Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

TRACULA (dmri_motion)
by John Anderson 06 Jun '17

06 Jun '17

Dear TRACULA experts, I plan to use TRACULA in freesurfer 6 to analyze DTI data. I want to kindly to inquire about the command "dmri_motion". This script,nicely, generates: the SNR, drop out score, # drop out slices and motion parameters. I highly appreciate if you can guide me to a method, so I can benefit from these numbers in my evaluation to motion in the data. I tried to plot SNR and Fa, or SNR and motion parameters and I found outliers consistent with more motion and less SNR. In this case is it healthy procedure just to remove the outliers?! Are there any ranges of safety for SNR and motion parameters that can be used to include/exclude the images. Thanks Jon

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recon-all: .md and .txt format
by 곽유나 06 Jun '17

06 Jun '17

Hello FS experts, I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the folder I found that FreeSurferColorLUT.txt , ASegStatsLUT.txt, and others were all stored in .md files. So I changed all of them into .txt, ran recon-all -make (to start from where it left off?), and now it seems to be working. Below is the output in the terminal when the error occurred (for the ASegStatsLUT.txt case) CTABreadASCII(/Applications/freesurfer/ASegStatsLUT.txt): could not open file Computing euler number orig.nofix lheno = -28, rheno = -16 orig.nofix lhholes = 15, rhholes = 9 Loading mri/aseg.mgz No such file or directory ERROR: reading /Applications/freesurfer/ASegStatsLUT.txt Darwin S-Yui-MacBook.local 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 recon-all -s yuna exited with ERRORS at Mon Jun 5 22:20:13 KST 2017 I want to ask if I'm doing this correctly, if it's okay to change the format to .txt and run recon-all -make. Best, Yuna. p.s. I posted a question on the list one or two days ago and for some reason I wasn't able to reply through the archive with the e-mail address I was using, so I wasn't able to thank you guys for your help. Now I'm posting with a new e-mail address, and I wanted to thank you for your replies!

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Recon Error
by Emily Rogers 06 Jun '17

06 Jun '17

Hello, I am trying to implement using Freesurfer segmentation in my analysis for MEG data. I am trying to segment this structural MRI (1400composite.dcm) and I keep getting errors. I have attached the log file. Any help is appreciated. Thank you, Emily Emily E. Rogers, MSc Wake Forest Graduate School of Arts and Sciences PhD Student, Neuroscience (336)-906-1103

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Re: [Freesurfer] computational neuroanatomy position (fwd)
by Bruce Fischl 06 Jun '17

06 Jun '17

FYI ---------- Forwarded message ---------- Date: Tue, 6 Jun 2017 18:33:39 +0000 From: "Reiser, Michael" <reiserm(a)janelia.hhmi.org> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: computational neuroanatomy position https://www.janelia.org/lab/reiser-lab/positions The Reiser lab at the Janelia Research Campus seeks a creative scientist to join our endeavor to understand circuit transformations in the Drosophila brain. We use imaging, electrophysiological, behavioral, anatomical, and computational techniques to crack the neural circuits for vision and navigation in Drosophila. This is an exciting time to be working on the fly visual system— one of the best described complex circuits in neuroscience. We are now living through the golden age of Drosophila anatomy, ushered by a much-improved genetic toolkit, advances in light microscopy (LM), and connectomic reconstructions from electron microscopy (EM) data. Brain regions that were once too complex to be studied at the level of identified neurons, can now have their cells and circuitry catalogued. But these efforts are held back by a lack of computational and analytical tools. Neurons of the fly visual system lend themselves directly to structure-function questions. How much of a neuron's function could be predicted from its morphology and circuit connectivity? In this position, you would lead our efforts to analyze several LM and EM datasets. A number of software tools already exist for anatomical analysis — you would evaluate and use the best of these, and contribute new code where needed. The specific aim is to establish the central representation of visual information in the fly. Many projects are possible, related to active research topics in the lab: • elucidating the circuit mechanisms giving rise to feature detection in identified neurons. Directional selectivity is an especially active topic. • predicting the flow field selectivity of optic flow sensing neurons from their morphology (and collaborating with others in the lab to measure these responses) • following visual pathways out of the visual system and into the central brain to identify the architecture of behavioral control centers • identifying feedback pathways from the central brain into the visual system that modulate of sensory neurons in response to the behavioral state of the animal • Post-connectome projects, such as localizing critical proteins, especially ion channels, to specific neuronal compartments. Analysis of Expansion Microscopy data. Several computational extensions of these research areas would be encouraged: • applications of machine learning to these data sets • single neuron biophysical modeling • dynamical systems and network modeling All of these projects would involve direct collaborations with experimentalist in the lab and computational neuroscientists within Janelia, forming a tight loop between anatomical discovery and experimental methods. A hybrid position is also possible, starting with a focus on the analysis of EM data and then moving on to a functional analysis of these neurons. Requirements: Ph.D. in a quantitative field, familiarity with diverse computing environments, comfort with geometric relationships in three-dimensions, and a keen interest in figuring out the brain. Experience in computational anatomy and/or neuroscience is a big plus. Janelia is an exciting research environment (near Washington, D.C.), with abundant opportunities for collaboration. Interested applicants should apply by email; please include your curriculum vitae and research interests, and arrange for three letters of reference to be sent to reiserm at janelia.hhmi.org. If you have specific salary requirements, please include them in your e-mail; all information is confidential. HHMI is an equal opportunity employer.

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computational neuroanatomy position (fwd)
by Bruce Fischl 06 Jun '17

06 Jun '17

FYI ---------- Forwarded message ---------- Date: Tue, 6 Jun 2017 18:22:18 +0000 From: "Reiser, Michael" <reiserm(a)janelia.hhmi.org> To: "fischl(a)nmr.mgh.harvard.edu" <fischl(a)nmr.mgh.harvard.edu> Subject: computational neuroanatomy position Dear Professor Fischl: I hope you are well. My lab (at the Janelia Research Campus) is embarking on a number of very exciting projects at the intersection of neuroanatomy and circuit function, and I am looking to hire a postdoc to help with the computational analysis of these data. Please find the advertisement linked below (and attached). I would be grateful if you could forward this ad to anyone you know who might be interested. https://www.janelia.org/lab/reiser-lab/positions With best wishes, Michael Reiser

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recon-all -all error end abruptly
by Ramesh Babu 06 Jun '17

06 Jun '17

Dear Expert, recon-all -all process for one subject end abruptly. I have attached the error report file. Please provide me some solution. Thanks Ramesh

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LME correction in longitudinal analysis
by Livia Liu 06 Jun '17

06 Jun '17

Dear FS experts, I are analysing longitudinal data - the difference between 2 groups (1 and 2) with 2 time points for each group (0, 1 --all the same time interval: a month). I followed http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels and with Jorge's early reply in http://www.mail-achive.com/freesurfer@nmr.mgh.harvard.edu/msg25750.html (1)qdec.table.dat fsid fsid-base time group sub04_MR1 sub04 0 1 sub04_MR2 sub04 1 1 sub05_MR1 sub05 0 1 sub05_MR1 sub05 1 1 ... con01_MR1 con01 0 2 con01_MR1 con01 1 2 con01_MR1 con01 0 2 con01_MR1 con01 1 2 ... (2) mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape (3) [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh'); lhsphere=fs_read_surf('$FsDir/freesurfer/subjects/fsaverage/surf/lh.sphere'); lhcortex=fs_read_label('$FsDir/freesurfer/subjects/fsaverage/surf/lh.cortex.label'); (4)Qdec = fReadQdec('qdec.table.dat'); Qdec = rmQdecCol(Qdec,1); sID = Qdec(2:end,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); [M,Y,ni] = sortData(M,1,Y,sID); X = [ones(length(M),1) M M(:,1).*M(:,2)]; But when I followed wiki,code[M,Y,ni]first, matrix X will be four columns: 1-A column of 1s(intercept term) 2-The time covariate (0s and 1s) 3-The group covariate (2s and 1s,but in my table group 1 in the first, I think maybe it upside down?So I used the code X before code[M,Y,ni],then it will be 1s and 2s) 4-The group and time interaction (It is also affected by the third column to change). Is my use correct here? I think it will be influn (5)Then I used voxel-wise mixed model analysis following Jorge's reply. lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex); CM.C = [0 0 0 1]; F_lhstats = lme_mass_F(lhstats,CM); (6)fs_write_fstats(F_stats,mri,'sig.mgh','sig'); How to do correction about the result 'sig.mgh'? May I use lme_mass_FDR or lme_mass_FDR2? How to do? And if I can have a file including clusters' massage like summary file? I can't do a mri_glmfit-sim or mc-z in QDEC, and FDR in QDEC, maybe the t-value to high,there are nothing left. Please give me some help.Thank you very much, and looking forward to your reply!

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recon-all error
by Maria Economou 05 Jun '17

05 Jun '17

Dear FreeSurfer developers, Sorry for cross-posting, perhaps my previous e-mail was missed. I've been trying to run recon-all for my first subject and I keep getting several errors like: ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 Too many open files ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt Loading pixel data ERROR: /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm is not a dicom file 70092 Requested element (18 82) not found in DCM_GetElementVM I have used the DICOM files from my 3D T1 MPRAGE SENSE images, so I don't understand why I get these errors. This is the command i used: uos$ recon-all -subjid 147364 -i /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm -all FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c platform: OS X El Capitan Version 10.11.6 Please find attached the recon-all.log Many thanks, Maria.

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Question regarding recon-all error
by 곽유나 05 Jun '17

05 Jun '17

Hello, I'm completely new to brain imaging and freesurfer, and I can't seem to find a solution to the error that I have with recon-all. I didn't even get to skull stripping yet, and something's wrong with the talairach transform. I attached recon-all.log and talairach_avi.log in the e-mail. Thanks for your help in advance. Yuna

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Freeview overlay, positive values only
by Rita Elena Loiotile 04 Jun '17

04 Jun '17

Hi, Is there an easy command to only load positive values of an overlay in Freeview. I know in tksurfer it's truncphaseflag. Freeview does have the "truncate" option in the surface pane of the GUI. But, I don't see a command line flag. I'm hoping there's a way that's not in the help documentation. Thanks! Rita

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Freesurfer June 2017