Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

qdec problem
by wanghaibao 07 Sep '16

07 Sep '16

Hi, Douglas thank you for your reply. yes, the number in the text box cannot be changed, including threshold and False Discovery Rate in display. and also when i Save the picture of Display in File menu, the name cannot be input into the text box. Can you not just change the number in the text box? On 09/06/2016 12:49 PM, wanghaibao wrote: > 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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mri_glmfit --pvr Assistance
by Timothy Hendrickson 07 Sep '16

07 Sep '16

FreeSurfer Experts, I have a data set which comprises one group and the co-variate IQ. I would like to correlate this data set with the dependent measure LGI. I originally performed this in QDEC, however I read elsewhere that a vertex-by-vertex correlation cannot be done in QDEC. Further, I read that it must be done via command line with mri_glmfit and the --pvr flag. I am confused as to what sort of file I should input into the --pvr flag (do I run a separate analysis?, etc). Any advice would be extremely helpful. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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recon-all error
by Liu Y 07 Sep '16

07 Sep '16

Dear Freesurfer Developers, After updating my op to Ubunto from 14 to 16.04, and re-installing the Freesurfer, when I run recon-all, it ended with an error message: /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s A2090_1 exited with ERRORS at ke 7.9.2016 10.20.05 +0300 I have searched the list and could not find answer, need your help. Best regards, Yawu 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu 16.04 LTS 3) recon-all.log: see attached

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Extracting aseg.stats data
by Tamara Tavares 07 Sep '16

07 Sep '16

Hello, I am trying to extract the volumes from the aseg file of multiple subjects using the command: asegstats2table --subjects C9F03_1 C9F03_2 C9F07_1 --meas volume --tablefile aseg_stats_test.txt I keep getting the following error: SUBJECTS_DIR : home/bmiadmin/Tamara/FreeSurfer_GENFI/analysis/output Parsing the .stats files ERROR: The stats file home/bmiadmin/Tamara/FreeSurfer_GENFI/analysis/output/C9F03_1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I have set my subject directory to where all my output files are located and the subjects/stats folder does contain a aseg.stats file. I have attached a aseg.stats file. Thank you in advance for your help! Tamara

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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>

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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

2 1

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

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Freesurfer September 2016