Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

Re: [Freesurfer] Problem running Tracula longitudinal analysis
by Anastasia Yendiki 09 Apr '13

09 Apr '13

Hi Dylan - Can you send your trac-all.log file? (When the baselist is included in the dmrirc, otherwise you're just running the cross-sectional tractography.) Thanks, a.y On Mon, 8 Apr 2013, Dylan Nielson wrote: > I'm running CentOS 6.4. I don't know if it matters, but I tried running the > command from both bash and tcsh and they both give an error. Also, I did the > bedpost outside of freesurfer and then copied the outputs from that into the > freesurfer directories where they're supposed to go. The dcmric file will > run if I take out the baselist portion. > Any ideas you have would be great. > > Thanks, > > Dylan > > > On Mon, Apr 8, 2013 at 8:04 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Dylan - First of all kudos for being a brave early adopter :) > The only thing wrong with the dmrirc that I see is that there > can be only one bvecfile and bvalfile, not one per time point > (it's assumed that you used the same protocol for all time > points). > > That said, I don't think that's what's causing the error. What > operating system and version are you running this on? > > a.y > > On Sat, 6 Apr 2013, Dylan Nielson wrote: > > I am trying to run Tracula on a single subject with > two time points. I get the following Error > below. I suspect it is because I am not setting my > dmrirc file up correctly, but I cannot > figure out what the error is. I've copied my dmrirc > file below as well. > > Thanks, > > Dylan > > Command: > trac-all -prep -nocorr -nointra -c > dmrirc.long.RP0603 > > Error: > > trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd > ; > ERROR: flag ; unrecognized > -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd > ; > > dmrirc.long > setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer > set dtroot = ~/fmri/RP0629_3T/freesurfer > set subjlist = ( tp1002.long.002 \ > tp2002.long.002 ) > set baselist = ( 002 002 ) > set dcmroot = ~/fmri/RP0629_3T/freesurfer/ > set dcmlist = ( tp1002.long.002/dmri/dwi.nii.gz \ > tp2002.long.002/dmri/dwi.nii.gz ) > set bvecfile = ( tp1002.long.002/dmri/bvec \ > tp2002.long.002/dmri/bvec ) > set bvalfile = ( tp1002.long.002/dmri/bval \ > tp2002.long.002/dmri/bval ) > set dob0 = 0 > set doeddy = 0 > set thrbet = 0.5 > set doregflt = 0 > set doregbbr = 1 > set doregmni = 0 > set doregcvs = 1 > set cvstemp = cvs_avg35 > set cvstempdir = $FREESURFER_HOME/subjects > set usemaskanat = 1 > set pathlist = ( lh.cst_AS rh.cst_AS \ > lh.unc_AS \ > lh.ilf_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.cab_PP rh.cab_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP ) > set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5) > set trainfile = > $FREESURFER_HOME/trctrain/trainlist.txt > set nstick = 2 > set nburnin = 200 > set nsample = 7500 > set nkeep = 5 > set reinit = 0 > > > > > 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. > > > >

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Rejoindre mon réseau sur LinkedIn
by Carl Anderson 09 Apr '13

09 Apr '13

LinkedIn ------------ Carl Anderson souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Carl Anderson http://www.linkedin.com/e/-qq80um-hfb2lg8j-68/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Carl Anderson http://www.linkedin.com/e/-qq80um-hfb2lg8j-68/rso/14130267/X9KR/name/664711… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hfb2lg8j-68/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Problem at tksurfer
by Roschinski, Benjamin 09 Apr '13

09 Apr '13

________________________________________ Von: Roschinski, Benjamin Gesendet: Donnerstag, 31. Januar 2013 13:37 An: freesurfer-owner(a)nmr.mgh.harvard.edu Betreff: Problem at tksurfer Dear Freesurfer users and experts, by doing the QC of our mri pictures, we found two unusual problems. The first problem is a strange appearance of insulas in many records of our patients by using recon checker as well as tksurfer. We would like to know, if this is a software problem or just a result of the young age(12-16) of our patients although we have a few older participants with the same problem. For a better understanding I have added a picture. Our second problem is a grey spot with "None" as description on the cuneus also in the parc pictures of recon checker and tksurfer. Do you have any ideas how to fix this problem? I have added a picture of this as well. I hope you can advise me how to fix these problems. Thanks and kind regards Benjamin

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Contrast file for cortical thickness 2 group 1 covariate analysis
by Alexandra Tanner 08 Apr '13

08 Apr '13

Dear Doug and Freesurfers, I'm running a group cortical thickness analysis covaried by age, and we're curious if there is a way to correlate thickness and age within groups and then look at whether or not there is a difference in the strength of the thickness/age relationship between groups. Originally the contrast file we used was the group-x-age.mtx (0 0 1 -1) looking at whether or not there was a difference between the group age slopes, but we then realized we're not interested in whether the slopes of the relationships are different, but rather if the strength of the cortical thickness/age relationship differs between groups. I ran mri_glmfit with an fsgd file that was set up as follows: GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Input subject1 Group1 30 Input subject2 Group2 40 I've taken a look at the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V) and can't seem to find a contrast file that does what we're looking for. Any advice on what sort of contrast file we should use, or whether we need to run a different analysis than glmfit, would be greatly appreciated! Thanks! Best, Alex

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Re: [Freesurfer] tracula fibers display question
by Anastasia Yendiki 08 Apr '13

08 Apr '13

Hi Sal - I'm cc-ing the list since this is of general interest. In 5.2 there's also a path.pd.trk file in the tracula output directory, which contains all the sample splines that were added up to create the probabilistic distribution in path.pd.nii.gz. The .trk format can be displayed in freeview or trackvis. These are still not like the pretty streamlines that you see visualized in deterministic tractography tools, simply b/c they haven't been smoothed. Hope this helps, a.y On Sun, 7 Apr 2013, Salil Soman wrote: > Dear Anastasia, > > Is there a way to display the merged_avg33_mni_flt.mgz file as a set of streamlines, rather > than the clay appearing structures generated by using freeview -tv /merged_avg33_mni_flt.mgz ? > I ask primarily because my collaborators in surgery and neurology are becoming increasingly > used to DTI fiber tracking images that give the appearance of multiple fibers (I recognize > that the modeling of white matter tracts using probabilities does not support delineation of > specific individual fibers, however, I think I am having a hard time even introducing > collaborators to the DTI data generated by Tracula due to the unusual appearance of its > output). > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS > >

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Re: [Freesurfer] Tracula the inverse of TBSS results
by Sean Hatton 08 Apr '13

08 Apr '13

This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: > Hi Freesurfer gurus, > > I have been using Tracula to investigate white matter abnormalities in a patient > cohort (n=20) compared to matched controls (n=40). In line with the literature, we > expected to see reductions in FA in the patients' tracts but instead they have > significantly higher FA means. To double-check, we ran TBSS over the same cohorts and > got the results as per the literature (I.e. reduced FA in the patient group). The FA, > RD, AD, MD and volume outputs are normally distributed and there are no extreme > outliners. So wondering: > 1. The patient group had significantly reduced tract volumes. If this volume > calculation is incorrect I expect it could influence the calculation of the mean > FA, RD, AD etc. Is there a way of checking the volume and subsequent > calculations? > 2. Yendiki et al 2011 had no corrections – do I need corrections? > 3. Should I be thresholding tract stats? > Thank you in advance, > > Sean Hatton > Brain and Mind Research Institute > University of Sydney > > > > > > > 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.

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Problem running Tracula longitudinal analysis
by Dylan Nielson 08 Apr '13

08 Apr '13

I am trying to run Tracula on a single subject with two time points. I get the following Error below. I suspect it is because I am not setting my dmrirc file up correctly, but I cannot figure out what the error is. I've copied my dmrirc file below as well. Thanks, Dylan Command: trac-all -prep -nocorr -nointra -c dmrirc.long.RP0603 Error: trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ; dmrirc.long setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer set dtroot = ~/fmri/RP0629_3T/freesurfer set subjlist = ( tp1002.long.002 \ tp2002.long.002 ) set baselist = ( 002 002 ) set dcmroot = ~/fmri/RP0629_3T/freesurfer/ set dcmlist = ( tp1002.long.002/dmri/dwi.nii. gz \ tp2002.long.002/dmri/dwi.nii.gz ) set bvecfile = ( tp1002.long.002/dmri/bvec \ tp2002.long.002/dmri/bvec ) set bvalfile = ( tp1002.long.002/dmri/bval \ tp2002.long.002/dmri/bval ) set dob0 = 0 set doeddy = 0 set thrbet = 0.5 set doregflt = 0 set doregbbr = 1 set doregmni = 0 set doregcvs = 1 set cvstemp = cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects set usemaskanat = 1 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS \ lh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5) set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt set nstick = 2 set nburnin = 200 set nsample = 7500 set nkeep = 5 set reinit = 0

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incomplete tracts
by stdp82＠virgilio.it 08 Apr '13

08 Apr '13

Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-apr-2013 18.57 A: <stdp82(a)virgilio.it> Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts What you say "again" you mean with 5.2? On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > yes, for some subject the low-b volume is in the end. > Some subjects have again incomplete tracts. > I'm attacking an example of configuration file that I'm using. > I hope that you can check it please. > > Thanks, > > > Stefano > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-apr-2013 18.45 > A: <stdp82(a)virgilio.it> > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > Hi Stefano - In your case we determined that the ones that had the low-b > volume in the end didn't run correctly, right? In that case, I didn't need > to see anything, you were going to try running 5.2. > > a.y > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > could I send you the data of a subject that I don't run correctly? > > > > I still have some subjects with tracts incomplete and I do not know if it depends > from > > my analysis or whether the images are not good. > > > > Thanks, > > > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-apr-2013 17.37 > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > tractography initialization issue, I strongly recommend running 5.2 with > > bbregister for the registration (which is the default in 5.2 anyway). > > > > You can also upload an example data set with issues (include: dmri, > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > Hope this helps, > > a.y > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > Dear Anastasia, > > > > > > thanks for the help. There is also a line option in freeview. However we still > have > > > brains with missing tracks, I rerun them with increasing the ncpts and registering > > to > > > bbr (since that is default in Tracula 5.2.). We are reasonable confident that our > > bvel > > > and bvac are correct, since we have roughly 20 cases out of 90 processed brains > > where > > > there are no missing tracts. Further sometimes only one tract is missing, > sometimes > > it > > > is more severe. We could not find any correlation with recon-all problems or DTI > raw > > > data issues (all but one were without moving artefacts). Since we are running > > bedpostx > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an > > issue > > > that is solved with installing the 5.2. version? Would that run in freesurfer > 5.1.0? > > > I guess we need to change the dcmrirc files only a bit. > > > > > > Kind regards > > > Gerit Pfuhl > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus > > > callosum follow the curvature of the corpus callosum, and in a sagittal > > > view to see if the lines in the cingulum follow the curvature of the > > > cingulum. Does this make sense? > > > > > > a.y > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > Dear Anastasia, > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our > > > gradient table is wrong but I am not really sure how to analyse > > > these informations. You wrote to Stefano the lines have to point in > > > the right direction and that the eigenvectors are not pointing along > > > his corpus callosum. Can you give me a more detailed description > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > > > dtifit_FA. > > > > > > Thanks and kind regards > > > Benjamin > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > http://gerit-orientation.blogspot.com > > > http://team-arzgebirg.blogspot.com > > > > > > > > _______________________________________________ > > 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 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.

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BA that are the begin and target of each tracts obtained in TRACULA
by stdp82＠virgilio.it 08 Apr '13

08 Apr '13

Hi list and Anastasia, how can I identify which are the Brodmann areas that are the begin and target of each tracts obtained in TRACULA analysis. Thanks, Stefano

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mri_normalize control in FS 5.2
by Michael Harms 08 Apr '13

08 Apr '13

Hi guys, I see that the recon-all for FS 5.2 now has flags for setting the -b and -n arguments to mri_normalize separately for the two different Normalization stages. Was that just for increased control/flexibility, or did you find that it was actually detrimental to use say "-b 20 -n 5" in the first Normalization stage, if for example using an expert options file for mri_normalize? thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu

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Freesurfer April 2013