Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Re: [Freesurfer] Problematic dilated ventricles
by Victor Kovac 03 Mar '14

03 Mar '14

Dear Bruce, A few weeks ago you made code mods to mri_em_register and got recon-all to process a subject of mine, MPS1036-1. You sent me the new aseg.auto_noCCseg.mgz and told me to run recon-all -make all -s MPS1036-1. I did this but I get the message make: Nothing to be done for 'all' and when I visualize the segmentation with tkmedit, there appears to be no change to the pial or wm surfaces. Could you please advise? Thank you. Victor On Mon, Dec 9, 2013 at 2:11 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > if you rename aseg.auto_noCCseg.new.mgz to be aseg.auto_noCCseg.mgz > > then run: > > recon-all -make all -s MPS1036-1 > > you should be all set > > Bruce > > > > On Mon, 9 Dec 2013, Victor Kovac wrote: > > I was hoping to MPS1036-1. I only got aseg.auto_noCCseg.new.mgz. Thank you >> for looking into MPS2002-3 -- it is quite the brain. And somehow, with all >> those morphological abnormalities, this subject has an IQ of 130. Very >> strange. >> Thanks, >> Victor >> >> >> On Mon, Dec 9, 2013 at 2:03 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> which one? I'm still messing with MPS2002-3 in my spare time >> On Mon, 9 Dec 2013, Victor Kovac wrote: >> >> Hi Bruce, >> Is there a way for you to send the subject(s) you >> analyzed to me? I know >> it's too big for email, but could you possibly >> upload it to GoogleDrive? >> >> Thanks! >> Victor >> >> >> On Wed, Dec 4, 2013 at 3:40 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> p.s. the other thing I did was run the graph >> cut skull >> stripping, which removed a bunch of extraneous >> stuff >> On Wed, 4 Dec 2013, kovac081(a)umn.edu wrote: >> >> Hey! >> >> Victor Kovac (kovac081(a)umn.edu) has uploaded >> some files >> for you at the Martinos Center FileDrop: >> >> -> MPS2002-3.zip (292.12 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=55xjt9pflsi> >> -> MPS2017-1.zip (264.15 MiB) >> <http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep& >> f=ak4v31bzu4p> >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here are the two subjects with ventriculomegaly that >> are causing >> the worst issues. The worst segmentation in >> MPS2002-3 is in the >> superior frontal (slices 150-180) and parietal >> (slices 50-95) >> cortical areas; this may be due to the numerous >> dilated >> Virchow-Robin spaces in his brain, which is another >> neuropathological feature of this disease. >> >> Thanks! >> Victor >> >> Please be aware, your upload will expire on December >> 31st. If >> you'd like to download these files, feel free to use >> the link >> below: >> >> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=8mo9zg0isep >> >> Cheers, >> The NMR Team >> >> >> >> >> >> 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. >> >> >> >> >> >> >>

3 6

reg-feat2anat problem
by Mariam Sood 25 Feb '14

25 Feb '14

Hello, I am running reg-feat2anat and facing some problems. First I ran the command in its default mode using FSL initialisation reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration. There is a warning coming up WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 Next I tried the command using -spm option. The within-subject registration (anat2exf) looks good, but the registration to the standard does not look that good, although not as bad as with -fsl option. The structural and the functional are using different conventions (structural is in radiological convention, whereas functional is neurological). I presume the determinants are associated with this and they have opposite signs. The orientations are also different. Additionally in both the log files (one with -fsl option and -spm option), I get another warning WARNING:: Flipping Left/Right orientation (as det < 0). Not sure whether this warning is something I should worry about. Much appreciate your help. Many thanks, Mariam.

2 4

Fwd: Tracula Error: bvecs and bvals don't have the same number of entries
by Francesco Baldacchini 14 Feb '14

14 Feb '14

Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Francesco - The bvecs file that you're attaching has only 3 vectors, > while the bvals file has 65 b-values. Are these your original files, or the > ones saved by trac-all in the dmri/ directory? > > a.y > > > On Mon, 13 Jan 2014, Francesco Baldacchini wrote: > > Hi everybody, >> I'm trying to run the trac all -prep command but after some times I get >> this >> error "bvecs and bvals don't have the same number of entries". I've >> checked >> my bvals and bvecs, which are in attach, but they seems to be formatted in >> the right way. What can I do? Thanks, >> >> Francesco Baldacchini >> >> >> > > 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. > >

2 9

Problem with reg-feat2anat and tcshell: Newer version of reg-feat2anat available?
by Greg Reckless 06 Feb '14

06 Feb '14

I am having the same problem with a newer version of tcshell and reg-feat2anat as discussed in threads below. Has this been resolved? If not, could a working link to the updated version mentioned previously be reposted. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-June/030473.html https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-September/033521… Thanks, Greg

5 8

dmri_motion Error bvals
by Liliana Maia 06 Feb '14

06 Feb '14

Hi, Within the new Tracula update and with outputs resulted from *trac-all -prep -noqa* I ran *: * *dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog'* And an error message appears: *machine x86_64Output motion measure file: /home/lapsi/test/motion.txtInput transform file: /home/lapsi/test/dwi.ecclogInput DWI file: /home/lapsi/test/dwi_orig.nii.gzInput b-value table: /home/lapsi/test/bvalsLow-b image intensity threshold: 100Nominal diffusivity: 0.001Loading volume-to-baseline affine transformationsComputing between-volume head motion measuresINFO: Processed transforms for 33 volumesLoading DWI volume series from /home/lapsi/test/dwi_orig.nii.gzLoading b-value table from /home/lapsi/test/bvalsERROR: Could not open /home/lapsi/test/bvals for reading* I tried with the b-values one value for each line in file bvalsT (see attachments): *dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' --mat 'dwi.ecclog'*,but the same error occurred. What can I do to verify this head motion? Thank you Best, -- Liliana Maia MEng Biomedical Engineering

2 2

Tracula only outputs merged flt file (and missing bbr)
by Salil Soman 06 Feb '14

06 Feb '14

Hi, Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt file and not the merged ... bbr file in paths? All of my dmrirc files have both bbr and flt =1, and most of my outputs have both, but occasionally I only get 1. Thanks! -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

2 2

upgrading to freesurfer 5.3
by Laura Christine Anderson 05 Feb '14

05 Feb '14

Hi Anastasia, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature? Thanks for your help! Laura Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112

2 4

"trac-all -prior" giving "Segmentation fault (core dumped)
by Yong-Hwan Kim 05 Feb '14

05 Feb '14

Hello, FreeSurfer community, I'm trying to run TRACULA sequentially. After running, "trac-all -prior -s <subject> -i <input_DWI.nii> -c <tracula_conf.txt>" that shows an error "Segmentation fault (core dumped)" in my server. (Other options, "-corr, -qa, -intra, -inter, -masks, -tensor", were have done without error) Server was configured as, 1. Fedora 13 - 64bit 2. FreeSurfer v5.1 3. Tracula v5.3 (updated from v5.1) Can anyone suggest a reason why this would be the case? Thank you, Yong-Hwan Kim *Captured Shell logs* -------------------------------------------------------------------------------------------------- . . . Loading cortex mask from /usr/local/freesurfer/trctrain/trc033/dlabel/mni/cortex+2mm.nii.gz Processing pathway 1 of 18... Matching streamline ends INFO: Have 4657 non-truncated streamlines (min/mean/max length: 60/99/137) . . . Finding center streamline INFO: Step is 5 voxels *Segmentation fault (core dumped)* Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 ... trac-preproc exited with ERRORS at Tue Jan 28 21:30:52 KST 2014 -------------------------------------------------------------------------------------------------- *Error Log from <subject>/scripts/trac-all.error* -------------------------------------------------------------------------------------------------- SUBJECT G001 DATE Tue Jan 28 21:30:52 KST 2014 USER user HOST localhost PROCESSOR x86_64 OS Linux Linux localhost 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.46 2013/12/04 17:02:25 ayendiki Exp $ /usr/local/freesurfer/bin/trac-preproc PWD /usr/local/freesurfer/subjects/G001 CMD /usr/local/freesurfer/bin/dmri_train --outdir /usr/local/freesurfer/subjects/G001/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.G001.14153.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /usr/local/freesurfer/subjects/G001/dlabel/mni/aparc+aseg_mask.nii.gz --fa /usr/local/freesurfer/subjects/G001/dmri/dtifit_FA.nii.gz --cptdir /usr/local/freesurfer/subjects/G001/dlabel/diff --reg /usr/local/freesurfer/subjects/G001/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc --------------------------------------------------------------------------------------------------

2 1

SLFP
by stdp82＠virgilio.it 05 Feb '14

05 Feb '14

Hi list, SLFP is SLF III? Is there a way to obtain by TRACULA also SLF I and II, knowing the the cortical targets of the tracts? Thanks, Stefano

2 1

TRACULA error: pre-processing
by Won Sang Jung 05 Feb '14

05 Feb '14

Hi, I have a problem running TRACULA in the pre-processing stage. The error message is the following; Loading streamline start ROI from /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz niiRead(): error opening file /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz ERROR: Could not read /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Linux localhost.localdomain 2.6.18-371.1.2.el5 #1 SMP Tue Oct 22 12:51:53 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at 2014. 01. 23. (목) 18:32:17 KST I guess this error started to happen after I updated Freesurfer version 5.3.0 (I could successfully run TRACULA with same data with the prior version of Freesurfer) In my setting, $TUTORIAL_DATA --> /usr/local/freesurfer/subjects/tracula/tutorialdata I tried re-download the file, diffusion_tutorial.tar.gz, from freesurfer server and extracted file again, but still I couldn't find the file "lh.cst_AS_roi1.flt.nii.gz" in Diff001/dlabel/mni folder. Thank you in advance for your advice. Wonsang Jung

2 1

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Freesurfer January 2014