Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Tracula: anatomical priors
by Jacobs H (NP) 16 Mar '17

16 Mar '17

Dear FreeSurfers, Where can I find the anatomical ROIs from the aparc/aseg (end and begin points) that are being used to reconstruct the tracts in Tracula? Many thanks Heidi

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Repost: tracula stats including NAs?
by Jacobs H (NP) 16 Mar '17

16 Mar '17

Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki). Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ? Look forward to your thoughts on this. Best wishes Heidi

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TRACULA tract reconstruction
by Joëlle Ismay Rosanne Van Der Molen 16 Mar '17

16 Mar '17

??Dear Tracula experts, I am applying Tracula on a longitudinal data set, and have some questions I am hoping you could help me with: Firstly, upon visual inspection, several tracts appear to be quite messy, or small (on the default freeview threshold) for most subjects. However, the -stat step from Tracula does not necessarily flag these tracts as outliers. What is then the best way to decide whether tracts are not correctly reconstructed and need to be rerun separately once more? Can I rely on the flagged outliers? Or should I rerun all the tracts that do not look ok after visual inspection? And in the last case, for tracts that look small, are they considered as correctly reconstructed if looking ok at lower thresholds than the default of freeview? Second, concerning the rerunning of poorly reconstructed tracts, I was wondering if there might be a more automated way to configure the dmrirc file in order to adapt it for each subject/each tract to rerun (and its corresponding control points). Third, I was wondering if there is a recommended software for obtaining bvecs and bvals. For the moment I used mrconvert (from MRtrix, using the -export_grad_fsl option) and the new mri_convert from freesurfer 6.0. As they give different outputs, I was wondering if this may impact the reconstruction. Lastly, would you recommend using freesurfer 5.3 or 6.0 for applying the longitudinal stream of Tracula? Related to this, is it recommended to use the same freesurfer version to obtain the long/base images, and to run Tracula? Thank you for your time, Best regards, Joëlle van der Molen

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Re: [Freesurfer] Intensity normalization in longitudinal processing
by Jaiashre Sridhar 16 Mar '17

16 Mar '17

Martin, Thank you for your response. I ran the subject completely (cross and long) in v6.0 and the white matter intensity distribution in the long brain looks similar to the one run with the mixed versions (v5.1 cross and v6.0 long). Since the surfaces also look fine, I understand that this is not an issue. Thank you again, Jaiashre.

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matrix is ill-conditioned or badly scaled, condno = 1e+08
by teodora petrova 16 Mar '17

16 Mar '17

Hello, I am trying to use the glm_fit to correlate a continuous variable (index) with cortical thickness, when controlling for age, education, and cognition (MMSE) (all continuous variables). However, I get the following error: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.index.thickness.10.mgh --fsgd index.fsgd dods --C index.mtx --surf fsaverage lh --cortex --glmdir lh.index.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Please find attached my fsgd file and the design matrix. I searched the archives and found out that a possible reason for this may be creating my file in Windows. Indeed, I created it by copy-pasting the data from an Excel spreadsheet into an empty txt file. I tried to convert it on Linux, using the command old.fsgd | sed 's/\r/\n/g' > new.fsgd, as well as making a new txt file on Linux (by copy -paste from a spreadsheet), but these did not work either. How can I solve this? Thank you for the help! Best, Teodora

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Postdoc position at Bangor University (Wales, UK)
by Kami Koldewyn 16 Mar '17

16 Mar '17

Applications are invited for a 3.5-year, full time postdoctoral position with Dr. Kami Koldewyn in the Developmental Social Vision lab<https://sites.google.com/view/devsocialvislab/> in the School of Psychology at Bangor University<https://www.bangor.ac.uk/psychology/> (Wales, UK). The post is part of a European Research Council funded Starting Grant focused on Developmental Social Neuroscience. The project, ‘Becoming Social’, investigates developmental change in social perception, social learning and the social brain in late-childhood/early adolescence. The successful applicant will be the coordinator of the first major research stream of the Becoming Social project, which focuses on understanding the typical adult system and developing tasks and methods that will be applied throughout the five-year project in the longitudinal developmental streams. Methods used may include behavioural, eye-tracking and neuroimaging (e.g. fMRI, DWI) measures and the postdoctoral researcher who fills this post will be very involved, both conceptually and technically, in the design and construction of research questions and the tasks to address them. Duties will include working to develop tasks and materials that will be used across the entire project (including not only typical adults but children/adolescents aged 9-16 both with and without an Autism Spectrum Disorder). The postdoctoral researcher will be a key member of the Becoming Social team and will work closely with other team members. A PhD or equivalent in a relevant field (e.g., Psychology, Neuroscience, Cognitive Science, Biomedical Imaging/Engineering or Computer Science), as well as outstanding written and spoken communication skills are essential. In addition, this particular post requires significant technical and/or neuroimaging abilities. The successful candidate needs to be comfortable with tackling new imaging and analysis methods and have the technical chops to do so. Closing date for applications: 10th April, 2017. Proposed start date: Between May 1st and July 1st 2017 (though exact timing is flexible for the right candidate). For full details see this document: PDF of advertisement<https://drive.google.com/open?id=0B2vETzZbbENDVkU4aVY1eWliVGc> To apply, visit: https://jobs.bangor.ac.uk/ Job #BU01403<https://jobs.bangor.ac.uk/details.php.en?id=QLYFK026203F3VBQB7V68LOTX&nPost…> For more information or to discuss eligibility please contact: Kami Koldewyn at k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk> Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Extract the cortical thickness
by Duy Nguyen 16 Mar '17

16 Mar '17

Dear FreeSurfer expert I wonder that whether I can use the command aparc2statstable to get the cortical thickness or is it better to get the cortical thickness of a volume defined ROI or is there the easy way to get the most accurate cortical thickness from ROI I am following the pipeline "VolumeRoiCorticalThickness" but I do not understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii. Sorry if this question is too obvious for me to overlook something. Any help is appreciated since I am newbie on FreeSurfer. Best regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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Recon-all : mri_watershed Error: indices out of bounds
by Matthieu Vanhoutte 16 Mar '17

16 Mar '17

Dear Freesurfer's experts, I ran a classic recon-all and got stucked on a problem I couldn't find in the mailing list: "*mri_watershed Error: indices out of bounds*" *mri_watershed -T1 -brain_atlas /home/global//freesurfer5.3//average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz * *Mode: T1 normalized volume* *Mode: Use the information of atlas (default parms, --help for details)* *********************************************************** *The input file is T1.mgz* *The output file is brainmask.auto.mgz* *Weighting the input with atlas information before watershed* **************************WATERSHED*************************** *Sorting...* * first estimation of the COG coord: x=125 y=200 z=49 r=52* * first estimation of the main basin volume: 593173 voxels* *mri_watershed Error: indices out of bounds* *Linux woody 4.4.0-31-generic #50~14.04.1-Ubuntu SMP Wed Jul 13 01:07:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 207078_M1_2013-01-29 exited with ERRORS at Thu Mar 16 14:57:24 CET 2017* Do you have idea or clue to this problem ? Best regards, Matthieu

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Hippocampal subfields huge memory demands
by Ferdi van de Kamp 16 Mar '17

16 Mar '17

Hi all, sorry for the double post, but I noticed an error in the chosen title. I believe the website warns for high demands of memory, claiming it may take up to 10G for this processing step. However, when I run this on cluster the memory demands go up to 30G. This is still for one subject using one scan. Is this to be expected, has something changed in the processing pipeline? Eventually I want to run the longitudinal version, should I expect an increase in memory demands? Running the parahippocampal subfields on our cluster using: recon-all -s $subject -hippocampal-subfields-T1 Version: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028- 4cfbf2a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Kind regards, Ferdi

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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?
by Antonin Skoch 15 Mar '17

15 Mar '17

Dear Doug, I have uploaded 3 subjects with 0.7mm3 data so that you can take a look: None of the subjects has macroscopical pathological changes, the juxtacortical hypointensities should be physiological finding. 1. example_subject_0.7mm.tar.gz This is subject processed by recon-all -all -T2pial -hires processed by dev version from 07/02/2017. In this subject you can see the cutting of the pial surface in the midline (due to the wrong aseg labeling to contralateral gray matter) at the RAS coords 2,-70,17 and juxtacortical hypointensity affecting pial/white surface in 7,29,43 2. juxtacortical_hypointensities_0.7mm_HCP_pipeline.tar.gz This is subject processed by HCP pipeline with quite large amount of juxtacortical hypointensities largely affecting pial/white surfaces, located for example at the RAS coords: 11,-64,54 15,-48,48 White surface produced by standard recon-all -hires -white is the file ?h.white.prehires. 3. test_first_wm_peak_HCP_pipeline_base.tar.gz This is subject processed by HCP pipeline with combination with 2nd step of longitudinal stream (-base). In this subject I tested -first_wm_peak behavior (option for mris_make_surfaces used in FreeSurferHiResWhite.sh in HCP pipeline). There has been change of implementation of -first_wm_peak in the December 2016. It seems that the recent implementation of -first_wm_peak positions the white surface too internally as I commented on here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51414.html White surface produced by standard recon-all -hires -white is the file ?h.white.prehires. Additionally, there are files lh.white.deformed_ver_201611 - file produced by using -first_wm_peak (original version before code change) lh.white.deformed_ver_201701 - file produced by using -first_wm_peak (version after code change with white surfaces positioned very internally, I consider it not anatomically relevant) lh.white.deformed_ver_201701_wo_first_wm_peak - file produced without using -first_wm_peak. Thank you for your time and looking forward to your comments! Regards, Antonin Hi Antonin, can you upload that subject? In one case using 700um, the white surface looked fine, and I did not see much of a difference with the 1mm scan. On 3/14/17 5:39 AM, Antonin Skoch wrote: Dear experts, can also be the difference between v5.3 and v6.0 behavior in HCP pipeline and possible sub-optimal behavior of v6.0 with HCP pipeline given by different in image input to mris_make_surfaces in HCP pipeline (FreeSurferHiResWhite.sh) ? For white surface estimation the recon-all input is brain.finalsurfs, which is very aggressively filtered so that the white matter voxels have typically values 110 and the SNR in deep white matter areas approach infinity. In contrast, for HCP pipeline the input T1w_hires_masked_norm image is filtered no to such an extent. Therefore there is much lower contrast-to-noise ratio in the region of GM-WM interface for mris_make_surfaces in FreSurferHiResWhite.sh. This maybe renders mris_make_surface more vulnerable to local deviations in intensity in GM-WM interface. My observation (without any thorougful tests) is that with v6.0 in HCP pipeline I had very often to edit wm.mgz in the region of GM-WM interface in the areas of (physiological) perivascular subcortical T1 hypointensities due to the ?h.white "leak" to these areas. And also, as I wrote in some of my previous (unanswered) posts: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51414.html the change of -first_wm_peak behaviour in v6.0 in fact worsened white surface estimation in my data I tested with HCP pipelines. I could upload some example subjects if you are interested and have time to dig in. In any case, it is probably hard to compare performance between standard recon-all and HCP pipeline and different versions of FreeSurfer due to different input to mris_make_surfaces and different flags used. The HCP pipeline, as it currently stands, would probably need different optimization of code or different command line options due to the different input used. Regards, Antonin Skoch Hi Bruce, I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the HCP 0.7mm data that I have looked at (and as I recall at least one other user had some similar issues, as did one of my collaborators), but that was all I meant to refer to. Sorry if my reply came across more general than that, as of course we want to move to using FreeSurfer V6+ in the future. It is the highres T1w and T2w stuff that my pipelines are designed to exploit, however. Also there are some changes I have to make to the HCP Pipelines for FreeSurfer V6+ because of differing file names, etc. Best, Matt. On 3/13/17, 9:40 PM, "Bruce Fischl" <freesurfer-boun...(a)nmr.mgh.harvard.edu on behalf of fis...(a)nmr.mgh.harvard.edu> wrote: >Hi Matt > >To state without qualification that "6.0 has some regressions as far as >surface placement" is incorrect. We quantified its test-retest >reliability, >accuracy and power to detect disease effects and all were improved >relative >to 5.3. We tested V6 on hundreds of datasets across an array of >pathologies >and different MR sequences, field strengths and scanners. We visually >inspected dozens of brains multiple times in the process of improving >accuracy and robustness. I can believe that on Wash U HCP data there >could >be some specific issues, but to imply that V6 is generally less accurate >is >simply incorrect. > >cheers >Bruce > > >On Mon, 13 Mar 2017, Matt Glasser wrote: > >> Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP >> Pipelines. For now version 6.0 has some regressions as far as surface >> placement goes and there are also some adaptations we need to make to >>the >> pipelines. >> >> Peace, >> >> Matt. >> >> From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of CAGNA >>Bastien >> <bastien.ca...(a)univ-amu.fr> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Monday, March 13, 2017 at 7:21 AM >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome >> project's pipeline ? >> >> Dear freesurfer experts, >> >> >> I'm wondering if it's possible to run the human connetome project's >>minimal >> processing pipeline using freesurfer 6 ? >> >> >> Does it require some update of the pipeline or is there anybody that >>have >> already enjoyed the new freesurfer version with this pipeline ? >> >> >> Thank you for your attention and your help, >> >> Bastien Cagna

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Freesurfer March 2017