Re: [Freesurfer] out of memory, fast_selxavg3.m

Does this happen with all parts your analysis (lh, rh, and mni305)? or only mni305 volumetric analysis? Because if it happens with only the volumetric part, you can resample with 3 mm (instead of 2 or 1mm). On Sun, May 3, 2015 at 7:57 PM, Xiaomin Yue wrote: > Hi, > > I hope that I can get some a

Re: [Freesurfer] Rendering in 3ds Max?

Hi, Have a look at Anderson's blog here http://brainder.org/2014/01/08/splitting-cortical-surface-into-independent-regions/ All the best, Arman Sent from a mobile device, please excuse my brevity/misspellings. > On May 2, 2014, at 1:04 AM, Sourena Soheili-Nezhad > wrote: > > Hi Dorian, > >

[Freesurfer] Post-doctoral Fellowship in longitudinal image analysis at UCL

more details and the application procedure. If you have any queries regarding the vacancy or the application process please contact Dr Neil Oxtoby n.oxt...@ucl.ac.uk. — Arman Eshaghi, MD PhD Student UCL Institute of Neurology Queen Square Multiple Sclerosis Centre 1st Floor

Re: [Freesurfer] Still confused by group analysis..

Dear Doug and others, I'm sorry to hijack this thread. I noticed in FSL list that it has been recommended to demean gender (and probably other categorical variables) in GLM. As far as I understand, this implies treating a categorical variable as a continuous one. However, I can also see that you r

Re: [Freesurfer] Displaying cortical thickness changes in volume images

Dear Venkat, I believe the most straight forward way is to use your gamma volumes. For example if your first contrast is the difference between two time-points, thickness difference could be extracted with this command line: mri_convert ~/glmdir/contrast/gamma.mgh difference_thickness.mgh --frame

[Freesurfer] TRACULA tract path failure

Dear all, I have difficulty sorting out the problem with some tracts in several subjects, tracts are incomplete or missing. As it has come up quite a few times on the list, for this sort of problem I have first set "reinit=1" and then increased control points to 7, and re-ran trac-all with "-prior

Re: [Freesurfer] TRACULA tract path failure

racts look better for many subjects but this one still has problems in forceps minor. Thanks, Arman On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi wrote: > Dear Anastasia, > > Thanks for your response. I have sent a subject that the problem in > forceps minor persists. > What I have

Re: [Freesurfer] TRACULA tract path failure

gt; > Hi Arman - One more thing. Do you mind sending me the original (non-skull > stripped) T1 as well? We'd like to test a different registration method on > it. Thanks! > > a.y > > > On Fri, 30 Nov 2012, Arman Eshaghi wrote: > > Dear Anastasia, >> Thanks for y

Re: [Freesurfer] TRACULA tract path failure

ile, please save it in the dlabel/diff/ > directory of your subject and rerun the path reconstruction, making sure > that reinit is not set to 1. You can rerun only the fmajor by editing the > pathlist variable in your configuration file. > > Hope this helps, > a.y > > &g

[Freesurfer] mri_normalize 5.4 vs v6

Dear All, When I run mri_normalize on the same image using two freesurfer versions I get distorted results only on the V6. Can someone let me know how I can get the same results with V6? command: mri_normalize V5 output: voxel value range: 0 - 182 [image: Inline image 1] v6 output: voxel valu

[Freesurfer] Longitudinal Pipeline

Hi, I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years. Thanks, Arman _

Re: [Freesurfer] Longitudinal Pipeline

nk I also > experimented around with a -base-affine flag to recon-all for that (instead > of -base). It is experimental! > > Best, Martin > > > > On 07 Apr 2017, at 13:34, Arman Eshaghi wrote: > > > > Hi, > > > > I wonder if there is a way for mri_robust_templ

[Freesurfer] PhD Studentship available at UCL

://www.findaphd.com/search/ProjectDetails.aspx?PJID=99251 I would be grateful if you could forward this email to potential candidates. Best wishes, — Arman Eshaghi, MD, PhD Queen Square Multiple Sclerosis Centre 1st Floor, Russell Square House 10-12 Russell Square London WC1B 5EH

[Freesurfer] FS GUI no glx extension

Hi, On a remote server forwarding X and running Ubuntu 14.04 I am having difficulty running tkregister2, with this error: *No glx extension!* *register: ### tkoInitWindow(name) failed* Also tried *export LIBGL_ALWAYS_INDIRECT=y* which did not work. Any input is highly appreciated.

[Freesurfer] RAS to voxel transform

Hi, I'm trying to understand the conversion from RAS (freesurfer surface coordinate) to volume space (x, y, and z.. According to Graham Wideman documentation here http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm (if it is not outdated), Right is negative x, *Anterior is positive z*, an

[Freesurfer] webiste is down

Just a heads up that the Freesurfer website is down as of 6:36 am EST 5 July Arman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only f

Re: [Freesurfer] retinotopic mapping using selxavg3-sess

Hi Alan, I can guess there are several problems here with your fsl installation. Are you on Neurodebian? For some historical reasons fsl5.0-command format for usual fsl commands were used so that when people wanted to use both fsl 4 and 5 at the time there wouldn't be any confusion. Anyway you can

[Freesurfer] Compiling Freesurfer from source ends with error regarding libtool version mismatch

Hi, I'm trying to compile Freesurfer current dev version from read only cvs repo according to developers guide on my machine with Ubuntu 14.04, gcc 4.8.2, I proceed as follows in dev/ directory: 1- ./setup_configure: which finishes without error 2- ./configure with vxl and mni library dir

Re: [Freesurfer] Compiling Freesurfer from source ends with error regarding libtool version mismatch

Have gcc 4.8) ac_have_gcc_48="yes" fi fi if test "$ac_have_gcc_48" = "yes"; then AC_MSG_NOTICE(Copying /usr/bin/libtool overtop the PROG_LIBTOOL) cp /usr/bin/libtool . fi This is not an elegant solution, but resolves the issue. All the best, Arman

[Freesurfer] Postdoctoral position at UCL

https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTc4NDY5OSZ2dF90ZW1wbGF0ZT05NjUmb3duZXI9NTA0MTE3OCZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJmpvYl9yZWZfY29kZT0xNzg0Njk5JnBvc3RpbmdfY29kZT0yMjQ You can get in touch with me (a.esha...@ucl.ac.uk) for more information. Best wishes, Arman Eshaghi, M

[Freesurfer] mri_robust_template

Hi, I have bias-corrected and co-registered longitudinal images, and I'm interested to use Freesurfer to construct unbiased within-subject templates (to be used in SPM). Using mri_roubust_template, I get the following error message on some (not all) of the subjects. I was wondering whether I could

[Freesurfer] mri_robust_template

Dear all, For a longitudinal analysis I need to have within subject templates. After some preprocessing that included FSL's BET, and linear registration of all time points to time-point 1, I fed images to mri_robust_template: mri_robust_template --mov tp1 tp2 tp3 --template --satit It runs fine

[Freesurfer] Averaging 3d-MPRAGE images before processing

Dear Freesurfer experts, We have acquired 2 sets of MPRAGE images in a single session to be averaged before processing in freesurfer. Is it valid if I use fslmaths command in fsl to average images and then feed the averaged image into freesurfer? Or do you recommend an equivalent of fslmath in

[Freesurfer] Feeding more than one MPRAGE into recon all

Dear freesurfer experts, Sorry to bother the list with this question again, but I searched the archive and documentation without success. I want to feed more than one MPRAGE datasets taken independently in a single session into recon all. How should I do that? Is there any command inside freesu