Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

extreme hydrocephalus -wm not recognized
by Andrea Horváth 02 Jun '14

02 Jun '14

Dear Freesurfers, I ran recon-all on a subject with extreme hydrocephalus. Registration to Talairach space and skull stripping were OK. However, a part of occipital white matter was not recognized as white matter even after adding control points and running recon-all -autorecon2-cp -autorecon3 due to the large ventricle as you can see in the attachment. What can you recommend to fix this problem? Thank you for your help! Andrea -- Dr. Horváth Andrea PhD hallgató Pécsi Diagnosztikai Központ

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Re: [Freesurfer] asegstats2table Longitudinal data.
by Victor Montal Blancafort 02 Jun '14

02 Jun '14

Thanks Martin, The provided command works! Best, Victor Hospital de Sant Pau, Barcelona

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invalid license key error
by Kristen Pammer 02 Jun '14

02 Jun '14

Hello, I have just downloaded and installed both CentOS and FreeSurfer. I am trying to run the installation tests, and a number of them do not work (e.g., tkmedit bert orig.mgz, recon etc). the error I get is as follows: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment I only recieved the license key a few days ago and copy/pasted the 3 lines exactly as sent to me. I found a thread from about a year ago, I tried to follow it through, but it didn't work. I also cannot find any other threads reporting a similar problem that follow through to a solution. Any help you could provide would be great Thanks KP

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tksurfer bug report, input from keyboard is not accepted in ubuntu 14.04
by Knut J Bjuland 01 Jun '14

01 Jun '14

Dear freesurfer I have used tksurfer on Ubunt 14.04. However, I have one problem. Tksurfer does not respond to any input from the keyboard when I am running it. I can only access it though the mouse. For instance, I can enter threshold values, in overlay configuration option? Are there any workaround? Knut J Bjuland

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aberrantly high LGI value with localGI on longitudinal subjects, What is the best curse of action?
by Knut J Bjuland 01 Jun '14

01 Jun '14

Dear Freesurfers, I have run localGI on longitudinal data. However, I got three longitudinal subject with value is aberrantly high LGI value. What is the best curse of action? Should I rerun the cross section with recon -all -s id -autorecon-2-wm -autorecon3 -randomness, and then recreate the base before running the localGI again? Or is there any other options? regards Knut J Bjuland

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problems with cortical surface area maps
by Lars M. Rimol 01 Jun '14

01 Jun '14

Hi Anderson, Thank you! How would you suggest I address this issue when I smooth these images before statistical analysis? I normally use the smoothing algorithm implemented in FreeSurfer (mri_surf2surf). -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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meshes/surfaces for sub-cortical structures
by Tanya 01 Jun '14

01 Jun '14

Hi Freesurfers, I'm wondering whether the meshes (list of vertices+faces) corresponding to structures such as the hippocampus and amigdala are available as part of the Freesurfer output? In the /surf folder there are only the meshes of whole brain structures (cortex, pial, WM...). Is there any utility function to generate the meshes for the smaller structures? Thank you!

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problems with cortical surface area maps
by Lars M. Rimol 31 May '14

31 May '14

Hi, I have generated surface area maps for a sample of subjects (using [mris_preproc --fsgd *.* --target fsaverage --hemi *h --meas area --out *.mgh). When I created a mean image across all subjects (163842 x 1) and looked at it in tksurfer, I noticed a pattern on the surface that's a little troubling. Please see the attached image file (patterninmeanareaimg_ allsubjs_unsmoothed.jpg). I sampled the curv files to ico (with *mris_preproc*) for all subjects and looked at them individually (I have attached a few figures). I did find four resampled curv.mgh's that looked unusual, but removing them did not change the pattern seen in the attached figure. I also looked at some of the individual area files resampled to ico (using make_average_subject) and the outliers there were identical with the ones identified using the resampled curv-files (perhaps unsurprisingly). All these images are unsmoothed. So I'm at a loss here. Any suggestions on what to do next in terms of trouble shooting? (PS! I have attached the resampled curv and area files for a normal subject in lh_104_curvsjekk_lateral.jpg and lh_104_areasjekk_lateral.jpg, and for an unusual subject in lh_81_UNUSUAL_curvsjekk_lateral.jpg and lh_81_areasjekk_lateral.jpg. The three other subjects that seemed unusual looked like subject 81, and all the other subjects looked like 104.) Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Re: [Freesurfer] Longitudinal data for cross sectional individual differences study
by Martin Reuter 31 May '14

31 May '14

Hi Mike, Yes, take the results from the longitudinal stream, they are less noisy. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Michael Kranz <mbkranz(a)gmail.com> Date:05/31/2014 10:09 AM (GMT-05:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal data for cross sectional individual differences study Hi Freesurfers, Just wanted to verify: I have ran my subjects through the longitudinal processing stream (two time points a couple weeks apart). I want to predict cognitive performance (from the first time point) with Freesurfer stats. As I have the longitudinal data available, would it be better to use longitudinally processed stats (as opposed to the cross sectional stats)? I ask because I'm not aware of any publications that do this... Thanks much, Mike Kranz Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323-1329

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Longitudinal data for cross sectional individual differences study
by Michael Kranz 31 May '14

31 May '14

Hi Freesurfers, Just wanted to verify: I have ran my subjects through the longitudinal processing stream (two time points a couple weeks apart). I want to predict cognitive performance (from the first time point) with Freesurfer stats. As I have the longitudinal data available, would it be better to use longitudinally processed stats (as opposed to the cross sectional stats)? I ask because I'm not aware of any publications that do this... Thanks much, Mike Kranz Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323-1329

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