Hi Neils,
on the 2nd error, there is a bug in the most recent (ie, as of last week) version of mri_vol2surf. I've placed a new version at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.
On the 1st, error, is mri_vol2surf actually being run with the * wild card? Or is that something you put in? If it is running with that wild card, it's definitely wrong.
doug
Strien, N van wrote:
Hi,
I am having several problems with the feat2surf script when using this on my own data. For privacy purposes I renamed my subject to bert, however this refers not to the sample dataset:
The problems that I face with the feat2surf script are as follows:
- If I do not edit the script manually it stops when not finding a
data file (zstat1.img) in analyze format. If I edit the feat2surf script so it only finds a zstat1.nii file it continues.
- Results are not stored under 4 new subdirectories in the .feat main
directory (as suggested in the tutorial). They are stored (and overwritten) in the /root directory. (I know it’s a bad habit of mine to work under the root account, but I expect the outputdir will only change to /home/$username/ if I change user. Ẃhen the script only looks for .nii files (and finds them) it exits nicely (after commenting away some of the images the feat2surf script looks for such as cluster* and rendered*).
- When opening for example the rh volume in tksurfer, I get an error
message that the .mgh volume is incorrect.
This is the output when I run the feat2surf script without editing it.
Mon Jan 30 13:32:00 CET 2006
/media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_level
mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh
srcvol = mblok1+.feat/stats/*.img
srcreg = mblok1+.feat/reg/freesurfer/anat2exf.register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = bert2
surfreg = sphere.reg
interp = nearest
float2int = round
INFO: float2int code = 0
ERROR: analyzeRead(): cannot find any files for mblok1+.feat/stats/*.img
ERROR: could not read mblok1+.feat/stats/*.img as type 16
ERROR: with mri_vol2surf --src mblok1+.feat/stats/*.img --srcreg mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out /*.mgh --surf white --out_type mgh
When I ran mri_vol2surf manually (see command line below; $out1 = the output dir I created manually to store the results in), the computer runs forever displaying a vol2surf_linear message. I left it running overnight and it didn't finish. Any suggestions in what I could alter to get it right? The functional overlay works fine with tkmedit.
Thanks in advance,
Niels van Strien
mri_vol2surf --src $datalocation/mblok1+.feat/stats/zstat1.nii --srcreg $datalocation/mblok1+.feat/reg/freesurfer/anat2exf.register.dat --trgsubject bert2 --hemi lh --out $out1/zstat1.nii.mgh --surf white --out_type mg
srcvol = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_level/mblok1+.feat/stats/zstat1.nii
srcreg = /media/userdata/experiments/stereo_mtl/pilot/bert/results/fwhm5_hp50/1st_level/mblok1+.feat/reg/freesurfer/anat2exf.register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = bert2
surfreg = sphere.reg
interp = nearest
float2int = round
INFO: float2int code = 0
WARNING: missing NIfTI-1 orientation (qform_code = 0)
WARNING: your volume will probably be incorrectly oriented
Done loading volume
Reading surface /media/userdata/subjects/bert2/surf/lh.white
INFO: NOT fixing vertex area
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 0
vol2surf_linear: nhits = 74277/126030
2 0 0 0
vol2surf_linear: nhits = 74277/126030
3 0 0 0
vol2surf_linear: nhits = 74277/126030
4 0 0 0
vol2surf_linear: nhits = 74277/126030
5 0 0 0
vol2surf_linear: nhits = 74277/126030
6 0 0 0
vol2surf_linear: nhits = 74277/126030
7 0 0 0
vol2surf_linear: nhits = 74277/126030
8 0 0 0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer