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30132 discussions

TRACULA and priors problem
by Juergen Haenggi 16 Mar '17

16 Mar '17

Dear TRACULA experts I run TRACULA FS 6.0 on a Mac and get the following error: #@# Priors Fri Feb 24 17:11:18 CET 2017 /tmp/subj33.interpreter_control_01/.15208.txt: No such file or directory. In the FS archive I found the following email https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50778.html However, in my situation, the directories of the FS preprocessed subjects are in /Applications/freesurfer/subjects folder, and therefore to solution proposed in the email (make symbolic links) does not make sense for me. Is there another work around? Thanks in advance Regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------

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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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