Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

TRACULA fornix tractography
by Barbara Kreilkamp 27 Jul '16

27 Jul '16

Dear Anastasia, As we are analyzing DTI data acquired in patients with epilepsy we are especially interested in the fornix. I've come across the mri_cc -f option for fornix segmentation (native space) but I've also read that manual tracing/labeling of the tracts would be needed in the 33 controls for TRACULA (training set - trctrain). In Wakana et al. 2011 I see that the fornix was not included due to low reproducibility and it further states: "the reason for the poor reproducibility is most likely due to not enough spatial resolution with respect to the diameter" I wonder if you could please guide us in how to best add this tract to TRACULA so that it would be consistent in the methods compared with the other tract ROI definitions or perhaps state what were the difficulties in adding this particular tract to TRACULA. Thank you very much, Best wishes, Barbara

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problems by running longitudinal mass univariate analysis
by Valsasina Paola 27 Jul '16

27 Jul '16

Dear FS experts I am trying to run the commands for performing the longitudinal mixed effect statistics with the LME Matlab toolbox. I am following the instructions on the web page; however, I have two questions: 1) when I run the command lme_mass_fit_vw, the script is running for a very long time, after 3 hours the estimation was just at 10% (unfortunately, my laptop is equipped with Windows and is not particularly powerful). I had to stop the script at that point; before restarting it again I would like to be sure: is this behavior normal? Is it correct that lme_mass_fit_vw is running for such a long time? 2) when the script was running, there were several warnings on the Matlab screen, saying that the algorithm was not converging (at most of locations). Is it also normal? How can I check the correctness of my input image? When I open with freeview the "lh.thickness_sm10.mgh" volume, I just see a black screen with valid timeseries values in the minority of voxels (I imagine that these timeseries are concatenated thickness values of my study subjects). Is there another way to better visualize and check a concatenated 4d mgh file? Failure of convergence is referring to empty/zero voxels of this image? Thank you for any advice on these two topics Kind regards Paola Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all'Ospedale San Raffaele: perch? al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c'? cura, senza ricerca. Non c'? ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg]

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Error with selxavg3-sess
by Luft, Marissa 27 Jul '16

27 Jul '16

I am running the following code: selxavg3-sess -s 1002a -analysis workmen.sm05.lh on data that was already preprocessed with preprocesses, mkanalysis-sess, and mkcontrast-sess. I get the following error message: outanadir = /Users/marissaluft/Documents/ROSE_Program/Jeff_Lab/Free_Surfer_Project/Project_Folder/1002a/bold/workmem.sm05.lh Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3 (line 115) flac = flac_customize(flac); Thank you, Marissa Luft

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TRACULA dmri_paths, single time point in longitudinal stream
by Harms, Michael 27 Jul '16

27 Jul '16

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doubts about pial surface
by Elias Vergílio Da Cás 27 Jul '16

27 Jul '16

Hi, My name is Silvia and I would like to know how to edit the pial surface conform image in the attachment. I've tried painting with grey color but it wasn't successful and when I erase the voxels around the region nothing happens too. *Freesurfer version*: 5.3 -- Atte. Elias Vergílio Da Cás - Físico UFES/HUCAM/EBSERH

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flipping TRACULA tracts
by Barbara Kreilkamp 27 Jul '16

27 Jul '16

Dear Freesurfers, I've got data pertaining to patients with left and right-sided temporal lobe epilepsy (TLE). My aim is to group those tracts according to side of epilepsy for waypoint comparisons. Basically for patients with right TLE I'd like to look at right tracts and at the same time for patients with left TLE I'd like to look at left tracts (ipsilateral tracts), I need to do the same for the contralateral tracts. Is there a straightforward way of doing this? I've already copied the tracts to respective ipsi and contralateral byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt; do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i ${i/byvoxel./byvoxel_contraRTLE.}; done Now I have to flip the x-coordinates in the patients with right TLE (to make them more comparable to the tracts of the patients with left TLE). That will not be a problem, but I wonder if I am missing something? Can I then just go ahead and run trac-all -stats -c dmrircfile to generate the mean waypoint tracts etc.? Thank you very much, Best wishes, Barbara

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TRACULA group stats visualization
by Derek Pisner 27 Jul '16

27 Jul '16

Dear Anastasia, I am running into an issue with the trac-all -stat option on our longitudinal TRACULA data. Everything runs smoothly through all earlier stages, and I checked individual subjects' merged outputs in freeview with -tv mode. Everything looks fine. Also, then when I run trac-all -c dmric_config -stat, everything finishes without error. But then when I open the results with the command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt I get the image seen in the attached .png file. Any idea what might be causing this? Many thanks in advance for you help. Best, Derek

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When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
by Knut J Bjuland 27 Jul '16

27 Jul '16

flirt.fsl -ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 -verbose 0 -omat/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat-init/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.schterminate called after throwing an instance of'NEWMAT::SingularException'Abort (core dumped) ERROR: flirtFedora 24glibc-2.23.1-8.fc24.x86_64gcc-6.1.1-3.fc24.x86_64libstdc++-6.1.1-3.fc24.x86_64ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x00007ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x00007feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6(0x00007feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x00007feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x00007feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x0000557ba6f46000)Knut Jørgen Bjuland

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New hippocampal subfields
by Jin Kyu Gahm 26 Jul '16

26 Jul '16

Hello, I was trying the new segmentation module of hippocampal subfields, but I also encountered the same errors as Pierre reported a week ago: ------------------------------------------------------------------------------------------------------------------ Invalid MEX-file '/tmp/MCR_1031368111/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': libkvlGEMSCommon.so: cannot open shared object file: No such file or directory Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 133) ------------------------------------------------------------------------------------------------------------------ Eugenio - I wonder if you already solved the problem. Thanks for your help! Best, Jin

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fMRI Postdoctoral Fellow
by Thomas Yeo 26 Jul '16

26 Jul '16

Dear All, I am looking to hire a postdoc with either strong machine learning background OR system neuroscience background. Prior experience with fMRI is a plus. Topics are flexible. Example topics include individual-subject brain parcellations, relationships between behavior and brain networks, dynamic functional connectivity, meta-analysis, neural mass modeling, graph theoretic modeling of brain networks, etc. Other details below. Regards, Thomas Requirements: Ph.D. in neuroscience, computer science, electrical engineering, statistics or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists. Research Webpage: https://sites.google.com/site/yeoyeo02/home Compensation: Competitive and commensurate with experience Attraction: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Contact: Email BT Thomas Yeo (ythomas(a)csail.mit.edu) with your CV. Deadline: Whenever the position is filled.

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Freesurfer July 2016