Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

Tracula registration failure
by Marena Manierka 03 Jun '21

03 Jun '21

External Email - Use Caution To the Tracula team: I am attempting to complete my first project using the Tracula pipeline on a mixed dataset of autism, schizophrenia, and control adult brains. I ran the tracula prep, bedp and path steps for the autistic subject in question without receiving any error messages. However, when I attempt to view the registration of the FA.bbr.nii.gz image to the MNI brain the registered image appears as a completely white, roughly brain-shaped mask. This has not occurred with other subjects from the dataset. I have attached a screenshot from freeview for reference. When I load the subject's dtifit_FA.nii.gz in freeview it appears to be relatively normal. Is this a fatal error in the registration process, and is there any way to correct it? I have also attached the log file for the subject in case this is helpful. Thank you for your help, Marena -- Marena Manierka, B.Sc Graduate Student, Integrative Program in Neuroscience Department of Psychology, MSS 414/ MS0296 University of Nevada, Reno marena.manierka(a)gmail.com

2 4

Recon-all running on a loop
by DIANA ORTEGA CRUZ 03 Jun '21

03 Jun '21

External Email - Use Caution Dear FreeSurfer team, My name is Diana Ortega, I am a Neuroscience PhD student at Universidad Politécnica of Madrid. I run a job to compute recon-all in parallel for 30 subjects remotely on a supercomputer at my research institution. This job finished due to timeout, and all subjects but one finished without errors. However, one of the subjects was not finished and it appears as if it was stuck on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB in size), and from *recon-all-status.log* it appears to be stuck in the "Fix Topology" step. Have you ever encountered a similar situation? Would you know why this could have occurred? Here are the details: FreeSurfer version: 7.1.1-centos8_x86_64 Operative System: CentOS8 Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem SD530 <https://secure-web.cisco.com/1Bch1AH1AvTKzQqcdunZ0FIqTIHtdhvL6XMYZuyZxpRjtV…> Line run for that subject: recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16 When opening *recon-all.log*, it keeps adding the following lines: Remesher::removeTria( 240873 ) Remesher::removeTria( 240876 ) NEXTIDX : 88755 Remesher::removeCollapsedTrias( 88755 , 120326 ) v_to_t[vidx] : Trias are identical : ... removing ... When opening the error.log of the complete job, there are several lines of this error: rm: No match. Any advice will be of great help! Thanks a big lot! Best, Diana Ortega Cruz. PhD Student Laboratory for Clinical Neuroscience Centro de Tecnología Biomédica - Universidad Politécnica de Madrid

2 3

'help: aparcstats2table'
by Zeynep Boz 02 Jun '21

02 Jun '21

External Email - Use Caution Hello, I am using Ubuntu 18.05 version and Freesurfer6 version. I've completed all the recon-all parts without any problems, but I'm having trouble with the "aparcstats2table" part. The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness --tablefile lh.thicknes.xlsx" gives the following error: File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas volume --stats = aseg.stats --table = segstats.txt" gives the following error: File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Thank you in advance for your support Dr.Zeynep YÜKSEL Ondokuz Mayis University Vocational School of Health Services, Medical İmaging 55139, Atakum, Samsun, Turkey Tel: +903623121919 Ext:5261

2 1

mris_fix_topology taking ages
by Ellen Ji 02 Jun '21

02 Jun '21

External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_…, but wasn't able to load the &h.defect_labels as I received the error below. Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong? FYI, I'm running recon-all thru the HCP Pipeline. Thanks! tksurfer avoss_01 lh defect_labels subject is avoss_01 hemi is lh surface is defect_labels surfer: current subjects dir: /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf checking for nofix files in 'defect_labels' Reading image info (/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01) Reading /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz surfer: Reading header info from /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz nquads=4063237, nvertices=664 ERROR: MRISread: file '/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory

4 7

Recon-all error :Segmentation fault (core dumped)
by liub 02 Jun '21

02 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of running,there was an error: mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul Segmentation fault (core dumped) Command exited with non-zero status 1 Also when I ran the command "recon-all -all -s bert" using the official data in */freesurfer/subjects/bert ,it raised the same error. I googled this error,but there's still no answer.I've attached the recon-all.log. The recon-all.log is belong to bert and recon-all(1).log is belong to my data. Here is my operating system info : uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Platform: CentOS Linux release 8.3.2011 FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1 Thank you for your kind help. Best regards.

2 5

mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)
by Diógenes Bispo 01 Jun '21

01 Jun '21

External Email - Use Caution Hi Freesurfer team. I made the following command: #!/bin/tcsh setenv study $argv[1] foreach hemi (lh rh) foreach smoothing (10) foreach meas (volume) mris_preproc --fsgd FSGD/{$study}.fsgd \ --cache-in {$meas}.fwhm{$smoothing}.fsaverage \ --target fsaverage \ --hemi {$hemi} \ --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh end end end ---- #!/bin/tcsh set study = $argv[1] foreach hemi (lh rh) foreach smoothness (10) foreach meas (volume) mri_glmfit \ --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \ --fsgd FSGD/{$study}.fsgd dods \ --C Contrasts/Contrast-1_group.diff.mtx \ --C Contrasts/Contrast-2_group-x-age.mtx \ --C Contrasts/Contrast-3_group-x-icv.mtx \ --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \ --C Contrasts/Contrast-5_GCCV.intercept.mtx \ --C Contrasts/Contrast-6_GCCV.age.mtx \ --surf fsaverage {$hemi} \ --cortex \ --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \ --eres-save end end end ---- #!/bin/tcsh setenv study $argv[1] foreach meas (volume) foreach hemi (lh rh) foreach smoothness (10) foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir) mri_glmfit-sim \ --glmdir {$dir} \ --grf 2.0 neg \ --cwp 0.05 \ --2spaces \ end end end end I have the following error: ... mri_surfcluster --in rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask rh.volume.covid.10.glmdir/mask.mgh --cwsig rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh --sum rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary --ocn rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh --no-fixmni --csd-out rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd --fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg --oannot rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot --bonferroni 2 --surf white ERROR: need --csd with --csd-out How should I proceed to solve this problem? Thanks Diógenes Bispo diogenesdiego(a)gmail.com

2 3

(no subject)
by Francisca Ferreira 01 Jun '21

01 Jun '21

External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I ran mri_glmfit using the following command mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this seems to have worked. I am now trying to visualise my results adapting the recommended wiki command freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d Freeview crashes and I'm getting the following error Number of vertices in overlay data (64 or 64) does not match with surface (163842). Number of vertices in overlay data (64 or 64) does not match with surface (163842). Is there something wrong with the commands priot to this step?

2 2

Acquisition/pipeline question
by Massieh Moayedi 31 May '21

31 May '21

External Email - Use Caution Hi, We’re collecting multiecho T1s. We have individual T1 images with different echoes, and the RMS files. I’ve run freesurfer using both the RMS files, and the multiple echo files (labelled as 001, 002…). I get slightly different results in the parcellation outcomes with the two different methods. Why would that be? What do you recommend for input — the RMS file, or the individual echo files? Thanks, massieh ______________________ Massieh Moayedi, PhD Assistant Professor and UTCSP Pain Scientist, Faculty of Dentistry Co-Director, Centre for Multimodal Sensorimotor and Pain Research University of Toronto http://secure-web.cisco.com/1K6w7Y_uJDRfNwqfL6uDO6MJy1eSSJ1WkHHxHgSG36WhM_v…<http://secure-web.cisco.com/1LEvYjhl0pitHhLUTNoJ9RpfqXnN1s5qlijKej9VsxU6jIk…> pronouns: he/him/his

2 1

extract % signal change in FSFAST analysis
by Star Xi 31 May '21

31 May '21

2 1

FW: mri_convert changing orientation but lose last coronal slice
by Melissa Marie Rundle 31 May '21

31 May '21

External Email - Use Caution Hi, I am using mri_convert to change the orientation of an image in its native space from LPS to PSR. Ex. Mri_convert -out_orientation PSR input_file output_file Sometime when I do this, I lose the last coronal slice(s) of the occipital lobe when the image is converted to PSR. Is there some way to ensure that when I change the orientation, I get the whole brain back? Thanks, Melissa

2 1

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Freesurfer May 2021