep.mgz *_dpv_tstat_uncp.mgz *_dpv_tstat.mgz I was wondering if there is a way to calculate volume values of C1 for each subject (i.e., controls and patients). Thanks.

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New hypothalamus segmentation tool in FreeSurfer
by Iglesias Gonzalez, Juan E. 05 Oct '20

05 Oct '20

Dear FreeSurfer users, We now have in the development version of FreeSurfer a machine learning tool to segment the hypothalamus and its subregions. Here is the description of the tool in the FreeSurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits The development version of FreeSurfer can be download as usual from: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ Any feedback on the tool is greatly appreciated. Kind regards, Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Macaque Brain Segmentation
by Jie Zhao 05 Oct '20

05 Oct '20

External Email - Use Caution Hello Freesurfer Team I am trying to segment the macaque brain. After skull strip, control point adding and white matter editing, I try to inflate the brain surface. My command is :recon-all -s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80 The output error is:need seg for ripping. But i used the noaseg flag for macaque brain segmentation. Can you help me explain this and how to solve this problem? I have attached the recon-all.error and brainmask.mgz and wm.mgz . Thanks in advances! All best, Jie

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mris_convert orientation problem when converting from FS to .vtk
by Schumann, Aicko 04 Oct '20

04 Oct '20

External Email - Use Caution Dear Freesurfer Developers, I must admit that I have not used Freesurfer for quite some time, i.e. I may be a little rusty. I vaguely remember having the same issue a few years ago, but I cannot find anything in the forum that seems to work for me. Hence, I apologize for a potentially trivial question: I am having problems with mris_convert when trying to convert a surface from FS format to .vtk. It seems that during the conversion the orientation of the surface is somehow changed to what looks like a rotation by 90 degrees (indeed the file information seems to suggest a [x,y,z] <-> [x,z,-y] transformation). For instance, after running "recon-all" on a standard MNI152 brain (here borrowed from FSL), I want to convert the pial surfaces to .vtk format for further processing. I use the following simple command: mris_convert lh.pial.T1 lh.pial.T1.vtk Opening both surfaces in, for instance, freeview shows lh.pial.T1.vtk somewhat rotated by 90 degrees. Other target surface formats have the same issue. My suspicion is that there is some intrinsic orientation change during the conversion. How can I preserve the orientation during mris_convert? Wouldn't that be the expected behavior? Alternatively, how can I change the orientation of a surface file after the conversion? Thank you for your advice! Best, Aicko ---- Dr. rer. nat. Aicko Yves Schumann Research Assistant Professor Physicist, Center Statistician, Big Data Scientist Institute of Psychiatry Medical University of South Carolina 67 President Street (Rm. BA506C) Charleston, South Carolina, 29425 United States Phone Office: +1 843-792-6470 Phone Cell: +1 843-532-8506

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How to draw streamlines and their corresponding ROIs using freeview
by Zhiyuan Yu 04 Oct '20

04 Oct '20

External Email - Use Caution Hi, I have extracted fibers and the corresponding ROIs. I would like to know how can I draw them together using freeview. Thank you, Zhiyuan

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