Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

more thinner parcelation borders
by Gonzalo Rojas Costa 30 Jul '10

30 Jul '10

Hi: I change the color palette of the parcelation borders to white... But, I need thinner parcelation borders... can I change that parameter ?... Or could I specify a transparency factor for the borders ?... Sincerely, Gonzalo Rojas Costa

2 1

[fsfast]: temporal overlap of stimuli and concurrent presentation
by Sebastian Moeller 30 Jul '10

30 Jul '10

Dear fellow Surfers, is it possible to model several independent event streams for fs-fast? That is, using the 5 column paradigm file, is it okay to have different condition ID codes that have identical stimulus onset time (well only some of the time)? Or would I have to model that by specifying a TER and have both staggered around the real onset time? I would be happy to receive any pointer. Thanks in advance & best regards Sebastian -- Sebastian Moeller telephone: 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Methods for white matter hypointensities measure
by Laluz, Victor 30 Jul '10

30 Jul '10

Hello guys, I am curious as to how white matter hypointensities (on T1 mprage) are measured automatically for the aseg.stats file in FS? A group at UCSF is interested in using this measure for a study and would like to have a nice explanation or citation to describe how it is generated. I have looked through what I think the likely citations would be on the Freesurfer techniques article listing and came up empty. Thanks! Victor Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center

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Motor areas from Talairach
by Ben Hamida Cammoun Leila Faiza 30 Jul '10

30 Jul '10

Hi I am trying to find different Talairach areas in the motor cortex. I used the mris_convert -t function on the inflated brain (.asc). I selected coordinates using ranges from a paper (for example range x -70 to 4; range y -43 to 7 and range z 19 to 76 for M1). But when I want to see if they are in the wright area with tksurf on the same surface (inflated), the coordinates change. Do you know how to find the wright coordinates? Thanks Leila

2 1

monkey brain recon outputs
by Arslan, Ali 29 Jul '10

29 Jul '10

Hi, I finished reconstructing a monkey's surface following the scripts on the wiki. The output surfaces seems to be a bit distorted and rough around the edges. This reconstruction is done with a volume normalized by using ~400 white matter control points. The resolution of the scan is 1x1x1 mm. Here are some pictures to look at: http://www.flickr.com/photos/52445793@N05/sets/72157624471174691/ Interestingly, white matter and gray matter boundaries seem to be intermingled for some reason. I was hoping control points would take care of that problem but they didn't. This can be observed by the 2 vol_surf images in the set. The most obvious defects can be seen on the white matter. There are small protrusions over the gyri, and the surfaces are generally very rough, unlike a successful human reconstruction. I was wondering if you have any ideas as to the source of the problem. Skull stripping was done with FSL's bet, and it looks successful. Can it be a problem with intensity normalization? Regards, Ali Arslan

2 1

Overlay Thickness Files in tkmedit
by Michael Scheel 29 Jul '10

29 Jul '10

Hi, is there a way to visualize the lh.thickness or rh.thickness files as an overlay in tkmedit. Thanks, Michael

2 1

skull strip
by Tara Brah 29 Jul '10

29 Jul '10

I have a question regarding the skull stripping process. I ran my data through recon-all but still had much skull intact. I then followed the recommended process per the freesurfer wiki to change the watershed threshold levels on the recon process. I did so at the 20, 15, 10, 5, and 0 threshold with little improvement to the amount of skull removed. I know a similar question has been asked but in that scenario freesurfer was not including the skull as part of the cortical matter while in my scenario it is. Do you have any further suggestions as to how to remove the skull from my images? Thank you.

1 0

recon-all error
by Watson, Christopher 29 Jul '10

29 Jul '10

I was running a subject, and got this error: recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010 make: *** [/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1 The disk is not full, and permissions are in order. I've run several other subjects with no problems. Initially my command line was "recon-all -autorecon2 -s zhang_r"; then I tried again except with "-make autorecon2", and saw the same error. It exits at SubCort Seg (mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/current/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz) The last several lines of output are: mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Any ideas? Chris

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Script to get recon processing time
by Chris Watson 29 Jul '10

29 Jul '10

Hello, Do you guys have a script that parses recon-all.log and spits out the processing time for each step? Something that would be similar to this in recon-all --help: -<no>motioncor < 5 min -<no>nuintensitycor 3 min -<no>talairach 4 min -<no>normalization 3 min -<no>skullstrip 1 min -<no>gcareg 8 min -<no>canorm 1 min -<no>careg 10 hours and so on. Thanks, Chris

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ALICE overlay files conversion
by Gregory Dierksen 28 Jul '10

28 Jul '10

Hello, My lab group has some scans with overlays identifying hemorrhages that were made using ALICE (the files have a .oly extension) that we'd really like to be able to use with FreeSurfer Obviously mri_convert won't do anything with these files, but I was hoping that perhaps you have some old tools for converting these files...? Thanks a lot, Greg --

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