Hi Balaji,
fslswapdim (a command line program which comes as part of fsl) should solve
your orientation problems.
If you have fsl installed (which you should do!) then typing
fslswapdim input_volume_name -x output_volume_name
into the terminal should swap RAS to LAS and vice versa.
Or you can
Hi Jeanette,
Which version of FreeSurfer are you running.
Also, can you try renaming the qdec.Qdecrc to .Qdecrc and try again.
Here's more info on editing the .Qdecrc file with the new measures.
https://surfer.nmr.mgh.harvard.edu/fswiki/.Qdecrc
Sita.
On Mon, 13 Jun 2011, Jeanette Berberich
Dear Freesurfer users,
I got different transformation matrices (shown below) when running ver 5.0 and
ver 5.1 on the same subject
- ver 5.0 was doing great but ver 5.1 failed:
I would appreciate it if you can give me some advice.
Yi-Yu Chou
that's weird. I'm not sure what to do. The log says that it is creating
T1.mgz and not t1.mgz. Can you try this:
cd $SUBJECTS_DIR/subject/mri
mri_normalize -g 1 nu.mgz T1.mgz
this should create T1.mgz and not t1.mgz
doug
tulu wrote:
Dear FS experts and Prof. Douglas N Greve,
Here is log
To go from mni152 to the MNI305 2mm space, use
mri_vol2vol --mov mni305.2mm.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--inv --o output.mni305.2mm.nii.gz
This will resample MNI152_T1_2mm.nii.gz (or
Hi Deryk ,
Thanks for checking...As Anastasia mentioned, If FSL's bedpostx runs well
then that should work as well...I'm not exactly sure about why the error
is coming up and I can't replicate it on my computer either. Can you check
one more thing in your terminal? In your dmri.bedpostX directory
Thanks for the response! I seem to be getting better results.
I was wondering if there was any way the same resampling can be achieved
using Freesurfer 4.5 since a
lot of analysis (including analysis with other tasks) has already been done
in it, or if it is okay to use JUST the
Thank you, Nick
This is much appreciated !!
It works now and the talairach.xfm is:
1.08349275588989 -0.0557942688465118 -0.0535474419593811 3.1632091999054
0.0642405077815056 1.0216326713562 0.235359072685242 -13.4880638122559
0.0452854037284851 -0.281521290540695 1.20965027809143
Hello, Freesurfers,
When I use *recon-all -all -s ...*
there exists the error *mris_volmask.bin: error while loading shared
libraries:
/usr/local/freesurfer//lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot
restore segment prot after reloc: Permission denied*
Would you please tell me how to
Hi,
I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject
THe process exits with error when it comes to fslroi (attached pls find
the log file). I try to re-run the fslroi command as follow:
fslroi
Hi Bruce,
It was a RAM issue, I only had 1 G for the virtual machine, put it to it's max
which I think is 1.7 on a 4G machine. Worked! Thanks!
Cheers,
Vanessa
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, 2 June 2011 10:31 a.m.
To: Vanessa
11 matches
Mail list logo