Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

Loading surfaces
by Nicole Rychagov 08 Nov '23

08 Nov '23

External Email - Use Caution Dear team: I am reaching out as I have encountered an error when loading surfaces on Freesurfer and am unsure what it means or how to address the error. I am including the error message below, and I would greatly appreciate any assistance you can provide. mrisReadTriangleFile(/mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/lh.pial): surface doesn't match /mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/lh.white No such file or directory mrisReadTriangleFile failed. No such file or directory Converting main surface: 100% done. Converting main surface: 100% done. mrisReadTriangleFile(/mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/rh.pial): surface doesn't match /mnt/d/chtt_edited_long_subjects_corrected/090324_CH8357/surf/rh.white No such file or directory mrisReadTriangleFile failed. No such file or directory reading colortable from MGH file... colortable with 14176 entries read (originally /fslhome/aaclouse/compute/research_bin/version7_2/freesurfer/FreeSurferColorLUT.txt) Thank you so much for your time! Sincerely, Nicole

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fsxvfb error: Falling back to using screens root_visual
by Dani Del Rubin 08 Nov '23

08 Nov '23

External Email - Use Caution Hello Developers, I’m trying to use fsxvfb to run freeview and save some snapshots, but I can’t get it to run. The command I’m executing is: “fsxvfb freeview -v brainmask.mgz -ss pic1.jpg --quit" The output I get is: this pid 23712 setting display to 86 [1] 23721 pid 23721 Starting command freeview -v brainmask.mgz -ss pic1.jpg --quit Falling back to using screens root_visual. Falling back to using screens root_visual. Falling back to using screens root_visual. Falling back to using screens root_visual. Segmentation fault (core dumped) Program exited normally. No image is saved. If I run the command without fsxvfb, it executes successfully ending up with a saved image, although it still gives an error: X server does not support XInput 2 QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code: 130 (Unknown), minor code: 47 QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code: 130 (Unknown), minor code: 47 Also, I can successfully run the AFNI command @snapshot_volreg to output an image, and that script also uses xvfb, so I don’t believe it’s a general problem with xvfb. Finally, my environment by default uses freesurfer version 6.0.0, but I’ve run the commands “export FREESURFER_HOME=/usr/global/freesurfer/7.4.1” followed by “source /usr/global/freesurfer/7.4.1/SetUpFreeSurfer.sh” to temporarily change the version. Other info: 1. Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 2. Platform: Ubuntu 16.04.7 LTS 3. uname -a: Linux [nodename] 4.4.0-206-generic #238-Ubuntu SMP Tue Mar 16 07:52:37 UTC 2021 x86_64 x86_64 x864_64 GNU/Linux 4. I am connecting remotely via X2Go to a MATE setup, which then connects to the compute node. I only saw 5 questions referring to xvfb on the archive, and most questions about xvfb I found online seem to not apply to my situation. Thanks very much for any help! Dani -- Dani Del Rubin, Ph.D. (he/him) Research Data Analyst, Psychiatry Oregon Health & Science University c: 301-437-7660 | rubinstd(a)ohsu.edu

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mri_cvs_register failure
by Antonín Škoch 08 Nov '23

08 Nov '23

External Email - Use Caution Dear experts, I have encountered an failure of mri_cvs_register --mov my_subject --mni The resulting output file final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz looks like in the attachment. Could you please give me a hint, where could be a problem, or how to troubleshoot the mri_cvs_register routine? Regards, Antonin Skoch

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.lta vs .dat questions
by Corinna Bauer 08 Nov '23

08 Nov '23

External Email - Use Caution Hi all, Can someone please explain the difference between .lta and .dat and why the registration looks different using the two file types? If bbregister outputs were already checked and edited (if needed) using the .dat file, is there a way to convert it to .lta? Thanks Corinna

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TR: Issues at the "tailarach_avi" transformation step of recon-all
by Hensenne, Eva (Stud. FHML) 08 Nov '23

08 Nov '23

External Email - Use Caution ________________________________ De : Hensenne, Eva (Stud. FHML) <e.hensenne(a)student.maastrichtuniversity.nl> Envoyé : mercredi 18 octobre 2023 14:41 À : freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Objet : Issues at the "tailarach_avi" transformation step of recon-all Dear Freesurfer Developers, I am currently running recon-all on a UNI scan. This scan has already been partly preprocessed by a script called "presurfer". This presurfered scan should work with recon-all (and it indeed works for my colleagues). However, I have systematically an error when I try to run recon-all on those files. The error says: "talairach_avi log file is transforms/talairach_avi.log... Error:mpr2mni305 failed, see transforms/talairach_avi.log Command exited with non-zero status 1". I attached you the talairach_avi.log and the recon_all.log files. 1. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2. Platform: Unbuntu 22.04 3. Recon-all.log: attached Best wishes, Eva Hensenne

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Atrophy Maps on Coronal Slices
by Daniel Gutstein 08 Nov '23

08 Nov '23

External Email - Use Caution Is there a methodology in FreeSurfer for creating atrophy maps and displaying them on individual coronal slices? Thank you. Daniel Gutstein Research Data Analyst Northwestern University | Mesulam Center for Cognitive Neurology & Alzheimer's Disease 300 E. Superior Street | Tarry 8-734 | Chicago, IL 60611 daniel.gutstein(a)northwestern.edu<mailto:daniel.gutstein@northwestern.edu> | (312) 503 - 8150

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Common space
by Alberto Del Cerro Leon 08 Nov '23

08 Nov '23

External Email - Use Caution Good morning, I would be interested in observing regional differences in cortical thickness without using predefined regions. However the results offered by FreeSurfer arrange the thickness results etc. in an individual space which is difficult to compare between subjects before labeling. Is there a possibility to transform the results to a common mesh (like a template) in order to perform an exploratory analysis?

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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

2 1

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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Freesurfer October 2023