Freesurfer

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30096 discussions

extract thickness values from clusters
by Clara Kühn 07 Sep '16

07 Sep '16

Dear Freesurfer Experts, I did a longitudinal 2 stage model and now I would like to extract the thickness and area values from significant clusters that survived the Monte Carlo correction. As I understood from the various e-mails in the archives expressing the same request there is a file "something.y.ocn.dat" where those thickness values are supposedly stored for each cluster and each subject. However, this file included "the average value of each subject in each cluster" (as it states in the group comparison tutorial), meaning the -log10(pvalue). I would like to show that the significant difference between two groups is driven by a certain group and to do that I want to display the thickness and area values of each cluster in bar graphs. What could I do to receive these values? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Cluster Forming Threshold
by Timothy Hendrickson 07 Sep '16

07 Sep '16

Freesurfer Experts, I am currently using a Monte Carlo Z-Simulation to perform multiple comparisons on a data set. I have played around with various cluster forming threshold and cluster wise thresholds. I have no idea what would be considered "too liberal" or "too conservative" of thresholds and I have not found much literature that decimates this either. Are there any general best practices I should follow when determining these thresholds? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Postdoctoral positions available in Sydney, Australia
by Jerome Maller 06 Sep '16

06 Sep '16

Hi everyone, An exciting opportunity exists to join a successful research group as part of a partnership between The Heart Research Institute and the University of Sydney’s Charles Perkins Centre, a world class research and education precinct. Interested postdoctoral applicant(s) will be joining a dynamic and highly successful collaborative research program aimed at applying cutting edge neuroimaging technology (multishell diffusion MRI, connectomics and resting-state functional MRI) to map normal patterns and disease-related alterations in neural networks. Our group has a novel neurocardiovascular focus and this role will develop and support projects including traumatic brain injury, perisurgical brain injury, depression and also explore the brain changes associated with cardiovascular and metabolic conditions such as diabetes, hypertension and heart failure. The group is headed by Professor Stuart Grieve (Director of Imaging at Charles Perkins Centre and group leader at HRI). A major focus is ultra high-resolution diffusion imaging (256-1014 directions, 5-8 shells) and in partnership with industry aim to spearhead the use of these clinically. Email: stuart.michael.grieve(a)gmail.com -- *Dr Jerome J Maller BSc,GradDipPsych,MSc,PhD* Neuroscientist Adjunct Senior Research Fellow *Monash Alfred Psychiatry Research Centre (MAPrc)* *Central Clinical School, Monash University and Alfred Hospital* *4th Floor, 607 St Kilda Rd, Melbourne VIC* Affiliate *Sydney Translational Imaging Lab (STIL)* *University of Sydney* Adjunct Associate Professor *Centre for Research on Ageing, Health and Wellbeing, Research School of Population Health, ANU College of Medicine, Biology and Environment at the Australian National University.* *T: +61 3 9076 2404 <%2B61%203%209076%202404>* *F: +61 3 9076 6588 <%2B61%203%209076%206588>* *M: +61 419 221 454 <%2B61%20419%20221%20454>* *E: jerome.maller(a)monash.edu <jerome.maller(a)monash.edu> *

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when to -qcache in longitudinal processing
by Linette Savage 06 Sep '16

06 Sep '16

Hello Freesurfers, My ultimate goal is a MLE analysis of 2 groups (n~25) at 2 time points. I have followed the longitudinal processing stream (cross, base, long) although only ran -qcache at the cross stage. Do I need to add this flag to the base and/or long recon-all command? Or is the same thing achieved by running this code (described in the LME wiki page under Preparing your data): mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.stack.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.stack.mgh --tval lh.thickness.stack.fwhm10.mgh --fwhm-trg 10 --cortex --noreshape I'm using Freesurferv5.3.0 on OS X El Capitan although about to move to a Linux system. Thanks kindly, Linette Savage University of Calgary Brain Training Study www.braintrainingstudy.ca<http://www.braintrainingstudy.ca>

2 1

qdec problem
by wanghaibao 06 Sep '16

06 Sep '16

Hello,Douglas I used the freesurfer 5.3 in fedora 20,there is a question in my reseach,may be not a question! When i view the results of analysis in the qdec window,why did i cannot change the value of the Threshold,such as min(which had been seted with the value of 2) ,in the same way,the max is 5?If i want to change the value of them,how can i do it? what wrong with it and how to solve it? thank you in advance haibao wang sep-6, 2016

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Navigation Tool error (tkmedit)
by Chester Kang 06 Sep '16

06 Sep '16

Hi, This occurs when executing the tkmedit command in order to perform white and grey matter edits. Clicking on zoom2 in order to enlarge the brain and then on Navigation Tool in order to drag the brain down. On clicking on the display window, the brain disappears to the bottom right hand corner (out of view). Clicking on dragging from the bottom-right and dragging to the top-left drags the brain up but with the contrast becoming "white"/oversaturated. With repeated click-n-dragging up, this get progressively worse. At times, while doing this, the following error is seen... "can't read "tViewPreset_None": no such variable" In all instances, once the disappearance happens, the contrast it no longer usable. Freesurfer version is 5.3.0, tkmedit stable5. Any help would be great! Regards, Chester

2 1

inflated surface - dots
by Fire Tech 06 Sep '16

06 Sep '16

2 1

sulcus measurement from aparcstat2table
by tulu 06 Sep '16

06 Sep '16

Dear FS expert I use the aparcstat2table and generate the cortical volume/thickness. I have a question regarding sulcus volume and thickness meaning. For example, it generate lh_S_front_inf volume and thickness, which represents as left inferior frontal sulcus. Did the volume represent as CSF volume in this sulcus ? and what is the thickness of sulcus meaning ? Thanks JLH

2 1

Recon-all GNU parallel Error. : Segmentation fault
by Dev vasu 06 Sep '16

06 Sep '16

Dear Sir / madam, I have tried running recon-all with GNU parallel and i am incurring following error kindly review the recon-all.log ( see below ). Could you please let me know why such problem persists for me. Is it the issue with memory space ? Thanks Vasudev Calling the GNU parallel in terminal " ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i {}.nii.gz -all -qcache " ------------------------recon-all-log................ Fr 2. Sep 17:59:48 CEST 2016 /media/vasudev/Daten/VBCT_results/PAT30 /usr/local/bin/freesurfer/bin/recon-all -s PAT30 -i PAT30.nii.gz -all -qcache subjid PAT30 setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results FREESURFER_HOME /usr/local/bin/freesurfer Actual FREESURFER_HOME /usr/local/bin/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15208 maxlocks unlimited maxsignal 15208 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3915432 3730516 184916 17476 21512 505448 -/+ buffers/cache: 3203556 711876 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ####################################### GCADIR /usr/local/bin/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/bin/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /media/vasudev/Daten/VBCT_results/PAT30 mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz /media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting

2 1

how to change threshold value in qdec window
by wanghaibao 06 Sep '16

06 Sep '16

hello,everyone I used the freesurfer 5.3 in fedora 20,there is a question in my reseach,may be not a question! When i view the results of analysis in the qdec window,why did i cannot change the value of the Threshold,such as min(which had been seted with the value of 2) ,in the same way,the max is 5?If i want to change the value of them,how can i do it? what wrong with it and how to solve it? thank you in advance haibao wang sep-6, 2016

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