[Freesurfer] Reenviar: signal dropouts in 7T scanners

I would be very grateful to receive your comments. Thanks in advance, --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34

Re: [Freesurfer] Reenviar: signal dropouts in 7T scanners

Hi Jose, people have told me that they are happy with the mp2rage sequence, but it hasn't been great for us. How do you propose to get good data in the bottom half of the brain in some scans and the top half in others? Change the flip angle? I guess you could try building an RMS image if you

[Freesurfer] Fwd: postdoctoral imaging position

Applications are invited for a position at the Unitat de Recerca en Neurociència Cognitiva (http://dpsiquiatria.uab.cat/en/grupRecerca_2.php) at the Fundació IMIM- Hospital del Mar, Barcelona, Spain. (www.imim.es). The position is full-time for 18 months. It entails working mainly on a grant

[Freesurfer] how to filp Fa maps

Hi, I would like to know if there is a way to flip FA maps (the FA.nii.gz file) before running TBSS. Many Thanks, Marcia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] postdoctoral imaging position

Applications are invited for a position at the Unitat de Recerca en Neurociència Cognitiva (http://dpsiquiatria.uab.cat/en/grupRecerca_2.php) at the Fundació IMIM- Hospital del Mar, Barcelona, Spain. (www.imim.es). The position is full-time for 18 months. It entails working mainly on a

[Freesurfer] writing out a transformed fmri volume

Hi, We have had several naive questions about registration recently, and thank you all very much for your patience. Here is another one. We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate

[Freesurfer] Qdec default design

Hello all, I'm running a cortical thickness group analysis in qdec with two groups and one covariate (age). By default, does qdec use the DODS option, or DOSS? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] writing out a transformed fmri volume

yep, use mri_vol2vol (with many of the same cmd line options). doug Hansen, Kathleen (NIH/NIMH) [F] wrote: Hi, We have had several naive questions about registration recently, and thank you all very much for your patience. Here is another one. We have used mrivol2surf with the output of

Re: [Freesurfer] Qdec default design

It uses DODS by default. doug Dankner, Nathan (NIH/NIMH) [F] wrote: Hello all, I'm running a cortical thickness group analysis in qdec with two groups and one covariate (age). By default, does qdec use the DODS option, or DOSS? ___ Freesurfer

[Freesurfer] Dummy Scans and Paradigm Files

Hello, My name is David Brohawn, and I am one of Dr. Roffman's research assistants. We run the SIRP and N-Back memory tests with our subjects. We have specified for 3 dummy scans to take place at the beginning of each of these protocols, which takes 6 seconds of scanning time, respectively.

Re: [Freesurfer] Dummy Scans and Paradigm Files

It depends exactly how you triggered your paradigm. If you used the scanner to trigger the start of your stimulation, then you do not include the 6 sec when preparing your paradigm files. doug Dave Brohawn wrote: Hello, My name is David Brohawn, and I am one of Dr. Roffman's research

[Freesurfer] FSFAST Users Group Meetings

Hi All, I have scheduled a series of three meetings to talk about FSFAST, particularly the new version that is coming out with FreeSurfer 5.0 (due out soon). THIS IS NOT A HANDS-ON COURSE ON HOW TO USE FS-FAST!!! The purpose of these meetings is to give an overview of FSFAST, including the

[Freesurfer] Methods doubt

Hello freesurfers Does anyone knows wich is the method in which the FS makes an average of 2 images, in the autorecon1 step when doing the motion correction?. I mean how can I explain it? Thanx Gabriel

Re: [Freesurfer] Methods doubt

Hi Gabriel, I'm pretty sure we use FSL's flirt for motion correction by default, but Nick or Doug can confirm. cheers Bruce On Thu, 1 Jul 2010, Gabriel Go.Es. wrote: Hello freesurfers Does anyone knows wich is the method in which the FS makes an average of 2 images, in the autorecon1

Re: [Freesurfer] Methods doubt

Thank you Bruce for you answer, but i still have the doubt, is motion correction from the FSL the method to average the images? or is another method... I wrote motion correction cuz in the -help of recon-all says that theyr made in the same step, but not to be the same process. but whatever is

Re: [Freesurfer] Methods doubt

Hi Gabriel, I'm not sure I know what you mean. I think we use flirt to compute the motion parameters, then we just average the images in the aligned space (which I think is to the first scan specified, but Doug would know) cheers Bruce On Thu, 1 Jul 2010, Gabriel Go.Es. wrote: Thank you

Re: [Freesurfer] Methods doubt

yes, the first image is the template. I think it uses flirt. Recent versions may use Martin's robust registration. doug Bruce Fischl wrote: Hi Gabriel, I'm not sure I know what you mean. I think we use flirt to compute the motion parameters, then we just average the images in the aligned

Re: [Freesurfer] Methods doubt

OK, so the alignment is to perform a simple average? that way, the real goal of the method is the registration before averaging, am I right? in versions like 4.05 what was the alignmen method, was the flirt? Do you know if Martin's robust registration is now implemented or will come in the

Re: [Freesurfer] FSFAST Users Group Meetings

To clarify, the material covered should be about the same in all the meetings, so no need to attend all of them, so you all do not need to attend the first one. There is no sign up, so just show up. First come, first serve. doug Douglas N Greve wrote: Hi All, I have scheduled a series of

[Freesurfer] Error in SubCort Seg.

Hi freesurfers, I have a few subjects failed at SubCort Seg step. The error message is: 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 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating