Hi,
I'm currently in the process of verifying that my install of Freesurfer
works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be
4 errors after running *recon-all -s bert -autorecon1.*
The last line I included here states that the command completed without
error, so I'm not
begin
> with), but resolving the nu_correct issue is the important thing to do.
>
> Nick
>
>
> On Wed, 2013-01-09 at 11:00 -0500, Susan Kuo wrote:
> > Hi,
> > I'm currently in the process of verifying that my install of
> > Freesurfer works. I have an Ubunt
Hi FreeSurfer community,
I am trying to run 'trac-all -corr -c ' on the tutorial
data, specifically for the single subject: Diff001. To start from
'scratch', I've deleted all but the './scripts' and the './orig'
directories in the Diff001 parent folder. When I run the following command:
> trac-a
Hi FreeSurfer community,
I am currently trying to troubleshoot my preprocessing part of TRACULA
with the tutorial dataset (for *Diff001* as the subject, specifically),
running *trac-all -corr -c *. I am running the commands in *
subjectID/scripts/trac-all.cmd* one by one because I've had problem
Hi,
I've been trying to email out for help to the FreeSurfer community, using
the below addresses. However, I am not receiving my own email back, though
I am a member of the mailing list via this email address. Can you tell me
what I'm doing wrong?
Thank you!
Susan Kuo
--
Hi FreeSurfer community,
I would like to run '-bedp' with TRACULA, to run the bedpostx option. I
see from the *./subjID/scripts/trac-all.cmd* file that the actual command
issued was *bedpostx_seychelles*, which allows for the PBS queueing system
running on seychelles and is used by the Martinos
Hi TRACULA Experts,
Is there a way of parallelizing BEDPOSTX on a cluster, not using the
bedpostx_seychelles option since I'm on a non-MGH cluster?
Thanks!
Susie Kuo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harva
>> all possible cluster setups at other centers is beyond the scope of our
>>> research, but perhaps the existing script is useful as a starting point for
>>> making it work on your cluster.
>>>
>>> Hope this helps,
>>> a.y
>>>
>>&g
Hi FreeSurfer Community,
I am trying to run TRACULA's last step, 'trac-all -path -c
', and am receiving the error:
Segmentation fault(core dumped)
Moreover, when I look to standard output (terminal), I noticed that the
initial 'dmri_paths' command is incomplete. The terminal shows that the
com
fusion-to-anatomical
> registration for the subjects that are failing? I'd check the
> aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if
> there are any holes or misregistration.
>
> a.y
>
>
> On Mon, 25 Mar 2013, Susan Kuo wrote:
>
t in the latest version of trac-all.
>
> Hope this helps,
> a.y
>
>
> On Tue, 26 Mar 2013, Susan Kuo wrote:
>
> Hi Anastasia, I did as you recommended and checked the
>> diffusion-to-anatomical
>> registration, and the overlay of aparc+aseg_mask on FA, and th
> wrote:
>
> Hi Susie - Everything under dlabel/diff is mapped to DWI space (either
> with flirt or with bbregister, whichever you use). The one in my screenshot
> was dlabel/diff/aparc+aseg.flt.**nii.gz.
>
> a.y
>
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
es of tracula. For a
> regular volume, use -v or no option at all. For best displaying the
> aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
> map menu.
>
> Hope this helps,
> a.y
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
> Hi
to it.
>
> So you just need to switch on bbregister and switch off flirt in your
> configuration file, and then rerun trac-all. If the DWI-to-T1 registration
> is good, then the masking issue will be solved too.
>
> Good luck!
>
> a.y
>
> On Wed, 27 Mar 2013, Susan Kuo
Hi Anastasia,
We were viewing the arcuate fasiculus tract created by TRACULA, and
noticed that the tract did not reach Broca's area. While there exists
literature that now challenges this neuroanatomical convention, I would
like to investigate the possibility of creating and inputting on our ow
Hi FreeSurfing researchers,
I am looking at the pathstats.overall.txt, and wanted to see if anybody
knew which space these voxels are in - I assume MNI space (given that I
used the MNI template) and not individual diffusion space, but would like
to confirm. Does anybody know for certain what spac
he native space, without any transformationon
> the DWIs to another space.
>
> a.y
>
>
> On Wed, 1 May 2013, Susan Kuo wrote:
>
> Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt,
>> and wanted to see if anybody knew
>> which space these vo
ust about transforming these files to the template space and
> passing the list to trac-all. I'm happy to document this part. The hard
> work is the manual labeling!
>
> Hope this helps,
> a.y
>
>
> On Wed, 1 May 2013, Susan Kuo wrote:
>
> Hi Anastasia, I wou
Hi Anastasia,
I apologize for jumping in here, but I have run bedpostx parallelized on
a cluster. Are there files that we can modify to run the script in
parallel? I noticed the '-prior' step is particularly long and cumbersome.
Thank you!
Susie Kuo
NIH
On Fri, May 17, 2013 at 12:47 PM, Anas
; BTW, the -prior step should be about 70% less long and cumbersome in
> 5.2/5.3 than it was in 5.1. Which version are you running?
>
> a.y
>
>
> On Fri, 17 May 2013, Susan Kuo wrote:
>
> Hi Anastasia,
>> I apologize for jumping in here, but I have run bedpostx paralle
Hi Anastasia,
For one of my subjects, I am noticing that the right uncinate fasciculus
is very diffuse and more importantly, erroneously crosses from the frontal
to the temporal lobe. I looked at the original endpoint ROI generated by
trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the
Hi Anastasia,
I noticed that my pathstats.byvoxel.txt files are missing the last four
values (AD_Avg RD_Avg MD_Avg FA_Avg) even though I'm certain I ran
trac-all -path -c correctly. Do you have any idea why this
might be? e.g. a configuration file change?
Thank you!
--
Susie Kuo
Mediocrity
Hi Anastasia,
I believe the issue I had with the pathstats.byvoxel.txt not displaying
the last four values (AD_Avg RD_Avg MD_Avg FA_Avg
) is owing to the fact that trac-all was run with FREESURFER 5.1. I believe
that FREESURFER 5.2 may be needed to generate path.pd.trk, and from that,
the above v
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