Re: [Freesurfer] DTI error

Correct. On Sunday, May 22, 2016, Anastasia Yendiki wrote: > > No idea, sorry. You used the -c option with the previous steps of trac-all > and didn't see this error, correct? > > On Sun, 22 May 2016, Jasmin Alves wrote: > > Hi Anastasia, >> Perhaps I was asking

Re: [Freesurfer] DTI error

No idea, sorry. You used the -c option with the previous steps of trac-all and didn't see this error, correct? On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Perhaps I was asking for advice regarding the wrong step in trac-all, do you have any ideas why I am still receiving the

Re: [Freesurfer] DTI error

Hi Anastasia, Perhaps I was asking for advice regarding the wrong step in trac-all, do you have any ideas why I am still receiving the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt This occurs when I do trac-all -path –c dmrirc1_sim.txt I tried looking at posts from

Re: [Freesurfer] DTI error

Ok, then you can ignore the error that you see when you run the bedpost step. `On Sun, 22 May 2016, Jasmin Alves wrote: Sorry for the mix-up. All of the bedpost output files are generated as well both 1 and 2 of each file.  On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki

Re: [Freesurfer] DTI error

Sorry for the mix-up. All of the bedpost output files are generated as well both 1 and 2 of each file. On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > These are output files from the -prep step. I'm asking about output files > from the bedpost step,

Re: [Freesurfer] DTI error

These are output files from the -prep step. I'm asking about output files from the bedpost step, since that's where you're encountering the error. https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputsfromtrac-all-bedp What's in the dmri.bedpostX/ directory? On Sun, 22 May 2016, Jasmin

Re: [Freesurfer] DTI error

Output files are being generated, ie. 1. dtifit_FA.nii.gz - Fractional Anisotropy 2. dtifit_MD.nii.gz - Mean Diffusivity 3. dtifit_MO.nii.gz - Mode of the Anisotropy 4. dtifit_S0.nii.gz - Non-Diffusion weighted image 5. dtifit_L1.nii.gz - Primary Eigenvalue 6. dtifit_L2.nii.gz

Re: [Freesurfer] DTI error

But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Thank you for the reply, when I do just let it run, I get the following error when I try to do trac-all -path –c

Re: [Freesurfer] DTI error

Hi Anastasia, Thank you for the reply, when I do just let it run, I get the following error when I try to do trac-all -path –c dmrirc1_sim.txt I get the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt Thanks, Jasmin On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki <

Re: [Freesurfer] DTI error

Hi Jasmin - Check if things are running despite that error. Are output files being generated? a.y On Sat, 21 May 2016, Jasmin Alves wrote: Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: