Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

-nofix topology command
by Stephan Wunderlich 20 Apr '21

20 Apr '21

External Email - Use Caution Dear all, I want to run recon-all with the -nofix command, so that no fix of the topology is done, because it takes too much time or never finishes. Especially these commands in the recon-all.log file never finish. PIDs (232383 232386)… But sometimes when I run recon-all with -nofix the surf/xh.orig files are not created since this is done by the fix topology command. Is there way to still create these files without fixing the topology of the brain so that recon-all finished successfully? I remember that in older version of freesurfer there was not fix topology and it worked as well. Best, Stephan

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FLAIR image analysis
by Jindal, Saurabh 20 Apr '21

20 Apr '21

External Email - Use Caution Hi experts, Could we analyze FLAIR images using freesurfer without having T1 images? Saurabh ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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problem running last step longitudinal analysis
by Zeng, Qi 20 Apr '21

20 Apr '21

External Email - Use Caution Hi Experts, I am running the last step (-long) for a longitudinal analysis, However, encountering an error message saying: "error: ERROR: number of asegs and norm volumes do not match" for all the subjects I run this time. A similar problem has been reported before as the following link. The answer to the question is 'Freesufer version too old'. I have been following the exact same steps two months ago for my last cohort and it was fine. However, this time all the subjects reporting error messages (attaching error.log). Re: [Freesurfer] mri_fuse_segmentations error in longitudinal stream (mail-archive.com) <https://secure-web.cisco.com/1xcCNPG6jeY7R3XZUuavTvtod8U5a5tYZLLrz9Kuekmq6u…> My system: x86_64 GNU/Linux Freesufer version: freesurfer/6.0.0 attached the error.log Best, Qi

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recon_all subcortical volume adjuested eTIV
by Jaime Gomez 20 Apr '21

20 Apr '21

External Email - Use Caution Hi, Does the asegs.stats produced by recon_all have the volume estimates of subcortical structures adjusted by the eTIV? I want to understand the effect of sex in the segmented structures. Should normalize the volumes of aseg.stats (Vol/eTIV) or is already done in recon_all? Thank you!

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Re: [Freesurfer] Native volume to fs_average surface
by Glasser, Matthew 20 Apr '21

20 Apr '21

External Email - Use Caution You would do that through the subject’s own surface. It does not work very well to map data directly from the volume onto group average surfaces (see e.g. Coalson et al., 2018 PNAS). Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>, "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Native volume to fs_average surface External Email - Use Caution Hi experts, I have some fMRI data that I have pre-processed in Feat. I want to resample a single subject's data to the fs_average surface but unsure of the most optimal way of doing this. At present I am warping the functional data to the MNI brain in the volume (using FSL's applywarp) and then resampling to fs_average using the following command. * mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh --hemi rh --mni152reg My question is whether you think this is the most appropriate approach, and/or if there is way to move directly from native volume to fs_average surface without needing to go via MNI volume? 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/1qGEoQnnU3besQKg-GQwdKq-WtCCzi1b5tl-HNLywYRQ48…> 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Building atlas by Xhemi: Segmentation fault (core dumped)
by Li-Zhen Chen 20 Apr '21

20 Apr '21

External Email - Use Caution Hello Freesurfer Developer， I'm building my own symmetric atlas by Xhemi, something is wrong at the final step(Make final iteration) Here is my code: make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --subjects sub_01 sub_02 --xhemi --lh When I ran this code, a problem emerged. Here is part of the log: mris_seg2annot --seg /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh --ctab /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab --s myatlas.i3 --hemi lh --o /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot $Id: mris_seg2annot.c,v 1.10 2014/11/15 00:07:19 greve Exp $ cwd /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3 cmdline mris_seg2annot --seg /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh --ctab /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab --s myatlas.i3 --hemi lh --o /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot sysname Linux hostname chenlz-HP-ZHAN-99-Pro-G2-Microtower-PC machine x86_64 user chenlz subject myatlas.i3 hemi lh surfseg /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh ctab /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab annotfile /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot Reading surface seg /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.vote.mgh Reading surface /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/surf/lh.white Reading ctab /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab Writing annot to /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot Annot2std-Run-Time-Sec 16 annot2std Done mri_annotation2label --subject myatlas.i3 --hemi lh --outdir /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214 --annotation aparc.a2009s subject = myatlas.i3 annotation = aparc.a2009s hemi = lh outdir = /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214 surface = white Reading surface /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/surf/lh.white Loading annotations from /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 11176 entries read (originally /media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/label/tmpdir.annot2std.8488/seg.1.sub_01.xhemi.ctab) Segmentation fault (core dumped) ERROR: make_average_surface I run Freesurfer 6.0 on Ubuntu 18.04. I've tried to rerun my script several times but I can't figure this problem out. What could be the possible reasons? Any answer will be appreciated! Kind regards, Jewel

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question about lesion segmentation using samseg
by Ritobrato Datta 19 Apr '21

19 Apr '21

External Email - Use Caution Hi All, I have T1w MPRAGE, T2w and PD images but I dont have FLAIR images from a Multiple Sclerosis study. Can I use samseg to segment the lesions ? Can you please suggest ? Many thanks Ri

2 1

Tracula group analysis in freesurfer
by Zeng, Qi 19 Apr '21

19 Apr '21

External Email - Use Caution Hi Experts, I understand there is surface-based group analysis in Freesurfer, which is for thickness, curvature, volume and etc. Is there a group analysis for DTI tracula results? Any links to recommend to conduct the analysis? Thank you so much! Best, Qi

2 1

Abormally high foldind index
by Ellen Ji 19 Apr '21

19 Apr '21

External Email - Use Caution Dear Experts, While the majority of our subjects have a folding index between 5-30, there are a couple of *extreme* outliers in the thousands or even negative. Could this hint that a particular part of recon-all failed and should be rerun? Thank you for your interpretation and advice! -Ellen

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Autorecon1 failure
by Abdollahi, Shervin (NIH/NINDS) [C] 19 Apr '21

19 Apr '21

External Email - Use Caution Hello Freesurfer Developers, am trying to use run freesurfer that is configured inside smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeline. this workflow, does the following: 1. T1w reference: realigning and then averaging T1w images 2. Brain Extraction and INU (bias field) correction (antsBrainExtraction.sh) 3. Brian tissue segmentation (@fsl_fast) 4. Spatial normalization to standard space (antsRegistration) 5. Surface reconstruction with Freesurfer When it gets to step 5, it takes skull-stripped t1, ants_segm, and bias_corrected image to use in freesurfer recon-all command. In the surface reconstruction section, it starts by running the following command: recon-all -autorecon1 -i /path-to /sub-03_ses-20140624_T1w.nii -T2 /path-to/sub-03_ses-20140624_T2w.nii -noskullstrip -hires -openmp 1 -subjid sub-03 -sd /Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer -expert /Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts And surely soon, it gives me an error that it can not read mgh file (brainmask.mgz). looking into freesurfer/sub-03/mri directory I can see that brainmask.mgz is not created and I am not sure if this is because the option -noskullstrip was used? I have attached the recon-all.log file. I would appreciate any suggestion on how to debug this problem. 1. Freesurfer version: 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551) 2. Platform: macOS Catalina, Version 10.15.7 3. uname -a: Darwin ndsd-eeg-cedar 19.6.0 Darwin Kernel Version 19.6.0: Tue Jan 12 22:13:05 PST 2021; root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64 4. Recon-all.log: see attached

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Freesurfer April 2021