Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

Tracula 5.2.0 -path step segmentation fault
by Gerit Pfuhl 26 Apr '13

26 Apr '13

Dear Freesurfer experts, Running tracula in freesurfer 5.2.0 gave me now an unsual errror. No problems in the trac-prep and trac-bedp step but suddenly segmentation fault in trac-path. The other threads state it is a problem in a previous step. However, the subject was processed fine in version 5.1.0 though some tracts were incomplete - that is why we try the new better algorithm. I found no difference in the dmri and dmribedpostx folders (a few more files in xfms compared to using tracula 5.1.0 version). I used the defaults in the dmrirc file and attach the log file. Kind regards Gerit Pfuhl

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Re: [Freesurfer] Problem running Tracula longitudinal analysis
by Anastasia Yendiki 26 Apr '13

26 Apr '13

Hi Dylan - Thanks for your patience. There was a small scripting bug that was causing trac-all in longitudinal mode not to process the command line properly on some systems. Can you please copy the two modified scripts I'm attaching to your $FREESURFER_HOME/bin, overwriting the existing versions? Please let me know if that fixes the error, and if so I'll post them to the wiki as an update for anyone else who wants to run longitudinal. Thanks, a.y On Tue, 9 Apr 2013, Dylan Nielson wrote: > This should be what you need, Let me know if I've sent the wrong one. > > > On Tue, Apr 9, 2013 at 11:30 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > 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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a question
by limeilingcheng 26 Apr '13

26 Apr '13

Hi all, Now I got some results by freesurfer, finally I selected two vertexs which the coordinate values were(Talx=-40.5, Taly= -14.5,Talz=-12.7 and Tal x=55.1, Tal y=-23.9, Tal z=-1.8 ), the corresponding regions reported by freesurfer were left superiortemporal and right superiortemporal. In the following step, I want to make the left and right superiortemporal as ROIs and observe the functional connectivity between the ROIs and the voxels in the whol brain. However, it is difficult for me to understand how to get the ROIs I want based on Harvard-Oxford atlas(?) according to my coordinate values from freesurfer,especially it was Talairach index, and if we get the transformed coordinate values in the Harvard-Oxford atlas, should I make the corresponding whole region as the ROI? Regards, Meiling

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asegstats2table error depending on subject sorting
by Andreas Berger 26 Apr '13

26 Apr '13

Hi Surfers, as of version 5.2, i'm getting an error using asegstats2table, depending on how i sort the subjects: andreas@psy058:~$ asegstats2table --subjects $(ls $SUBJECTS_DIR | sort -t _ -k 1 -nk 2) -t segstats.csv --skip -d comma SUBJECTS_DIR : /mnt/raid/freesurfer/subjects Parsing the .stats files Skipping /mnt/raid/freesurfer/subjects/fsaverage/stats/aseg.stats Skipping /mnt/raid/freesurfer/subjects/lh.EC_average/stats/aseg.stats Skipping /mnt/raid/freesurfer/subjects/qdec/stats/aseg.stats Skipping /mnt/raid/freesurfer/subjects/rh.EC_average/stats/aseg.stats Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 553, in <module> if(nmeasures != nmeasures0 and not options.common_flag and not options.all_flag): NameError: name 'nmeasures0' is not defined i don't get that error if i either: 1) remove the non-subjects (fsaverage, qdec, etc..) from the list, or: 2) do not sort the list like i do the subjects list is attached, sorted the way it produces the error greetings, Andreas

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Re: [Freesurfer] convert labels to volumetric masks
by limengsecret 25 Apr '13

25 Apr '13

Hi Doug, Thanks for your reply. The mask created is used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. The .w file I download from http://ltl.tkk.fi/wiki/Atlas, indicates the maximum probability map. Best wishes, Meng Dear FreeSurfers, I want to convert cortical labels to volumetric masks, and I run the following commands: 1. /tkregister2 -mov sub/mri/rawavg.mgz -noedit -s sub -regheader -reg ./register.dat/ 2. /mri_label2vol -label ./lh.entorhinal.label -temp sub/mri/rawavg.mgz -subject sub -hemi lh -o sub_lh_entorhinal.nii.gz -proj frac 0 1 .1 -fillthresh .3 -reg ../mri/register.dat/ if I do not run the recon-all command, could I change the rawavg.mgz to sub.nii (original data)? What is sub.nii? The second problem is that when I convert the annotation file to volumetric mask, whether I should convert the file to labels using mri_annotation2label first, then run the commands as decribed above, or there is a way that could convert the annotation file to volumetric mask directly? You can use the same label2vol command above but spec --annot instead of --label The last problem is that how to convert the .curv file and .w file to volumetic mask? mri_surf2vol should work for the curv file. Why do you have a .w file? BTW, for our standard annotations (aparc and aparc.a2009s) you will probably be happier with the results if you use mri_label2vol with --seg aparc+aseg.mgz or --seg aparc.a2009s+aseg.mgz. Otherwise, there are some holes that are created if you use the surface labels. doug

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Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files
by Jeni Chen 25 Apr '13

25 Apr '13

The original command line: > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd To which you suggested > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim 1GroupAvg-Cor-thickness-Mod-VAS And it did not work either. Thanks. jeni Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 > what was your orignal mri_glmfit-sim command line? On 04/25/2013 05:17 PM, Jeni Chen wrote: > Hi Doug, > > Sorry; didn't realize it wasn't included. > > So to state the original problem, I tried running mri_glmfit-sim with > the following options (previous message included below): > > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd > > I get an error message saying "cannot find any csd files". You > suggested putting just the csd base > (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I > did, but still gave the same error message. I've attached the error > log if you want to have a look. > > Thanks. > > Jeni > > > > >> Hi Jeni, what is your command line and terminal output? In general, >> just saying that something does not work is not enough information to >> track down the problem. Also, please include previous correspondence. >> We answer a lot of emails here, and the easier you make it on us, the >> faster we can solve your problem. thanks! doug > On 04/25/2013 04:41 PM, Jeni Chen wrote: > > Thansk Doug. I tried it but still doesn't work. Any other thoughts? > > > > jeni > > > > > > _______________________________________________ > > Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> Hi Jeni, done pass that path to the csd, just the csd base. In your >> case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS >> doug >>> On 4/24/13 8:47 PM, Jeni Chen wrote: >> >> Hello, >> >> I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I >> specified the --no-sim option to avoid re-running the entire >> simulation again. I entered my DSC file but in the end I get the >> error message: "cannot find any csd files". Here is what I entered: >> >> mri_glmfit-sim \ >> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ >> --cwpvalthresh .999 \ >> >> --no-sim >> >> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI >> copied and pasted the csd file from its own folder to the top >> directory, but it gave the same error. I've attached the error >> log in case you want to have a look. >> >> Thanks for your help! >> >> Jeni >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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-autorecon2-pial
by obregon＠nmr.mgh.harvard.edu 25 Apr '13

25 Apr '13

Hi, I was wondering if the -autorecon2-pial flag has been superseded on the newer release of Freesurfer, for it isn't being recognized? Also, is the use of this flag equivalent to running recon-all with the -autorecon-pial option? Thanks, Gabriel

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Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files
by Jeni Chen 25 Apr '13

25 Apr '13

Hi Doug, Sorry; didn't realize it wasn't included. So to state the original problem, I tried running mri_glmfit-sim with the following options (previous message included below): mri_glmfit-sim \ --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ --cwpvalthresh .999 \ --no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd I get an error message saying "cannot find any csd files". You suggested putting just the csd base (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I did, but still gave the same error message. I've attached the error log if you want to have a look. Thanks. Jeni > Hi Jeni, what is your command line and terminal output? In general, just > saying that something does not work is not enough information to track > down the problem. Also, please include previous correspondence. We > answer a lot of emails here, and the easier you make it on us, the > faster we can solve your problem. > thanks! > doug On 04/25/2013 04:41 PM, Jeni Chen wrote: > Thansk Doug. I tried it but still doesn't work. Any other thoughts? > > jeni > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Hi Jeni, done pass that path to the csd, just the csd base. In your case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS > doug > > >> On 4/24/13 8:47 PM, Jeni Chen wrote: > Hello, > > I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered: > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd > I copied and pasted the csd file from its own folder to the top directory, but it gave the same error. I've attached the error log in case you want to have a look. > Thanks for your help! > > Jeni

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Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files
by Jeni Chen 25 Apr '13

25 Apr '13

Thansk Doug. I tried it but still doesn't work. Any other thoughts? jeni

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HeadSurface to MEG fiducials
by José Ángel Pineda 25 Apr '13

25 Apr '13

Dear expert, I am doing source reconstruction with MEG. First, I am corregistering my head surface mesh from the freesurfer (obtained with mkheadsurf) to the headshape of the subject obtained with the Polhemus tracking system. So I already have one affine transformation (Aff_1) The head surface was obtained over the T1 image in voxel native space (not orig.nii) The next step is to apply an affine transformation to the T1 to bring it into the same coordinates as the headshape (and fiducials). Then I apply Aff_1 to the T1 and check the results. I observe there is an offset displacement between the T1 and the fiducial points. I dont know what to do to solve this. I read that as my head surface is in RAS space I should consider that, but Ive tried to correct this introducing the affine tranformation matrices that are mentioned on the web for Coordinates in Freesurfer, but Im not able to correct it. Could you please give me any advice? Thanks Jose -- José Angel Pineda Pardo Center of Biomedical Technology (CTB) Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES

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