Dear Freesurfer experts
I am trying to process the data of a Longitudinal DTI Study with 2 Timepoints
I have encountered the following error while running the tracula
pre-processing:
-
Dear Freesurfer experts,
> thank you very much for your suggestion. This is the error message
> when I specify the -analysis folder. It seems coming from the
> preprocessing registration step.
Any of your advice will be greatly appreciated.
> best regards
> yongxia
>
> fslregister --s andrew_fsa
yongxia, did you see my reply from yesterday?
On 5/24/13 6:08 PM, Douglas N Greve wrote:
> where did your raw data come from? Specifically, how were the nifti
> files created? There is a warning in there that indicates that there
> is some problem with them.
> doug
>
>
> On 05/24/2013 05:56 PM,
Hi Sal, yes you can. Use bbregister to register the lowb image to the
anatomical. This creates a registration matrix. Use mri_vol2vol and the
registration to map the ADC map to the anatomical, then use mri_segstats
to extract the values
doug
ps. Please post questions to the FS list instead of
Thank you Doug.
Just so I am clear - is the anatomical the nifti T1.mgz or is it a
different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This
creates a registration matrix.*
bbregister -s SUBJECTNAME --mov lowb.nii --
On 5/25/13 1:39 PM, Salil Soman wrote:
Thank you Doug.
Just so I am clear - is the anatomical the nifti T1.mgz or is it a
different file. From your email I gather should do the following:
*1) Use bbregister to register the lowb image to the anatomical. This
creates a registration matrix.*
Hi!
I have been running the mri_glmfit-sim command to do the correction for
multiple comparisons for my group analysis and for some voxel-based thresholds
(not all) there is an error that comes up when reading the colortable from the
annotation file:
reading colortable from annotation file...
-- Forwarded message --
From: Salil Soman
Date: Sat, May 25, 2013 at 8:00 PM
Subject: BBR Register failing
To: Douglas N Greve
Dear Doug,
I attempted to run the process we discussed earlier today for registering a
different tissue contrast to the T1 after freesurfer 5.3 was run
Done. Thank you for your consideration. The best I can figure so far is
1) the script's attempt to make the tmp.bbregister.7392 directory fails
and 2) (after I manually make this directory),
there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 r
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having
some problems with the fslregister script. From what I have been able to
investigate. It looks like there is an issue that fsvol may not get named
if you are not dealing .cor files.
Code in question
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