Re: [Freesurfer] DTI error

2016-05-25 Thread Anastasia Yendiki
Hi Jasmin - On my screen the dash "-" symbol before the "c" looks different than the one before "path". I'd check if you are indeed typing a plain "-c". Best, a.y On Wed, 25 May 2016, Jasmin Alves wrote: Hi Anastasia,  I am still receiving the following error message when I run a different

Re: [Freesurfer] DTI error

2016-05-25 Thread Jasmin Alves
Good call! Thanks Anastasia! It worked! On Wed, May 25, 2016 at 8:46 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Jasmin - On my screen the dash "-" symbol before the "c" looks > different than the one before "path". I'd check if you are indeed typing a > plain "-c". > > Be

Re: [Freesurfer] DTI error

2016-05-25 Thread Jasmin Alves
Hi Anastasia, I am still receiving the following error message when I run a different participant doing, trac-all -path –c dmrirc1_sim.txt: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt If you have any ideas for what i can try it would be very appreciated! Thanks! Jasmin On Sun, Ma

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves
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 for advice regarding the wrong st

Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki
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 follo

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves
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 prev

Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki
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 wrote: T

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves
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, s

Re: [Freesurfer] DTI error

2016-05-22 Thread Anastasia Yendiki
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 A

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves
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

2016-05-22 Thread Anastasia Yendiki
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 dmrirc1_sim.tx

Re: [Freesurfer] DTI error

2016-05-22 Thread Jasmin Alves
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

2016-05-22 Thread Anastasia Yendiki
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: /Applications/freesur

[Freesurfer] DTI error

2016-05-21 Thread Jasmin Alves
Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Grad