Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

Regarding a problem in spatiotemporal linear mixed effects model analysis
by yildirim adalioglu 06 Nov '23

06 Nov '23

External Email - Use Caution To whom it may concern, Hello! We are currently trying to do a ST-LME (Spatiotemporal-LME) analysis based on bipolar disorder brain MRI images. We are having 2 problems: 1)In the lme_mass_fit_EMinit step, we get a warning that says matrix is singular, close to singular or badly scaled. 2)In the lme_mass_RgGrow step, it says "computing seeds" indefinitely and it never ends. We looked for people having similar problems, however we could not find a solution. Currently, we suspect that this may be due to the zeros in the columns of fs_read_Y('lh.thickness_sm10.mgh'). Do you happen to know the reasons of these problems? Thank you for your time. Sincerely,Yıldırım Adalıoğlu

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Longitudinal multimodal processing
by gabriel robert 04 Nov '23

04 Nov '23

External Email - Use Caution Dear experts in longitudinal neuroimaging We carefully read the papers about possible biases introduced by treating timepoints images differently (Reuter and Fischl NI 2011, for example) to estimate unbiased anatomical and functional changes of brain development in healthy individuals. We took good note that treating each time point independently would remove asymmetry biases at the cost of reduced power. In our project, we would like to analyze about 800 scans both 3DT1, diffusion (FA preprocessed with fsl TBSS) and functional task BOLD at 3 time points (14 years-old, 19 years-old and 23 years-old). Each time point scans are preprocessed individually and normalized to a specific group-based template at the corresponding time point (not a within-subject midpoint symmetric space) and to the standard MNI space. Our question: We'd like to use a home-made study-specific multimodal atlas to resample ROI BOLD mean contrasts and fractional anisotropy at each time point but this atlas is *based on the last time point only (23 years-old).* Does this situation fall into the 'asymmetry-induced bias in longitudinal processing' ? Our feeling is most probably yes but given the sample size this is likely to be marginal compared to the effect size and results would still be interpretable... ? Many thanks for time, interest and insight, Best wishes Gabriel

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Problem with mri_robust_register when using segmentThalamicNuclei.sh
by Xingyu Liu 02 Nov '23

02 Nov '23

External Email - Use Caution Dear freesurfer experts, I was trying to segment thalamic nuclei using segmentThalamicNuclei.sh after a preprocessing using fMRIPrep 23.1.4 with fs recon-all. But it turned out with an error regarding mri_robust_register. Log shown below. ------------------------------ PROCESSID 41966 PROCESSOR x86_64 OS Darwin ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin liu-imac 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:42:42 PDT 2023; root:xnu-10002.1.13~1/RELEASE_X86_64 x86_64 ------------------------------ freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 setenv SUBJECTS_DIR /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer cd /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer /Applications/freesurfer/7.4.1/bin/segmentThalamicNuclei.sh sub-01 /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer #-------------------------------------------- #@# Thalamic Nuclei processing Wed Oct 11 13:29:13 EDT 2023 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.4.1/MCRv97//runtime/maci64:/Applications/freesurfer/7.4.1/MCRv97//bin/maci64:/Applications/freesurfer/7.4.1/MCRv97//sys/os/maci64:/Applications/freesurfer/7.4.1/lib/gcc/lib: Registering imageDump.mgz to mask from ASEG /Applications/freesurfer/7.4.1/bin//fs_run_from_mcr /Applications/freesurfer/7.4.1/bin///mri_convert /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer/sub-01/tmp/THnuclei_v13_useTwoComponents_1_T1//THDEbinaryMask.mgz aux.mgz -odt float -vs 1 1 1 -rt nearest >/dev/null: Signal 127 mv: aux.mgz: No such file or directory /Applications/freesurfer/7.4.1/bin//fs_run_from_mcr /Applications/freesurfer/7.4.1/bin///mri_robust_register --mov imageDump.mgz --dst /Users/xingyuliu/dataset/neuro/MPG/ds001168_custom/derivatives/sourcedata/freesurfer/sub-01/tmp/THnuclei_v13_useTwoComponents_1_T1//THDEbinaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50 >/dev/null: Signal 127 Error using SegmentThalamicNuclei (line 249) Problem with mri_robust_register Darwin liu-imac 23.0.0 Darwin Kernel Version 23.0.0: Fri Sep 15 14:42:42 PDT 2023; root:xnu-10002.1.13~1/RELEASE_X86_64 x86_64 Thalamic nuclei exited with ERRORS at Wed Oct 11 13:29:23 EDT 2023 ------------------------------ Thank you very much for your help! Best, Xingyu

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FSPGR Recon All Error
by Massimo Valerio 02 Nov '23

02 Nov '23

External Email - Use Caution Il giorno dom 8 ott 2023 alle ore 16:58 Massimo Valerio < massimo.valerio(a)unito.it> ha scritto: > Hello FreeSurfer Developers, > > I'm attempting to compute the recon-all of my patient FSPGR (fast > spoiled gradient-echo) of three-dimensional MRI data > ERROR: mri_cc: no WM voxels found with norm > 40 -- check skull stripping > > > I've searched the list and no same errors have been reported. > Does anyone have any thoughts on how to trouble-shoot this one? > Also, Ive attached the recon-all.log in case it's of any use. > > 1) FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275 > 2) Platform: MacOs Ventura 13.6 > 3) uname -a: Darwin MacBook-Pro-di-Neuroland.fritz.box 22.6.0 Darwin > Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; > root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64 > 4) recon-all.log: see attached > > > Dott. Massimo VALERIO > > Neuropsichiatra Infantile > SSD Neurologia Pediatrica > Dipartimento di Patologia e Cura del Bambino Regina Margherita > A.O.U Citta della Salute e della Scienza della Citta di Torino > Presidio Ospedale Infantile Regina Margherita > Email: massimo.valerio(a)unito.it > > > <https://secure-web.cisco.com/1hGQ2Ktox86EwpKDERFOjsru_gSyhek2B23t1VWBMgvO6S…> Privo > di virus.http://secure-web.cisco.com/1OmCce9Gor4-SmaxBnuSXzDcrgpxIAHB9uE5V6KmR… > <https://secure-web.cisco.com/1hGQ2Ktox86EwpKDERFOjsru_gSyhek2B23t1VWBMgvO6S…> > <#m_-561044188468629674_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >

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Advice for measuring cortical thickness from a custom label
by Tyler J Ward 02 Nov '23

02 Nov '23

External Email - Use Caution Hi FreeSurfer developers and community, I have a template space statistical surface map that I want to extract cortical thickness and volume from several thousand MRIs with freesurfer parcellations. I converted the map to a cortical label using *mri_surfcluster.* > *mri_surfcluster --in sig.mgh --thmin 4 --sign neg --hemi lh --subject > fsaverage --olab ./my_label --cortex* > [image: unnamed.png][image: unnamed2.png] I then converted these template space labels to subject space labels using mri_label2label. > *mri_label2label --srcsubject fsaverage --srclabel ./**my_label**.label > --trgsubject bert --trglabel ./**burts_label* > *.label --regmethod surface --hemi lh* > Lastly I extracted thickness and created volumes from these labels. > *mri_segstats --slabel bert lh **burts_label* > > *.label --i $SUBJECTS_DIR/bert/surf/lh.thickness --nonempty --excludeid 0 > --sum ./bert_thickness_table**mri_label2vol --o ./berts_mask.mgh --label > ./**berts_label**.label --temp $SUBJECTS_DIR/bert/mri/nu.mgz --subject > bert --hemi lh --fillthresh 0.3 --proj frac 0 1 .1 --identity* > The results look okay but the voxels are not as clean as other freesurfer volumes and ROIs. For example, the cortical masks created from the label have small holes inside the mask. [image: 2023-10-06T16:24:00,146947999-07:00.png] I decided to smooth this by 3mm^3 fwhm and threshold by the left hemisphere cortical parcellation in aparc+aseg.mgz file to get a better looking ROI that is contained by and filled into the freesurfer cortical parcellation: [image: 2023-10-06T16:23:51,051653286-07:00.png] [image: 2023-10-06T16:37:34,665543751-07:00.png] From this, I have a couple questions: 1.) Can I expect my custom ROI thickness to be comparable to the thickness values outputted by Freesurfer for the Deikan-Killiany atlas? 2.) Is there anything I can do to verify the accuracy of the cortical thickness within this ROI? 3.) How can I extract volume from this ROI (should I just count voxels?) and will it be valid to do a cross-sectional analysis of volume from a region derived from a surface label, just as we look at any other region (tiv adjusted hippocampal volume for example)? Thanks in advance for your time and advice, Tyler

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registration of a rescaled volume
by Malav Shah 02 Nov '23

02 Nov '23

External Email - Use Caution Hi there, I have an animal brain's MRI with 3 volumes, each with a good resolution in one of the planes. (i. 768x768x88, ii. 768x768x150, iii. 768x768x140) As far as I understand freeSurfere doesn't have a 3D ihgh-res reconstruction tool, right? So I tried to reconstruct a high-resolution 3D volume with NiftyMIC ( [ https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBm… | https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBm… ] ), but unfortunately it didn't work for me. My final goal is to get good tissue segmentation (pial-, grey-, and white-matter labels). So now I am considering rescaling one of the scans in a high-dim. space (768x768x768) using imresize3 (or something similar for interpolation) with MATLAB. The rescaling works, but the non-high-resolution planes turn out to be elongated. I am not sure how to get past this issue, and register the new rescale volume with one of the old ones (trying some params with mri_vol2vol might work?) At the end I want to visualize rescaled 3D volume on top of the original scans, so I can at least (semi-automatically and then) manually segment it. thanks in advance :) - malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) on fMRIprep
by Siegel-Ramsay, Jennifer 02 Nov '23

02 Nov '23

External Email - Use Caution Hello, We are trying to run freesurfer through fMRIprep and for the first time ever, I have a series of anatomical scans that are failing during registration. Normally we run this on the normalized T1 scan outputs and have no problem, but these are the original images non-normalized images. My random guess is that there might be too much inhomogeneity in the T1 signal to run freesurfer? I am very new and have rarely used freesurfer. Here is the fMRIprep error (full log attached) #@# Talairach Failure Detection Mon Oct 2 15:32:02 CDT 2023 /work/06950/j/ls6/project_nndcbipolar/derivatives/fmriprep-v23.1.3/sourcedata/freesurfer/sub-ut0006/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1kkJIUzEvH0ScGRNqsTstzKtzyE2xMeizp0oaQP3-n-ioGW… Ok, I've tried going through this https://secure-web.cisco.com/1QtKKJUk_dNKuv9HQvIxbFlVKsOnN9ROC0VGd25vitNurR… to figure out what is going wrong with the T1 images during the freesurfer registration with fMRIprep. Freesurfer isn't liking our T1 images. This image is the freesurfer output (output under derivatives/frmiprep/sourcedata/sub-ut0002/mri/T1.mgz [cid:image005.png@01D9F782.EC5FF0E0] The above should come out registered to this one which is the sub-ut0002/mri/brainmask.mgz:reg=sub-ut0002/mri/transforms/talairach.xfm [cid:image006.png@01D9F782.EC5FF0E0] I can't go in and manually alter the T1 to be in alignment in tkregisterfv because I don't have any of the needed files output in the surf folder. Getting... ERROR: cannot find /home/jovyan/freesurfer-subjects-dir/sub_ut0002/surf/lh.white I am attaching the full crash log from fMRIprep and also the script output. I wonder if you could help me understand what might be going wrong? Thanks, Jennifer Jennifer Siegel-Ramsay, PhD Postdoctoral Fellow Department of Psychiatry and Behavioral Sciences Dell Medical School | The University of Texas at Austin dellmedschool.utexas.edu<../../../../../lep66/AppData/Local/Microsoft/Windows/INetCache/Content.Outlook/H3ICGTO9/dellmedschool.utexas.edu>

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Project volumetric MTR data on surface
by Davide Tabarelli 02 Nov '23

02 Nov '23

External Email - Use Caution Dea FreeSurfer experts, I’m writing in order to ask how to map on a surface data from a volumetric MTR image. I have volumetric Magnetization Transfer Ratio data co-registered to the subject native space of a subject (as produced by recon-all on a T1 acquisition). The subject, for which I have also the T1 and T2 scans, has been already processed with recon-all, then I have the complete folder of the subject, as produced by the recon-all standard pipeline. I need a surface in the native subject space containing the MTR data, averaged along the surface normals for a certain amount of millimeters. It would also be useful to define the surface as in a certain midway between the pial and the white surfaces. I tried to understand the mri_vol2surf tool but I’m stuck in understanding the correct way to do this and if this is the correct command to be used. I would greatly appreciate your help ! Thank you in advance. Davide

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Possible Skull-Stripping Error in Many Subjects (FS7.2)
by Carly McIntyre-Wood 02 Nov '23

02 Nov '23

2 1

FSGD file and constrast
by Steve Petersen 02 Nov '23

02 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have MRI data of one group of subjects and would like to evaluate positive and negative correlations between cortical thickness and some biomarkers by excluding the potential effects of age and sex. I followed the FS tutorials ( https://secure-web.cisco.com/1Y5TdIEJ9ARZSn2I1-6PLi22V0MhAKTkmre4K1MKlAmgQh…) and have read previous posts on the FS´s mail archive but I would appreciate if you can check if my FSGD file and contrasts are right. The FSGD file looks as follows: GroupDescriptorFile 1 Title CTh_Bioma Class Female Class Male Variables age biomarker Input 4009 Female 60 222.0 Input 4014 Male 70 195.6 Input 4022 Male 68 230.2 Input 4027 Female 65 250.0 Input 4039 Male 62 205.6 Input 4001 Male 63 270.2 Input 4002 Male 78 245.5 Input 4004 Male 66 234.1 Input 4050 Female 62 210.0 And these would be my contrasts: positive correlation between thickness and the biomarker: 0 0 0 1 negative correlation between thickness and the biomarker: 0 0 0 -1 Thank you very much in advance. Best regards, Steve.

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Freesurfer November 2023