Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

If you are running on Ubuntu, I have a build of the freesurfer source checked out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system using gcc 4.9. However, I did not have the test data to run tests, so I must add the disclaimer that the binaries have not gone thru the

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce > On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com> wrote: > > Hi Bruce, > > Thanks so much for pointing that out, I totally missed that part. > > Also, the

Re: [Freesurfer] [FSFAST]

Thank you, i will! Walid > On Apr 10, 2018, at 8:03 AM, Douglas N. Greve wrote: > > You can do it with the tpexclude file. Do a search through the archives > for docs on how to use it > > > On 04/09/2018 06:56 PM, Walid Yassin wrote: >> Hello Doug, >> >> Thank you

Re: [Freesurfer] [FSFAST]

You can do it with the tpexclude file. Do a search through the archives for docs on how to use it On 04/09/2018 06:56 PM, Walid Yassin wrote: > Hello Doug, > > Thank you for your previous answer. > I have another question in the mkanalysis. When I run mkanalysis is it > possible to analyse

Re: [Freesurfer] [FSFAST]

Hello Doug, Thank you for your previous answer. I have another question in the mkanalysis. When I run mkanalysis is it possible to analyse only a part of my run? I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore the first 20s and the last 30s and analyse the 50 in the

[Freesurfer] recon-all | ln -s error

Hello All, My $SUBJECTS_DIR is located on an external disk that was mounted and recon-all exited with errors at ln -s lh.white.preaparc.H lh.white.H I was not able to perform this operation with sudo as well 4172_vsl/surf$ sudo ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Anna, Unfortunately, we’re not able to build the dev code right now due to a compile error, but this should get sorted out within the next day or two, so I can help you out with getting this new mri_normalize then best Andrew From: on behalf of Anna

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

I am indeed considering LME model since I have multiple visits (4) for each subject and multiple groups (3). Based on your response, I am inclined to include the following. Intercept - random variable Slope (time_base_scan) - random variable As I am including time_base_scan as the random

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

Hello, this is somewhat difficult to answer, so the following is a personal opinion. I think the first question is whether your would like to go for a) a cross-sectional design or b) a longitudinal design. If a), you'd have a single scan per subject (e.g., baseline) and could discard the

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Bruce, thank you for the quick reply! Ubuntu 16.04 LTS 64-bit freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Please let me know how to incorporate the new version into the installation. Thank you very much and best, Anna Hi Anna no attachments :< Srishti's issue stemmed from

Re: [Freesurfer] FSGD design for multi-centre study

That looks right to me. If you use a DOSS model and have a lot of subjects, I don't think there should be a problem with so many classes. On 04/09/2018 09:50 AM, C.P.E. Rollins wrote: > Hi Douglas, > > Thanks for your response. I just wanted to confirm how the FSGD and > contrast files might

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Anna no attachments :< Srishti's issue stemmed from control points outside of the head. The current (dev) version of mri_normalize detects and removes them. Can you grab a new version of mri_normalize and see if it fixes your problem? Let us know your hardware/software environment and we

[Freesurfer] how to control for head size differences when measuring global atrophy?

Dear freesurfers my study aims to measure volumetric differences between patients X and controls. As dependent variables, I have (i) a-priori ROIs and (ii) global brain measures (total gm, total wm and CFS). In the ROIs analysis, I use eTVI to control for for head size variability. Now my

Re: [Freesurfer] FSGD design for multi-centre study

Hi Douglas, Thanks for your response. I just wanted to confirm how the FSGD and contrast files might look for the multicentre study. If I'm to create a separate class for each combination of diagnosis, sex, and center, would there then be 24 classes? (as there are 2 diagnoses (patient vs.