Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

cotrolling for total gray matter volume
by Clara Kühn 02 Jul '16

02 Jul '16

Dear FreeSurfer experts, I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was wondering if it is useful to control for total gray matter volume when looking at surface area? Thanks for your help! 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

2 1

Intensity normalization issues leading to improper segmentation
by Elodie Cauvet 01 Jul '16

01 Jul '16

Dear Freesurfer list, Maybe I am hoping for a miracle with my question, but I am bit desperate after unsuccessfully trying things around for over a year. In a nutshell, I need advice on the intensity normalization options. We have T1 data from twins (8-25years) acquired on a 3T MR750 GE scanner with a 32 channel coil (IR-FSPGR 3D volume). This coil has a huge problem in a field inhomogeneity resulting in strong occipital hypersignal and frontal hyposignal, from which I believe all my problems originate. - The standard pipeline provide an incomplete temporal and frontal segmentation (white and pial surfaces do not include enough) while over including in occipital and parietal. - We tried using the watershed 40 value from the skulltrip to get more of the occipital (we had a few subjects having holes in occipital within the brain segmentation). This option changed also the segmentation resulting in better segmentation for temporal and frontal but worse in parietal and occipital. - We tried control points as well, without success (as you can imagine due to the fronto-occipital inhomogeneity). We also tried manually removing extra voxels from the white surface to correct it. But unfortunately, this is not an option because we have about 200 scans to process. - We tried using N4 intensity bias correction on the raw images before feeding it to freesurfer, but the segmentation did not run through for all participants (stuck in fixing topology for more than a week) and for those working, the pial surface did not include enough grey matter. I am now thinking about playing with the option of intensity normalization (mri_ca_normalize) within freesurfer but would like to have your expert opinion on that before roaming. Any advice on how to set up mri_ca_normalize to retrieve a good white matter homogeneity? Or any other functions I should be playing around with? Thanks a lot in advance for your help, Kind regards, Élodie Élodie CAUVET | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B, floor 8 | 113 30 Stockholm +46 (0)8 514 527 10 | +46 (0)728 774 058 elodie<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…>.cauvet(a)ki.se<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…> http://ki.se/en/kind/startpage<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…> http://elodiecauvet.wordpress.com/<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…> Karolinska Institutet – a medical university

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Re: [Freesurfer] qdec load error missing BLT
by Antonin Skoch 30 Jun '16

30 Jun '16

Dear Joshua, we had the same problem with freeSurfer 5.3.0 on Debian GNU/Linux 8.3 (jessie). In our case this was warning, the qdec launched, however the fsgd plot functionality (interactive vertex-wise GLM plot display) did not work. It seems that the error is caused by interference of tk/blt libraries packaged with freeSurfer with those installed on the system. We were able to resolve this issue by uninstalling following installed packages: tk8.6-blt2.5 blt If this do not help to you, try to run strace -f qdec and inspect, which libraries are loaded during initialization on your system before the error is issued. Regards, Antonin Skoch

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REPOST: Skull Strip and Bad Surfaces
by Katherine Reiter 30 Jun '16

30 Jun '16

Dear FreeSurfer experts, I am working on a data set and am having particular difficulty with one subject. It appeared the skull strip was mistakenly removing occipital regions. These regions were absent from the brainmask, T1, and resulting surfaces. I attempted to solve this in 2 different ways. I first adjusted the watershed and reran the recon-all -autorecon2 in order to redraw the surfaces. Adjusting the watershed worked to include these regions in both the brainmask and T1 but the resulting surfaces hugely inaccurate (see the attached screenshot '4003_badsurfs_parietal_cerebellum2'; Oddly enough, the frontal surfaces are largely accurate but the parietal regions include gray matter in the white surface and even large amounts of the cerebellum, while excluding occipital regions. I then reran it from the raw dicoms and had the same issue with occipital regions being excluded so I adjusted the watershed and tried to manually fix the surfaces, but this resulted in similar inaccurate surfaces. See the second attached screenshot '4003_badsurfs'. ll surfaces are fairly messy, but some regions are more accurage, where the appears to distinguish between gray and white and other areas are over inclusive, but cerebellar and some superior and medial regions are excluded. Any and all help would be much appreciated. Thanks in advance! Kate Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.reiter(a)marquette.edu

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REPOST: Longitudinal Stream: Recon-all and template
by Tamara Tavares 30 Jun '16

30 Jun '16

Hello All, I am planning to run the longitudinal stream on my data set and I have a few questions: 1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individually through recon-all? My understanding is that some motion correction will occur if I specify more than one T1 which may alter the results versus if I specify one T1? 2) What input files should I use to create my base templates? Are the input files the norm.mgz files from each subject? Thank you in advance for your help! Best, Tamara

2 1

mean cortical thickness not equal to averaged ROIs cortical thickness
by Nabin Koirala 30 Jun '16

30 Jun '16

Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ? Thank you. Regards, Nabin

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Get a given point's ROI
by Yuan Lin 29 Jun '16

29 Jun '16

Dear FreeSurfer experts, I am a beginner to learn to use FreeSurfer. Now I have a question to be solved. I have gotten the reconstruction results of a subject after using the command recon-all. How can I know a given point belongs to which region of interest? For example, how can I know whether a give point belongs to the superior frontal or inferior temporal? Which commands should I use? Thank you so much. Best, Lin

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arkadiy Maksimovskiy 29 Jun '16

29 Jun '16

Thank you for catching this. Really appreciate your help. - Arkadiiy

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28
by Arkadiy Maksimovskiy 29 Jun '16

29 Jun '16

Thank you!!

1 0

longitudinal tracula
by Harms, Michael 29 Jun '16

29 Jun '16

1 0

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Freesurfer June 2016