Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

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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creating norm.mgz
by Borzello, Mia 31 May '14

31 May '14

Hi all, I'm trying to use tkmedit to pick electrode points for a patient. For the mri, I'm using the average brain provided by freesurfer. I realized that I have no norm.mgz file which tkmedit calls. How do I create this? Thanks, Mia

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Control point error
by Victor Kovac 30 May '14

30 May '14

Hello, I ran recon-all on few subjects but noticed that much of the temporal lobes were excluded from segmentation, so I added control points to missed white matter voxels in this area, and subsequently ran recon-all -autorecon2-cp -autorecon3. The control points fixed much of the segmentation errors in the temporal lobes; however, errors in segmentation of other areas of the brain -- far from where I had placed control points -- were introduced. Attached are images of the same subject and same coronal slice, before and after running -autorecon2-cp -autorecon3, and, as you can see, much of the right superior frontal lobe is now missed. Is there any way to fix this, other than by simply adding more control points to the newly missed areas? One note is that the cores I am running these subjects on have a memory limit of 3.75 GB and I see that the recommended memory per subject is at least 4.0 GB. Could this be the problem? Also attached is the recon-all log. Thank you! Victor

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Re: [Freesurfer] Registration of Functional Data to the Inflated Brain
by Sherryse Corrow 30 May '14

30 May '14

Thanks Bruce. The problem is that the registration itself is not working properly. Recap: The goal is to view the functional data on the inflated brain. We ran recon-all, checked that registration, then attempted to register the functional data to the free surfer anatomical. My understanding is that running reg-feat2anat should create a folder (featdir/reg/freesurfer) with register.dat and anat2exf.register.dat files in (among others). The folder is created and some of the files are created, but those two are not. Although, I should note that there is a file created within this folder called anat2exf.register.dat.init. But I am not sure what the ³init² is for or what it means. The terminal output from running reg-feat2anat is attached. I can see now that there are errors in the output (I am slowly figuring how how to use FreeSurfer!). Any suggestions you have are greatly appreciated! Thanks! Sherryse Date: Tue, 27 May 2014 12:21:30 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Registration of Functional Data to the Inflated Brain Hi Sherryse you only need to register the anatomicals to the funtionals once, then sample the functional data onto the surface using mri_vol2surf. This will create a surface overlay that can be visualized on any of the surfaces for that subject (e.g. lh.white, lh.pial, lh.inflated) cheers Bruce On Tue, 27 May 2014, Sherryse Corrow wrote: >Hi FreeSurfer Team,? >Please help out a FreeSurfer newbie! ?We are having an issue with mapping >our functional data onto the inflated brain. ?When we finish the mapping, >it >seems that much of the data is showing up in white-matter space, and >therefore, cannot be seen on the external surface of the brain. We later >discovered that we were likely using the wrong registration matrix. >However, >it doesn?t seem like the one we are supposed to use is being produced >during >recon-all. ?I am new to FreeSurfer and would greatly appreciate some >assistance! ? >To provide you with more detail.? >Problem: When we run the command line below, and then open the folder >experiment.feat/reg/freesurfer, there is no >anat2exf.register.dat file.??However, there is a file called: >anat2exf.register.dat.init. >Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143 >Terminal Output: There is no terminal output.??No error of any kind. >Log File: Attached. >Thanks, >Sherryse >P.S. We submitted this issue previously but were not getting a response, >so >we tried again in case our thread wasn?t working properly.? >--? >Sherryse Corrow, Ph.D. / Postdoctoral Fellow >Human Vision and Eye Movement Lab >Department of Ophthalmology & Visual Sciences >UBC/VGH Eye Care Centre >360A-2550 Willow Street >Vancouver, BC, V5Z 3N9 >Tel: 604-875-4111 ext 67672 >Cell: 604-315-6717 >sherryse.corrow(a)eyecarecentre.org > >

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