I found out why it didn't work. One of the script that bedpostx_postproc.sh
calls is written in python2. I set my default to python3 and therefore caused
the error in the last step. After I loaded python2 environment, i got the
merged files and finished properly. Thanks for your help as
Dear FS expert
I use the aparcstat2table and generate the cortical volume/thickness. I have
a question regarding sulcus volume and thickness meaning.
For example, it generate lh_S_front_inf volume and thickness, which
represents as left inferior frontal sulcus. Did the volume represent as CSF
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in
Hi Bruce and Clara,
Thanks for your comments. Indeed the bright points are segmented as WM in
wm.mgz, however these errors do not occur only in a few places but in many
slices throughout the brain so manual edits will be quite extensive, which
is why we wanted to double check that there is no
Hello Ben,
I am no expert, I can only talk from my experience.
I've had similar images in my data. Those might be blood vessels or dura that
were included in the surface. If they are included in the surface on more than
5 slices and pretty well visible you could delete those voxels from the
Hi Yoon - It sounds like FSL's bedpostx postprocessing script
failed. You can run it like this:
bedpostx_postproc.sh /path/to/your/subject/dmri
This script merges the results from all the slices. It's possible that
something went wrong with the slices (you ran out disk space for
Hi Anastasia,
trac-all -prep completed without error.
I thought trac-all -bedp starts and ends without any error but trac-all path
failed with these messages.
Loading BEDPOST parameter samples from */dmri.bedpostX
niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR:
