Re: [Freesurfer] [Freesurfer/FSFAST]

Oh, yes. I used mriconvert. Sure! So ill convert it again (using mriconvert?), and run preproc-sess and send you the terminal output. P.S. I can still view the file after conversion normally. Thank you, DWY From: freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] [Freesurfer/FSFAST]

but using what program? mri_convert? Can you try converting it again and sending me the terminal output? On 4/3/18 11:38 PM, Dave Yas wrote: By hand. I followed the FSFAST hierarchy and just simply created the files and named them.

Re: [Freesurfer] [Freesurfer/FSFAST]

By hand. I followed the FSFAST hierarchy and just simply created the files and named them. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Wednesday, April 4, 2018 3:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurf

Re: [Freesurfer] [Freesurfer/FSFAST]

The version should not matter here. How did you create /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ? On 4/3/18 7:51 PM, Dave Yas wrote: Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts for anything here).

Re: [Freesurfer] using T2 for hippo subfields

Per an earlier post below, is an 'expert_file' always required when using the -hires option? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Sunday, March 25, 2018 9:47:07 PM To: Freesurfer support list Subject: Re: [

Re: [Freesurfer] [Freesurfer/FSFAST]

Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts for anything here). From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Tuesday, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Fr

Re: [Freesurfer] [Freesurfer/FSFAST]

Only ~80%, but there is space for this run.. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Tuesday, April 3, 2018 11:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Freesurfer/FSFAST] Is the disk full? O

Re: [Freesurfer] [Freesurfer/FSFAST]

Is the disk full? On 4/3/18 6:48 PM, Dave Yas wrote: Yes, the file exists! Here is the full output: -- preproc-sess logfile is log/preproc-sess.sess01.log -- $Id: preproc

Re: [Freesurfer] [Freesurfer/FSFAST]

Yes, the file exists! Here is the full output: -- preproc-sess logfile is log/preproc-sess.sess01.log -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ Davey set

Re: [Freesurfer] Surface label to volume and then back to surface

Hi David, I've tried to answer your questions below. doug On 03/30/2018 01:48 PM, David Beeler wrote: > Hi all, > Sorry in advance, this is a bit of an annoying one! > > I am trying to use freesurfer's automatically generated MT label as a > parcel to constrain activity measured during a functi

Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1

you can generate them with cd $FREESURFER_HOME/subjects/fsaverage/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right should take less than an hour to run On 04/03/2018 03:28 PM, Abigail Noyce wrote: > > Date: Mon, 2 Apr 2018 14:55:47 -0400 > Fro

Re: [Freesurfer] FSGD file error

Sorry, one more thing. I think that it should work if you demean your covariate, no need to have multiple subjects from that group On 04/03/2018 03:16 PM, Douglas N. Greve wrote: > you should also demean your covariate > > > On 04/03/2018 03:13 PM, Douglas N. Greve wrote: >> The problem is that

Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1

> Date: Mon, 2 Apr 2018 14:55:47 -0400 > From: Douglas Greve > Subject: Re: [Freesurfer] mirroring fsaverage labels between > hemispheres > > If you have a label defined on the lh or rh of fsaverage, you can map it > to the contralateral hemi with something like > > mris_apply_reg --src-la

Re: [Freesurfer] FSGD file error

you should also demean your covariate On 04/03/2018 03:13 PM, Douglas N. Greve wrote: > The problem is that you only have one subject for group haemorrhage. If > you are going to include a covariate, then you need more than one subject > > > On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrot

Re: [Freesurfer] FSGD file error

The problem is that you only have one subject for group haemorrhage. If you are going to include a covariate, then you need more than one subject On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote: > Dear free surfer developers, > > When I try to run the mri_glmfit free surfer does not see

Re: [Freesurfer] Percent Signal Change

fmn is the mean image averaging over all time points, so it should have the same dimensions as one of your images. The repmat() call is supposed to replicate the image over the number of time points, but there is a bug. It should be f.vol,4 not 3. Try that On 04/03/2018 02:33 PM, Sarah Cole wr

Re: [Freesurfer] Percent Signal Change

Doug, Could you please let me know what this line is doing? "fmnrep = repmat(fmn,[1 1 1 size(f.vol,3)]);" When I try to assign f.vol/fmnrep to s.vol (this line s.vol = f.vol./fmnrep;), matrices do not match in dimension. Thanks, S On Thu, Feb 15, 2018 at 1:05 PM, Douglas N Greve wrote: > That

Re: [Freesurfer] Hemodynamic Lag Shift

Please ignore my previous post. I was wrong on so many levels! Thanks S On Fri, Mar 30, 2018 at 8:34 AM, Sarah Cole wrote: > Hi Doug, > > Sure. I have attached an excel sheet. > I have averaged the signal magnitude across 16 blocks of objects, and 16 > blocks of scenes, separately. Each block

Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41

Hi Bruce, I attached the recon-all.log! Thanks in advance for taking a look! Darko Message: 3 Date: Sat, 31 Mar 2018 06:47:12 -0400 From: Bruce Fischl Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds To: Freesurfer support list Message-ID: <23b23889-c042-4a04-9316-4c8ed5468.

[Freesurfer] Fwd: Learning Workshop in Bloomington IN (fwd)

FYI -- Forwarded message -- Date: Tue, 3 Apr 2018 11:14:38 -0400 From: Satrajit Ghosh To: Bruce Fischl , "Jog, Amod" Subject: Fwd: Learning Workshop in Bloomington IN hi,  this may be of interest. please forward. cheers, satra -- satrajit ghosh  |  satra.cogitatum.org p

Re: [Freesurfer] Freesurfer for canine

I will check with the Emory group that I know has been scanning canines. Don't know if they are interested in the extra work to get FreeSurfer output but since they are doing FMRI maybe they would be OK with sharing their AMRI data. It would be good to ask C. Destrieux on the progress with pig and

[Freesurfer] Brainhack Ireland 2018 - Brainhack Global

Join us for Brainhack Ireland 2018 , a 2.5-day event at which you can team up with neuroscience researchers, data scientists, hackers, philosophers and anyone else with an interest in working on innovative projects related to neuroscience. There will be prizes for

Re: [Freesurfer] [Freesurfer/FSFAST]

does that file exist? CAn you send the full terminal output? On 4/2/18 9:53 PM, Dave Yas wrote: Hi, I am running preproc-sess on one subject. I got the following error after running preproc-sess: Error: niiRead(): error reading from /Users/Studies/Directory/Study_Directory/sess01/bold/00

Re: [Freesurfer] FSGD file error

please send the fsgd file. Also, send the full text output from mri_glmfit On 4/3/18 5:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote: Dear free surfer developers, When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underly

[Freesurfer] FSGD file error

Dear free surfer developers, When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and ad

[Freesurfer] Download FreeSurfer for Virtualbox

Hi! I've tried downloading the FreeSurfer Virtualbox-file several times, but when I try to unzip, I get a message that the file is broken and that the file cannot be unzipped. What am I doing wrong? I realise that this message doesn't contain a whole lot of information but this is all I know... Be