[Freesurfer] recon-all -all error end abruptly

Dear Expert, recon-all -all process for one subject end abruptly. I have attached the error report file. Please provide me some solution. Thanks Ramesh Sun Jun 4 21:09:32 IST 2017 /mnt/research/freesurfer_analysis/subjects/grp127 /usr/local/freesurfer/bin/recon-all -all -i grp127_t1.nii -s grp1

[Freesurfer] TRACULA (dmri_motion)

Dear TRACULA experts, I plan to use TRACULA in freesurfer 6 to analyze DTI data. I want to kindly to inquire about the command "dmri_motion". This script,nicely, generates: the SNR, drop out score, # drop out slices and motion parameters. I highly appreciate if you can guide me to a method, so I

Re: [Freesurfer] Question regarding recon-all error

Hi Yuna can you run mri_info on the input to recon-all (the .IMA file) and send us the entire screen output? Ideally as text in the email, not an attachment. thanks Bruce On Mon, 5 Jun 2017, 곽유나 wrote: Hello,   I'm completely new to brain imaging and freesurfer, and I can't seem to fi

Re: [Freesurfer] recon-all -all error end abruptly

it looks like you are trying to run the cuda version but your GPU doesn't have enough memory cheers Bruce On Mon, 5 Jun 2017, Ramesh Babu wrote: > Dear Expert, > > recon-all -all process for one subject end abruptly. I have attached the > error report file. Please provide me some solution. > >

Re: [Freesurfer] Cortical thickness_Group analysis

what is your mri_glmfit command? On 6/4/17 8:10 PM, Ali Radaideh wrote: Dear FS experts, I am trying to analyse the cortical thickness for a group of MS patients and healthy controls. I have followed the instructions on how to perform group analysis but I am still unable to achieve what I am

Re: [Freesurfer] Question regarding recon-all error

There is something wrong with your input data as it should have 256 files but only 33 were found On 6/4/17 10:36 PM, 곽유나 wrote: Hello, I'm completely new to brain imaging and freesurfer, and I can't seem to find a solution to the error that I have with recon-all. I didn't even get to skull

Re: [Freesurfer] recon-all -all error end abruptly

Dear Bruce, Two days back I ran 6 image processing simultaneous in different terminal. Everything finished without any error and took 8.2 hrs (4.5 hrs if I use only one terminal). But yesterday this problem has happened for the first time. I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 process

Re: [Freesurfer] recon-all -all error end abruptly

Hi Ramesh the error log has a line where the GPU says it ran out of memory. Possibly other things were running? cheers Bruce On Mon, 5 Jun 2017, Ramesh Babu wrote: Dear Bruce, Two days back I ran 6 image processing simultaneous in different terminal. Everything finished without any error and

[Freesurfer] recon-all error

Dear FreeSurfer developers, Sorry for cross-posting, perhaps my previous e-mail was missed. I've been trying to run recon-all for my first subject and I keep getting several errors like: ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParam

Re: [Freesurfer] recon-all error

Dear Maria, I am also faced the similar problem when I used Philips DICOM. Then I converted to nifti format by using dcm2nii tool. It is working fine. You can also try. Best Ramesh On Mon, Jun 5, 2017 at 7:56 PM, Maria Economou wrote: > Dear FreeSurfer developers, > > Sorry for cross-posting,

Re: [Freesurfer] recon-all -all error end abruptly

Hi Ramesh we don't do any automatic updating. Can you try running one of them again with nothing else running and see if it completes? cheers Bruce On Mon, 5 Jun 2017, Ramesh Babu wrote: Dear Bruce, Please see the attached file which was completed normally. Earlier I have done this with 6

Re: [Freesurfer] recon-all -all error end abruptly

Sure. I will start now. Tomorrow I will send the report. Thanks Ramesh On Mon, Jun 5, 2017 at 8:26 PM, Bruce Fischl wrote: > Hi Ramesh > > we don't do any automatic updating. Can you try running one of them again > with nothing else running and see if it completes? > > > cheers > Bruce > On Mon

[Freesurfer] Freeview Application

Hello FS team, Is there any way to download FreeView as a standalone application on a Windows computer, or would I need to download freesurfer as a whole and then VPN? Thanks in advance! Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts Genera

Re: [Freesurfer] Cortical thickness_Group analysis

Thanks alot. Below are the commands I used in order: mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.disease_Healthy_Age.thickness.00.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --

[Freesurfer] LME correction in longitudinal analysis

Dear FS experts, I are analysing longitudinal data - the difference between 2 groups (1 and 2) with 2 time points for each group (0, 1 --all the same time interval: a month). I followed http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels and with Jorge's early reply in http://www.

Re: [Freesurfer] LME correction in longitudinal analysis

Dear FS experts, I want to add some in my early mail. If the contrast CM.C= [0 0 0 1] is designed for the interaction effect(time and group). How to design contrasts to do the main effect about the time and group? CM.C=[0 1 0 1] and CM.C=[0 0 1 1]? Or other? I wonder I may be wrong in designing mat