Hi Ansgar - If the 2 series are in register with each other, you can just
concatenate them with mri_concat. You'd also have to concatenate the
respective bvals and bvecs in the same order.
For average FA, look in the pathstats.overall.txt file of each
reconstructed pathway. For more on this see the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
Hope this helps,
a.y
On Fri, 28 Oct 2011, Ansgar Furst wrote:
Dear Anastasia,
Re-running bedpostX just did it and I didn't encounter the problem on any
subjects after that.
Everything is running great now. I just had 2 more follow-up questions:
what's the best way to concatenate the 2 repeat DICOM DWI series into 1 NIFTI
file (you mentioned that
below)?
How do I extract average FA values constrained by the extracted fiber tracts?
Thanks so much for all your help,
Ansgar
On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Ansgar - Most likely everything is fine. Sometimes the script that's
built into bedpost
to monitor its progress gives this error but in fact everything has ran
fine. You should
check that all the outputs are there in the dmri.bedpostX directory. See
for list of
bedpost output files:
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
a.y
On Wed, 28 Sep 2011, Ansgar Furst wrote:
Hi Anastasia,
Thanks so much for your message. You were right about the recon
directory, the
contents had been accidentally moved elsewhere (sorry!) and once I moved
them
back and reran the script everything worked like a charm without any
errors.
However, it looks like I'm now stuck at the next processing stage (fsl's
bedpostX). I pasted the output with the error message below. FYI: I'm
unfortunately forced to run the bedpostX on a single Linux box (64-bit
dual core
with 8GB of RAM) which I hope is OK?
Thanks so much for all your help,
Ansgar
==================================================
trac-all -bedp -c scripts/dmrirc_single_subject_1only
INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC
INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf
/home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz
ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
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Queuing post processing stage
58 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
/usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) -
No such
process
===================================================
On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Ansgar - Currently there's no way to specify multiple scans for
the same subject as dicom files, sorry. You can concatenate the DWIs
from the 2 scans in one nifti file, and also concatenate the
bvecs/bvals from the two scans, and pass the concatenation to
dmrirc.
As for your error, it looks like maybe the freesurfer recon wasn't
found, so it skipped some steps (diffusion-to-anatomical
registration and mask creation). Does the freesurfer recon dir
/home/ajfurst/Data/WRIISC/014/ exist?
a.y
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