Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Tracula error: libnetcdf.so.6
by Garikoitz Lerma-Usabiaga 17 Dec '13

17 Dec '13

Hi Anastasia, I've got this error when running -prep Tracula step. /usr/local/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory We have RedHat 6 (I tried in 2 different machines). Do you think it is some missconfiguration on our side? Can you think in anything we could try? thanks! Gari

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Longitudinal Freesurfer & TRACULA quality control
by vbrunsch＠nmr.mgh.harvard.edu 17 Dec '13

17 Dec '13

Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per subject (2 cross-sectional runs, 2 long runs and the base). 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 folders per subject for the SBA? 2. Independent of the previous question, for the longitudinal version of TRACULA would you recommend to use (all of) the QA_TOOLS on the freesurfer base folder only / additional folders? 3. In addition to the late visual check for well reconstructed pathways with freeview, is there another automated possibility to check the quality of the diffusion weighted images beforehand/do you think this is necessary? 4. On another note: If I understand correctly, in TRACULA bedpostX is used to reconstruct the pathways but then the mean over the voxels that were hit (by the MCMC sampling of the paths) of measures from the tensor model are taken as outputs. I wonder, is there also the possibility of using the partial volumes f1, f2,.. as output measures? Best, Vincent

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Re: [Freesurfer] New features in TRACULA
by Anastasia Yendiki 17 Dec '13

17 Dec '13

Hi Ruth - If you download the update and unzip it, you'll see an executable called dmri_motion. You can run it without any arguments to see the help text. Try something like this: dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out output.txt a.y On Fri, 13 Dec 2013, Ruth Carper wrote: > > Thanks. We haven't yet implemented TRACULA but have run eddy_correct on all > the brains in our existing pipeline and still have the ecc.log files. Is > there a command line that would let us generate your motion measures without > running TRACULA? > > --Ruth > > > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Ruth Carper <rcarper_99(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, December 10, 2013 8:28 PM > Subject: Re: [Freesurfer] New features in TRACULA > > > Hi Ruth - Glad to hear this is useful to you. The rotation and translation > parameters are extracted from the affine registration of each DWI volume > to the first volume, which in trac-all is performed by eddy_correct. > > a.y > > On Tue, 10 Dec 2013, Ruth Carper wrote: > > > Hi Anastasia, > > We discussed your paper at our lab meeting yesterday so this was perfect > > timing on the release of motion measures in your updated TRACULA. But I > > wasn't clear where the numbers are coming from in your new update. Is > this > > from EDDY? eddy_correct? Some other registration step? > > > > Thanks, > > Ruth > > > > > > > > > > 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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Tracula error when running bedpostX (2nd step af trac-all)
by Matthieu Vanhoutte 17 Dec '13

17 Dec '13

Hello experts, I am running the ball-and-stick model fit in Tracula on FS 5.1 and come across the error: *WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri subjectdir is /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri Making bedpostx directory structure Queuing preprocessing stages /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected operator Queuing parallel processing stage /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x66: unexpected operator Queuing post processing stage /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected operator Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/monitor to show progress. Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. * I have attached my dmrirc file and trac-all.log. Best regards, Matthieu

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Re: [Freesurfer] trac-all inquiry
by David Soto 17 Dec '13

17 Dec '13

thanks Anastasia, see the link below pls https://dl.dropboxusercontent.com/u/8209026/regs.zip you will find 2 pairs of images pair one: there are 2 files starting by ind2anat, one showing the T1 and the other the FA in the same coordinates, you will see that align well pair two: here are 2 files starting by MNI, one showing the FA in mni space and the other the mni T1_1mm template..seem fine to me, though there seem to be some coverage deficit in the FA map in the bottom right of the image cheers ds On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi David - I am not convinced that all the regisrtrations have worked well > for this subject. The fact that some of the coordinates of the control > points, which are mapped from template to individual space, are negative > in individual space (see INFO messages in log file), means that some part > of the brain in templated space is mapped outside the field of view in > individual DWI space. Can you send any screenshots that show the quality > of the DWI to anatomical and DWI to MNI registrations? > > Thanks, > a.y > > On Mon, 2 Dec 2013, David Soto wrote: > > > hi - thanks , not sure though...the no_dif brain maskseems ok, if that is > > what you meant... > > > > I did re-run the processing and > > in the last run I can not see the WARN you mentioned > > the latest preprocessing output from the preprocessing can be > > found here: https://dl.dropboxusercontent.com/u/8209026/prepro.txt > > > > the dlabel/diff output got stuck with the > > rh.ilf_AS_avg33 which only contains thee _mni_bbr_cpts_5.txt but nothing > > else > > > > thanks so much > > > > ds > > > > > > > > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > Hi David - Sorry for the delayed response due to traveling. > > > > There's a warning about the right ILF in the log file that may > > offer a > > clue: > > > > WARN: Initial control point 37 56 -6 is not in DWI volume - is > > DWI cropped? > > WARN: Replacing with closest point in volume (37 56 0) > > WARN: Initial control point 38 45 -1 is not in DWI volume - is > > DWI cropped? > > WARN: Replacing with closest point in volume (38 45 0) > > WARN: Initial start point 37 56 0 is not in start ROI > > WARN: Replacing with closest point in start ROI (31 56 0) > > > > Is the brain mask cropped on either end of the right ILF? You > > mentioned > > that you already checked the registration of the FA map to the > > template > > space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's > > nothing > > wrong there. > > > > a.y > > > > On Sat, 16 Nov 2013, David Soto wrote: > > > > > Thanks! > > > for some weird unknown reason > > > the log for the preprocessing file of this > > > subject is unusually big (2.8 megabytes) > > > please get it from this link > > > https://dl.dropboxusercontent.com/u/8209026/Archive.zip > > > cheers > > > ds > > > > > > > > > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > Hi David - This log only shows output from the -path > > step and > > > not from the -prep step. The file that's missing should > > be > > > created during the -prep step, so there's no way to > > figure out > > > what went wrong without seeing the output from the > > > pre-processing. > > > > > > Please cc the freesurfer list on your reply. > > > > > > Thank you, > > > a.y > > > > > > > > > On Sat, 16 Nov 2013, David Soto wrote: > > > > > > Thanks, please see attachedI only noticed this > > > ERROR: > Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_ > > avg > > > 33_m > > > ni_bbr_cpts_5_std.txt > > > cheers > > > DS > > > > > > > > > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > Hi David - Can you please send us the > > > trac-all.log file for this > > > subject? > > > Without seeing where it stopped and what > > error > > > messages there > > > are it's > > > hard to guess what's going on. > > > > > > Thanks, > > > a.y > > > > > > On Fri, 15 Nov 2013, David Soto wrote: > > > > > > > Hi - > > > > trac-all completed in all my Ps except one > > > > and I noticed that the dlabel/diff output > > > does not contain > > > all the files > > > > > > > > I assessed whether it could be do to poor > > > registration, by > > > checking > > > > the aparc+aseg > > > > file and looks allright > > > > > > > > I also checked the registration of FA maps > > > to standard space > > > by > > > > freeview -v > > > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > > > > dtifit_FA.bbr.nii.gz > > > > and seems fine > > > > > > > > also > > > > > > > > freeview -v brain_anat_orig.nii.gz > > > lowb_brain.nii.gz > > > > > > > > which also seems fine > > > > > > > > any ideas pls? > > > > > > > > thanks! > > > > > > > > ds > > > > > > > > > > > > > > > > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia > > > Yendiki > > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > I suspect the current problem is > > > caused by poor > > > registration. > > > > Have you checked the aparc+aseg > > and/or > > > the registration > > > from > > > > diffusion to anatomical and from > > > anatomical to MNI? > > > > > > > > On Fri, 16 Aug 2013, David Soto > > > wrote: > > > > > > > > > > > > > > > > -- > > > > > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > -- > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > > > > > > > -- > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > -- http://www1.imperial.ac.uk/medicine/people/d.soto/

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talairach transformation error and general recon-all error
by JARED NIELSEN 17 Dec '13

17 Dec '13

Hi, I'm new to FreeSurfer and have been going through the tutorials, YouTube videos, and Mail Archive. I've run recon-all on a handful of scans with variable success. Some of the scans are processed after five or six hours without any problems, and the output looks good. Others are processed "without any errors" after a matter of minutes, and logically I don't see any output. Finally, others hit a hard error after a few minutes of processing during the talairach transformation step. I looked at the orig.mgz file (for the scan that failed at transformation step) through tkmedit, and it is a blank white rectangle. I don't see anything that resembles a head or brain. I've attached examples of each recon-all.log (i.e., good, bad, and bad_talairach). Any help would be greatly appreciated. Thanks, Jared

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GLM p value display
by Celine Louapre 17 Dec '13

17 Dec '13

Hi all I am wondering what is the best to present GLM results in a table on top of the visual display. For the significant clusters after clusterwise correction, should we display the Max -log10(p) as in the summary file itself, or the p value directly, or a transformed pvalue like a Z score? Thanks for advices Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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mri_glmfit-sim Error
by Jon Wieser 17 Dec '13

17 Dec '13

After running a group comparison using qdec I wanted to use mc-z for multiple comparison correction I tried running: mri_glmfit-sim \ --glmdir MTA_ADHD_MJ2 \ --sim mc-z 1000 2.0 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite ERROR: dimension mismatch between X and contrast MTA_ADHD_MJ2/tmp.mri_glmfit-sim-9440/lh-Avg-thickness-Age-Cor.mtx X has 4 cols, C has 8 cols What does this mean and how to fix it? -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Tracula upgrading to Freesurfer 5.3
by Laura Christine Anderson 17 Dec '13

17 Dec '13

Tracula experts, 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

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data uploaded
by Rujing Zha 17 Dec '13

17 Dec '13

Hi Bruce, I uploaded the data to your server. All files can be divided into 2 subjects. And one subject has incorrect segmentation (subject), the other has a multiframe ERROR(LJH_error). Thanks. All the best. 2013-12-17 Rujing Zha

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Freesurfer December 2013