yes, but if the information is lost in analyze (which it is) then we are
just guessing about orientations when we are converting back to .mgz
On Tue,
4 May 2010, Ilana Hairston wrote:
trying to make sense of this:
1. ran the initial recon-all to convert analyze to .mgz
2. then mri_convert on the DICOMs overwriting 001.mgz.
Now running the full autorecon-all to see what it looks like, but is seems
that mri_convert added spatial cosine information to the 001.mgz. this was
the output:
------------------------------
reading from 090725kc9b/e8845s5i1...
Starting DICOMRead2()
dcmfile = 090725kc9b/e8845s5i1
dcmdir = 090725kc9b
Ref Series No = 5
Found 103 files, checking for dicoms
Found 100 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 1.4
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 1
nslices = 100
ndcmfiles = 100
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
jpegUID: --1.2.840.10008.1.2.4--
Loading pixel data
TR=8.96, TE=1.79, TI=400.00, flip angle=15.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to FS090725kc9b/mri/orig/001.mgz...
On 4 May 2010 10:48, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
usually you create an mri/orig/001.mgz, but you can also just point
recon-all directly at the dicoms I think
On Tue, 4 May 2010, Antoine Leflon wrote:
So I have to write : mri_convert -it dicom -i (first image) -o (name
of the file) ?
I did it outputing orig.mgz as usually before getting the error .
Antoine
________________________________________________________________________________
Bruce Fischl <fis...@nmr.mgh.harvard.edu> a écrit :
mri_convert can be used to change the format, assuming it is standard
dicom.
cheers
Bruce
On Tue, 4 May 2010, Antoine Leflon wrote:
My files are dicoms and have no extension in the end of their name
(IM_0465 for example) . Is it possible to change the format ?
thanks ,
Antoine
________________________________________________________________________________
Talairach is about orientation. What is the format of your file? If it
is .hdr and.img, it will fail.
On 4 May 2010 11:43, Antoine Leflon
<antoine1.lef...@etudiant.univ-lille1.fr> wrote:
Hi all ,
I've used data from another Doctor , freesurfer told me the FOV was
330 so I put the flag -cw256 in the command recon-all but the
Talairach just failed ...
I got this error message . Can someone explain please ?
________________________________________________________________________________
#...@# Talairach Failure Detection Tue May 4 12:31:55 IST 2010
/home/cami/freesurfer/subjects/a1/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC
2009 i686 GNU/Linux
recon-all exited with ERRORS at Tue May 4 12:31:55 IST 2010
________________________________________________________________________________
thanks ,
Antoine
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