Freesurfer

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30132 discussions

Urgent help with preprocessing pipeline
by Martin Juneja 19 Sep '18

19 Sep '18

External Email - Use Caution Hi, I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version of FreeSurfer. I used cross-sectional pipeline to identify ROIs (from Desikan atlas) with significant difference in cortical volume (CV) between controls and *patients (subjects 1-40, baseline)*, say I get ROIs: R1, R2 and R3. I am using these ROIs (R1, R2 and R3) for further analysis to determine the effect of two treatments: *T1 (placebo) (for subjects 1 to 20) and T2 (active) (for subjects 21 to 40)*, compared to their corresponding baseline. I compared CV of these ROIs (R1, R2 and R3): *T1 vs. baseline and T2 vs. baseline* using both cross-sectional as well as longitudinal pipeline. *Using cross-sectional pipeline:* I found there is significant improvement in CV (p = 0.019) for these ROIs for treatment T2 compared to baseline and no change for placebo treatment T1. *Using longitudinal pipeline: *There is little improvement in CV (p = 0.2) for these ROIs for treatment T2 compared to baseline and no change for placebo treatment T1. I was wondering why I am getting results so different between these pipelines, and which pipeline suits better in such comparison when my ROIs are identified using cross-sectional pipeline, but further analysis of these ROIs involved longitudinal comparison. I would really appreciate any help (as early as possible). Thank you so much !

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Using freesurfer without intensity normalization
by Raquib Ridwan 19 Sep '18

19 Sep '18

External Email - Use Caution Hi, I would like to know if intensity normalization(not bias field correction) so that white-matter is ~110 and gm is ~60 is necessary for freesurfer segmentation. Will intensity normalization using other methods still work for freesurfer segmentation?

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Re: [Freesurfer] if: missing file name
by Yacila Isabela Deza Araujo 19 Sep '18

19 Sep '18

External Email - Use Caution Hello, Please, find in the attachment the capture of the terminal output. It is basically the same that I get when I run it from the freesurfer/subjects directory. I also need to say that the problem is only with this Mac. It runs without any problem in a Linux computer. Thanks a lot for your support Yacila > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Sep 2018 15:35:08 +0000 > From: Yacila Isabela Deza Araujo > <yacila_isabela.deza_araujo(a)tu-dresden.de> > Subject: [Freesurfer] if: missing file name > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <DC2EE6A5-D782-4874-B1CC-B864B0FC84EF(a)msx.tu-dresden.de> > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Dear Freesurfer experts, > > Please find in the attachment a file with the errors I get when I try to follow the examples of recon-all > > Thanks a lot for your support, > > Yacila >

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Freesurfer 6.0 - Tracula - Segmentation fault
by Matthew Grecsek 19 Sep '18

19 Sep '18

External Email - Use Caution I ran standard recon-all on a single subject and then trac-all -prep. The process ran for approximately 1 hour and exited with errors: Segmentation fault. This is my first time testing Tracula, so user error likely. Here are the final lines from the console and trac-all.log attached: INFO: Distances between consecutive points in test subject's space are 9 13 13 12 WARN: Could not find satisfactory control point fit - try 912 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 114 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 15 INFO: Minimum allowable curvature at a dominant point is 0.0447089 INFO: Points where local peeks in curvature occur are 67 116 39 (curv = 0.0963721) 77 75 87 (curv = 0.114559) 75 76 95 (curv = 0.0564307) 69 74 105 (curv = 0.126918) 74 67 115 (curv = 0.0809615) INFO: Intermediate dominant points are 67 135 33 67 116 39 75 82 76 69 74 105 74 49 116 INFO: Final dominant points are 67 135 33 67 116 39 77 75 88 69 74 105 74 49 116 WARN: Defaulting to equidistant control points INFO: Selected control points are 67 135 33 68 108 46 75 83 75 69 74 105 74 49 116 INFO: Distances between consecutive points are 30 39 32 28 INFO: Selected control points in test subject's space are 56 58 -8 56 46 -3 58 35 9 55 30 22 57 19 26 INFO: Distances between consecutive points in test subject's space are 13 16 14 12 WARN: Could not find satisfactory control point fit - try 913 Writing output files to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_* Writing spline volume to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz Segmentation fault Darwin Matthews-MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Sep 17 16:26:23 EDT 2018 Thanks, -Matt

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if: missing file name
by Yacila Isabela Deza Araujo 19 Sep '18

19 Sep '18

External Email - Use Caution Dear Freesurfer experts, Please find in the attachment a file with the errors I get when I try to follow the examples of recon-all Thanks a lot for your support, Yacila

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if:missing file name
by Yacila Isabela Deza Araujo 19 Sep '18

19 Sep '18

External Email - Use Caution Hello, I just started with Freesurfer and got the following error during the call of the command recon-all If: missing file name I should say that other commands work well. I looked for the error and it seems that it is a change in the script. I install Freesurfer in my Mac and did not change anything during installation. Why do I have this error then? Thanks a lot for your support, Yacila

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Question about register
by 薛倩雯 19 Sep '18

19 Sep '18

External Email - Use Caution Dear Freesurfer experts, I need to transform a bunch of MNI coordinates of fiber tracts to native space. I have already registered my subjects to cvs_avg35_inMNI152 using mri_cvs_register. How can I transform the MNI coordinates back into the native space? Thanks!Qianwen

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postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 19 Sep '18

19 Sep '18

External Email - Use Caution Job description: Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort study over the world. The GUSTO mothers were recruited during pregnancy between 2009 and 2010. We have followed the GUSTO family since then. The GUSTO study collects the unique data on cognitive functions, children behaviors, psychopathology, and brain imaging at multiple points from birth to 7 years of age. We aim to study whether mothers mood, diet, and family lifestyle since pregnancy affect 1) their babies cognitive and brain development; 2) psychopathology later in life. We also aim to examine the role of genetics in such maternal influences. We are looking for postdoctoral fellows who are interested in the GUSTO study. Requirements: 1. PHD in Cognitive Neuroscience, or Psychology, or Imaging Genetics; 2. Experience with MRI-based neuroimage techniques; 3. Knowledge in statistical analysis is necessary; 4. Good communication and writing skills in English language; 5. Knowledge in longitudinal analysis will be plus plus. If you are interested in the jobs listed above, please send your CV to Deans Chair, Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 19 Sep '18

19 Sep '18

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Re: [Freesurfer] Surface Area in Toddlers/Children
by Douglas Greve 18 Sep '18

18 Sep '18

The flag to preserve area is not being turned on there. You can try running mris_preproc separately for area and including the --jac flag. If that does not work, you can download version6 and just use it to run mris_preproc On 8/10/18 4:41 PM, Derek Sayre Andrews wrote: > > External Email - Use Caution > > Hi Douglas, > > Of course, please find attached a copy of the recon-all.log file. > > Best, Derek > > PS: Apologies for the direct email in order to get you the attachment > > cid:image001.png@01D430A0.A5153C80 > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas > Greve <dgreve(a)mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Friday, August 10, 2018 at 11:12 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children > > Yes. -qcache actually calls mris_preproc. At one point, FS did not > preserve total area when mapping to fsaverage. I fixed it a while > ago, but maybe something was still off in 5.1 > > On 8/10/18 2:06 PM, Derek Sayre Andrews wrote: > > * External Email - Use Caution * > > Hi Douglas, > > Thank you for the response. > > I did not use mris_preproc to prepared the data. > > The data was mapped to fsaverage using recon-all with -qcache. I > then loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into > MATLAB using SurfStatReadData > <http://www.math.mcgill.ca/keith/surfstat/> and summed them across > each vertex. > > Would the terminal output of recon-all -qcache be helpful? > > Best, Derek > > cid:part2.2B5BCEFF.1D6DDEE5@mgh.harvard.edu > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of > Douglas Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> > *Reply-To: *Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, August 10, 2018 at 10:25 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" > <mailto:freesurfer@nmr.mgh.harvard.edu> > <freesurfer(a)nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children > > It should be preserving total surface area. Can you send your > mris_preproc command line and the terminal output? It might be > something with 5.1 as well. > > > > On 8/9/18 3:49 PM, Derek Sayre Andrews wrote: > > * External Email - Use Caution * > > Dear Freesurfer Developers and Experts, > > I have been exploring various vertex wise (mass univariate) > effects using freesurfer measures of cortical thickness and > surface area in a cohort of toddlers/children aged 25-70 months. > > When looking at the effect of age on surface area using > individuals’ measures mapped to fsaverage and smoothed at 15mm > fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread > negative effect of age (i.e. decreased surface area with age). > Given the age group of the cohort this seems implausible. > Plotting the sum of each individuals > lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the > relationship: > > cid:image001.png@01D42FCE.C197B360 > > However, plotting the lh+rh total surface area returned by > mris_anatomical_stats reveals a much more plausible > relationship between surface area and age: > > cid:image002.png@01D42FCE.C197B360 > > My working hypothesis is that the significantly smaller brain > sizes of our cohort compared to fsaverage, and the fact(?) > that -qcache does not preserve global surface area, is causing > an “over adjustment” in our cohorts smallest brains when > mapped to fsaverage. > > Thus, my questions are three fold > > 1. Is the mapping of our significantly smaller brains to > fsaverage a potential explanation for the results we are > seeing in our mass univariate analyses of surface area? > > 2. If this is the case, would this effect be limited to > surface area or also extend to other freesurfer measures > including cortical thickness, lGI, sulcal depth etc. > > 3. How would you recommend approaching vertex wise analyses > in a cohort of this age? Create a study specific average > subject using make_average_subject to map onto? > > Thank you for your insight and guidance! > > Best, Derek > > PS: All processing was performed using freesurfer v5.1 > > cid:image003.png@01D42FCE.C197B360 > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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