Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Freeview recon button
by Walid Yassin 30 Jun '16

30 Jun '16

Hello freesurfers, I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have the Recon edit button. I saw that someone asked about this questions twice in the archive but was never answered. There was a note in the wiki page that reads "*Note*: Recon edit mode is only available in the most recent release of freeview". I thought that the most recent release of freeview comes with the most recent release of freesurfer. Can someone please let me know if there is a separate download link to the recent release of freeview? Thank you in advance, Also If someone can answer my previous question regarding the Gyrification i would really really appreciate it. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html Thank you again, Best regards, Walid

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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

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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

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

29 Jun '16

Thank you!!

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longitudinal tracula
by Harms, Michael 29 Jun '16

29 Jun '16

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Announcement: fsurf, a command line tool for running freesurfer on the Open Science Grid
by Krieger, Donald N. 29 Jun '16

29 Jun '16

Dear FreeSurfer community, The Open Science Grid (http://www.opensciencegrid.org) is a federation of university and laboratory HPC facilities which share computing capacity to support science. We have developed a command line tool "fsurf" you can use from your laptop or desktop computer to submit scans for FreeSurfer processing on these clusters. In the initial release it is capable of executing "recon-all -all -i SubjectName.mgz" using FreeSurfer 5.3. No allocation is required. We only request that you cite the OSG in publications that benefit from its use. Instructions for getting started are found here: http://bit.ly/freesurferopensciencegrid. Please post questions and problems to OSG user support at user-support(a)opensciencegrid.org<mailto:user-support@opensciencegrid.org>. We hope you find it useful. Best regards, The OSG fsurf support team

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