Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

Recon-all killed during mris_fix_topology
by Daan de Jong 21 Dec '17

21 Dec '17

Hello FreeSurfer Developers, I'm attempting to run recon-all on a MPRAGE acquisition (just a single one), and for many subjects the process gets killed during the mris_fix_topology script. An example of the message I get: CORRECTING DEFECT 5 (vertices=22062, convex hull=4299, v0=4005) Killed Linux RAD-MEMORYCL Recon-all –s PINxxx_t0 exited with ERRORS at Tue Dec 19 07:14:34 CET 2017 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I’ve attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 6.8 (Final) 3) uname -a: Linux RAD-MEMORYCL004 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached With kind regards, *Daan de Jong, MSc*

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Question about LME modle
by lanbo Wang 21 Dec '17

21 Dec '17

Dear all freesurfer experts, Hi, When use lme_lowessPlot, the plot shows black and green two lines. What the meaning of two line? Thank you, Lanbo

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T1 problem after reprocessing
by Romella Durrani 20 Dec '17

20 Dec '17

Hi, I'm having problems with T1 after reprocessing. The original scan has no problems on T1 (screenshot attached), but after I edited and reprocessed (edited subcortical aseg and added control points to correct surfaces), the T1 now has problems (screenshot attached). What's causing this issue on T1, which wasn't present on the original scan? Thanks [image: Inline image 1][image: Inline image 2]

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Dec '17

20 Dec '17

Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thank you for your help. > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > system language everything was genereted correctly and trac-all -prep ran without any errors. > I'm so glad. > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > Sincerely, > Florian > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > Hi Florian - Can you please change the decimal commas to points and try > again? > > a.y > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Here are the bvec and bval files you asked me about. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > > > Hi Florian - Can you please also attach the bvecs/bvals files from the > > dmri directory? > > > > Thanks, > > a.y > > > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > > worked for the moment. > > > However, then I got another error: "bvecs and bvals don't have the same > > > number of entries." > > > I don't know why, because they actually have the same number of entries. > > > > > > I attached the logfile so that you may see what is going on. The error > > > occours at line 1463. > > > > > > Thank you in advance for your help. > > > > > > Sincerely, > > > Florian > > > > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > > > Hi Florian - I see what's going on. Can you please rename the directory > > > /data/physics/florian/nii into something that doesn't include "nii", and > > > rerun? Because "nii" is a file extension, this confuses some of the > > > scripts. > > > > > > Thanks, > > > a.y > > > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > I ran the command you sent me and it runs without any errors. > > > > I also attached the command line for you. > > > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > > same kind of problems. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > > >>> > > > > > > > > Hi Florian - Can you please run this command directly on the command line > > > > and see if there are any errors? > > > > > > > > flip4fsl > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > > > Thanks, > > > > a.y > > > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > > > Hi Anastasia > > > > > > > > > > Thank you for your answer. > > > > > > > > > > Yes, those files exist. > > > > > I also extracted the bvec an bval files with anotther software then > > > > dcm2nii > > > > > and i keep getting the same kind of error. > > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > > testdata for running tracula. > > > > > > > > > > sincerely > > > > > Florian > > > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > > >>> > > > > > > > > > > Hi Florian - Do these files exist? > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > > s > > > > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > > s > > > > > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > > this > > > > > has nothing to do with the error you're getting) I have to warn you that > > > > > you may not be able to get good results running probabilistic > > > tractography > > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > > tracula). Your scan time is better spent acquiring 48 different > > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > > > a.y > > > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > > same > > > > > > kind of error repeatedly. > > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > > data > > > > > out > > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > > the > > > > > > config file. > > > > > > After doing so, I got the error which says that tracula cannot find > > > the > > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > > I have tried many options, but still cannot find a solution. > > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > > files. > > > > > > To uphold patient confidentiality, I have encode the name patient's > > > data > > > > > as > > > > > > "AAAAAA". > > > > > > > > > > > > I believe the problems are the bvec and bval files or their > > > structures. > > > > > The > > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > > 268 > > > > > and > > > > > > 1480 - 1484. > > > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > > > With kind regards, > > > > > > > > > > > > Florian Borsodi > > > > > > Department of Neurology > > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > > > it > > > > is > > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > > e-mail > > > > > contains patient information, please contact the Partners Compliance > > > > > HelpLine at > > > > > http://www.partners.org/complianceline . If the e-mail was sent to you > > > in > > > > > error > > > > > but does not contain patient information, please contact the sender and > > > > > properly > > > > > dispose of the e-mail. > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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tractstats2table error
by Juergen Haenggi 20 Dec '17

20 Dec '17

Dear FS and TRACULA experts I use FS6 on a Mac and I am trying to extract path statistics using the tractstats2table command, but faced the following error always for the last file in the list: …. /dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt is not found or is too small to be a valid statsfile if I replace the last subject by another subject of the list for which no error occurred, then the error will occurr for that subject also. although the problem is also reported by others on the FS mailing list, no solution is offered. Thanks in advance Regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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about the "fake" 1mm resolution
by Luqi Cheng 19 Dec '17

19 Dec '17

Deer Freesurfer Experts, I'm dealing with the monkey data. I convert the 0.5mm resolution monkey data into "fake" 1mm space using "mri_convert -iis 1 -ijs 1 -iks 1 "and create surfaces. I want to obtain the white/grey matter inferface in the raw 0.5mm volume space from white surface. I use the mri_surf2vol command but it is larger than the raw 0.5mm space. How could I acquire the white/grey matter inferface in the raw 0.5mm space ? Thank you very much. Best, Luqi

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bbregister issues with ?h.only
by Dorit Kliemann 19 Dec '17

19 Dec '17

Hi, I’m having some troubles with using bbregister on hemispherectomy brains (i.e only one hemisphere; data is successfully processed with recon-all dev version - thanks to Bruce). I use bbregister to create a register.dat for the functional (preprocessed with fmriprep and registered -but not resampled- to standard space with fmriprep) to structural. Goal is to use the aparc+aseg with mri_label2vol to transform to functional volume space. Ultimate goal is then to extract time series with mrisegstats. And this seems to work fine for 3 out of 5 subjects with hemispherectomy. However for two subjects the bbregister steps produced a bad output (as in the input tilts vertically, see screenshot overlaid on T1). One reason might be that for those subjects two heads are in a bid of a ‘funky tilted’ position, which maybe causes the automatic registration in bbregister to fail? Regardless of the reason, I was just wondering if any of you (Doug?) have further suggestions? One issue I noticed in the log is its suggested to use the T1 flag (not the bold) but its a bold input, just weird intensities probably bc of the ‘empty’ hemisphere. I also tried to run it with the T1 flag..same issue Thank you, Dorit Here is the command I use for bbregister bbregister --s subjx --mov func.nii.gz --init-fsl --reg subjx_register.dat --bold --lh-only Also happy to upload the relevant data or paste the whole log. I use Fs 6.0 to run bbregister,mri_label2vol and mri_segstats.

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Labeling gray matter as white matter after removing dura and adding control points
by Mulder, Hailey 19 Dec '17

19 Dec '17

Hello, I have a participant with an error in their white matter segmentation, and after troubleshooting, it still doesn’t look right. Hoping someone on here will let me know how to fix it. Skull stripping left some dura on the superior part of the brain, and initially it was labeling the dura as white matter. I ran gcut, then manually edited the rest of the dura out. It was then labeling some of the gray matter as white matter, so I put in control points along the actual white matter in that area. After my interventions, the segmentation is better but still looks funky. And when I run my mouse over the area incorrectly labeled as white matter, it shows a wm value of 0. So I’m not sure why it’s labeling it as white matter at all. I’ve included pictures of an affected slice just after recon-all as well as after all the interventions (both with and without surfaces). I also included the inflated surface before and after. Thank you, Hailey Mulder

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Hippocampus subfield ROI
by 강준영 19 Dec '17

19 Dec '17

Deer Freesurfer Experts. I'm currently working on hippocampus subfield parcellation in freesurfer version 6.0.0 In the previous version, freesurfer gave me CA1, CA3 and other subfields with separate mgz files so I could easily analyze them by AFNI separately. (make afni files for each subfields) However, in the current version, it gives me a whole file hippoSflabels-T1.v1.mgz and I tried to extract a specific subfield information (e.g. CA1, subiculum) only but failed. How can I make separate volume files of hippocampus subfields out of the 'hippoSfLabels-T1.v1.mgz file? I used 3dcalc function but got no idea to specify a region I'm interested in. Please help me out guys.. Thanks! Sincerely, Joonyoung Kang.

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mri_surf2surf after recon edits
by Sims, Sara A 18 Dec '17

18 Dec '17

Hello, I am trying to transfer Yeo2011 parcellations to a subject’s surface after I fixed an issue with the wm surface and reran recon. The recon had no errors and the surface is fixed. However, when I tried to run mri_surf2surf I got “MRISreadAnnotationIntoArray: vertex index out of range” and the output is clearly wrong (see attached), despite it working before the recon edits. Any help would be much appreciated! This is the re-run of recon on the edited subject: recon-all -autorecon2-wm -subjid 200614 This is the mri_surf2surf on the edited subject: mri_surf2surf --srcsubject fsaverage --trgsubject 200614 --hemi lh --sval-annot fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval 200614/label/lh.Yeo2011_7Networks_N1000.annot This is the output: sysname Linux hostname c0012 machine x86_64 user snolin srcsubject = fsaverage srcval = (null) srctype = trgsubject = 200614 trgval = 200614/label/lh.Yeo2011_7Networks_N1000.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/lh.sphere.reg Loading source data Reading surface file /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/lh.orig reading colortable from annotation file... colortable with 8 entries read (originally MyColorLUT) Reading target surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/200614/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (136080) Surf2Surf: Dividing by number of hits (136080) INFO: nSrcLost = 54959 nTrg121 = 136080, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 87475, nSrcLost = 54959, nSrcMulti = 76367, MnSrcMultiHits = 0.636466 Saving target data Converting to target annot Saving to target annot 200614/label/lh.Yeo2011_7Networks_N1000.annot mri_surf2surf --srcsubject fsaverage --trgsubject 200614 --hemi rh --sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval 200614/label/rh.Yeo2011_7Networks_N1000.annot sysname Linux hostname c0012 machine x86_64 user snolin srcsubject = fsaverage srcval = (null) srctype = trgsubject = 200614 trgval = 200614/label/rh.Yeo2011_7Networks_N1000.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/rh.sphere.reg Loading source data Reading surface file /data/project/vislab/raw/HCP_900sub/subjects_reconall/fsaverage/surf/rh.orig reading colortable from annotation file... colortable with 8 entries read (originally MyColorLUT) Reading target surface reg /data/project/vislab/raw/HCP_900sub/subjects_reconall/200614/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (137933) Surf2Surf: Dividing by number of hits (137933) INFO: nSrcLost = 54189 nTrg121 = 137933, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 87617, nSrcLost = 54189, nSrcMulti = 76225, MnSrcMultiHits = 0.660098 Saving target data Converting to target annot Saving to target annot 200614/label/rh.Yeo2011_7Networks_N1000.annot subject = 200614 annotation = 200614/label/rh.Yeo2011_7Networks_N1000.annot hemi = rh outdir = 200614/label/Yeolabels surface = white Reading surface /data/project/vislab/raw/HCP_900sub/subjects_reconall/200614/surf/rh.white Loading annotations from 200614/label/rh.Yeo2011_7Networks_N1000.annot MRISreadAnnotationIntoArray: vertex index out of range: 137425 i=00010101, in_array_size=137425 annot file: 200614/label/rh.Yeo2011_7Networks_N1000.annot MRISreadAnnotationIntoArray: vertex index out of range: 137426 i=00010101, in_array_size=137425 annot file: 200614/label/rh.Yeo2011_7Networks_N1000.annot MRISreadAnnotationIntoArray: vertex index out of range: 137427 i=00010101, in_array_size=137425 annot file: 200614/label/rh.Yeo2011_7Networks_N1000.annot

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Freesurfer December 2017