Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data

External Email - Use Caution I’d be happy to. This is the call: mri_vol2vol --targ ${target} \ --m3z $cvsmorph \ --noDefM3zPath --reg ${b0toT1mat_bet} \ --mov ${meanb0_bet} \ --o ${b0_to040_2_t1w} \ --interp trilin Thank

Re: [Freesurfer] Question about de-meaning the covariates and variables

On 3/2/2020 7:30 PM, Hengameh Marzbani wrote: External Email - Use Caution Hi Freesurfers, I'm stuck with the centering (de-meaning) issue. I have two discrete variables,gender and patient-control, and 2 continuous variables which are memory and age.I want to look for group differen

Re: [Freesurfer] timeseries question

Hi Mona, I don't understand your question. Only the mean will be removd from the time series, no drift term. One usually does not consider the hemodyamic response delay to be a drift term On 3/2/2020 5:45 PM, Nasiriavanaki, Zahra wrote: Hi I wanted to follow up on this question and clarify it

Re: [Freesurfer] recon-all failure

Does it run ok if you don't use -parallel? On 3/2/2020 6:16 AM, Ian wrote: External Email - Use Caution Hi all. I have a T1 scan which I run through recon-all with: recon-all -all -parallel -subjid freesurfer (after mksubjdirs etc) On my office machine, recon-all completes successf

Re: [Freesurfer] ERROR: fast_selxavg3() failed\n

My guess is that something is going wrong with your paradigm file. Can you send them? On 3/1/2020 2:06 AM, mahdiyeh khanbagi wrote: External Email - Use Caution Dear FreeSurfer Developers, I am trying to do FSFAST analysis on Mac OS Catalina 10.15.3, and I have completed the preproc

Re: [Freesurfer] make_average_subject

dev or 7beta On 2/29/2020 10:24 AM, Benjamin Ineichen wrote: External Email - Use Caution Ok. It says that for mac, I need to download the dev release, I assume that refers to Freesurfer version 7.0? Am Fr., 28. Feb. 2020 um 22:15 Uhr schrieb Douglas N. Greve mailto:dgr...@mgh.harv

Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data

Can you send the mri_vol2vol command line? On 2/28/2020 4:46 PM, Austin Patrick wrote: External Email - Use Caution The b0-to-anat look fine. I’m using mri_vol2vol with trilinear interpolation to apply the CVS warps. Thanks, -Austin *From: * on behalf of "Douglas N. Greve" *Rep

[Freesurfer] Question about de-meaning the covariates and variables

External Email - Use Caution Hi Freesurfers, I'm stuck with the centering (de-meaning) issue. I have two discrete variables,gender and patient-control, and 2 continuous variables which are memory and age.I want to look for group differences as well as differences in relation to t

Re: [Freesurfer] timeseries question

Hi I wanted to follow up on this question and clarify it a little bit more. My question is if the temporal drift (hemodynamic response delay) has been counted in considering that I used the preprocessed data as the input? I deeply appreciate any help. Thanks Mona On Feb 28, 2020, at 5:50 PM

Re: [Freesurfer] registrations

External Email - Use Caution Dear Bruce & All, Sure, I wanted some advice from the greats before registering pre and posteresection (intrasubject) scans. I tried both registrations on several patient data, bbregister clearly superior to mri_robust_register (used with orig/mgz) for

[Freesurfer] Freesurfer Digest, Vol 193, Issue 3

External Email - Use Caution Thanks, Lauren. Faith From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Monday, March 2, 2020 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Free

[Freesurfer] Issue with make_average_subject

External Email - Use CautionHi,   I'm having trouble making an average subject. Initially, I had the same error that was discussed here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57012.html; so I installed the patch of FS 6.0.0. After that, this is the ERROR I'

[Freesurfer] recon-all-failure with file links

External Email - Use Caution Oops, looks like the files didn't attach.  Here are links to the logs: https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-standard_out_log.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-status.log https://obd-public.s3.eu-west-2.ama

Re: [Freesurfer] group analysis for same group in 2 conditions

External Email - Use Caution Since that each subject undergoes to both conditions and functional images are in 2 different folders, I modify my folder structure and put functional folders together. It means that now I have a main functional folder (pRFs_functionals) in which I have

[Freesurfer] DPABI V4.3, DPABISurf V1.3 and DPARSF V5.0 were released!

External Email - Use Caution Dear colleagues, We are pleased to announce the release of DPABI V4.3, DPABISurf V1.3 and DPARSF V5.0. New features of DPABI_V4.3_200301 (download at http://rfmri.org/dpabi, please also update the docker file by: docker pull cgyan/dpabi): 1. Stabilit