Hi,
Yes, it is right. I am in the right folder.
What I did was following.
1. Merge files as 4D
2. do eddy current correction; I actually do not need it because I know my data do not have much eddy current distortion, but I did it anyway.
3. run bedpostx_datacheck because I cannot do 'dtifit'.
I have 7 volumes such as b0 to b5 so that my vectors and values are 7.
Any suggestion?
Sincerely,
Mi Jung
On Tue, Mar 10, 2009 at 8:21 AM, Mareike Menz <
[log in to unmask] <mailto:
[log in to unmask]>> wrote:
Hi Mi Jung,
the 4D file is needed anyway - that was missing before.
For bedpostx_datacheck you should name it data.
Funnily you have a file called data.ecclog - this is output of
eddy_current correction (for whatever Input - b-all?). You should
merge the volumes first, then correct for eddy currents and motion
(eddy_correct) and finally run bedostx_datacheck.
Your number of volumes needs to be exactly the same as entries in
bvals and entries/line in bvecs.
Without renaming you can also check the number of volumes with
fslnvols <4D> (e.g. b-all).
Greetings,
Mareike
Mi Jung Kim wrote:
Hi Saad and Matt,
Picture 1 is from when i ran 'dtifit'.
I attached my bvecs and bvals. Could you take a look at them
because bedpostx_datacheck shows that I do not have that files.
I have ascii file and link them.
I have 6 gradient directions with 16 NEX along with b=0 images.
I used 'fslmerge -t b-all b0 b1 b2 b3 b4 b5 b6' to make a 4D file.
Sincerely,
Mi Jung
On Tue, Mar 10, 2009 at 7:50 AM, Saad Jbabdi
<
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<mailto:
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[log in to unmask]>>> wrote:
Hi Mi Jung
Can you please tell us what command you are running and what
error
messages you get?
Cheers,
Saad.
On 10 Mar 2009, at 14:40, Mi Jung Kim wrote:
Hi Matt,
I think that I am supposed to some sort of data
information after
bedpostx_datacheck, am I right? But I do not see anything.
The folder has following data sets;
b-all.nii.gz b4.nii.gz bvecs
b0.nii.gz b5.nii.gz bvecs.txt
b1.nii.gz b6.nii.gz nodif.nii.gz
b2.nii.gz bvals nodif_brain.nii.gz
b3.nii.gz bvals.txt nodif_brain_mask.nii.gz
Do I miss something?
Sincerely,
Mi Jung
On Tue, Mar 10, 2009 at 7:05 AM, Matt Glasser
<
[log in to unmask] <mailto:
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<mailto:
[log in to unmask] <mailto:
[log in to unmask]>>> wrote:
1) Open a commandline terminal
2) Navigate to the folder that your data is
stored in
3) Type bedpostx_datacheck
Peace,
Matt.
------------------------------------------------------------------------
*From:* FSL - FMRIB's Software Library
[mailto:
[log in to unmask]
*Subject:* Re: [FSL] capillary phantom for muscle dti
Hi Matt,
I am actually sort of beginner with dti analysis.
Could you
tell me how to run bedpostx_datacheck please?
Sincerely,
Mi Jung
On Mon, Mar 9, 2009 at 7:54 PM, Matt Glasser
<
[log in to unmask] <mailto:
[log in to unmask]>
<mailto:
[log in to unmask] <mailto:
[log in to unmask]>>> wrote:
Please run bedpostx_datacheck in your data folder,
and post
the result here.
Peace,
Matt.
------------------------------------------------------------------------
*From:* FSL - FMRIB's Software Library
[mailto:
[log in to unmask]
*Subject:* Re: [FSL] capillary phantom for muscle dti
Hi Mark,
Thanks a lot. I also tested with b0 images, but it
still gives
same error.
Thanks,
Mi Jung
On Mon, Mar 9, 2009 at 6:04 PM, Matt Glasser
<
[log in to unmask] <mailto:
[log in to unmask]>
<mailto:
[log in to unmask] <mailto:
[log in to unmask]>>> wrote:
It looks like you are missing the b0 image. Amend
your bvecs
to be:
{0.0 1.0 0.446 0.447 0.448 0.447 -0.449
0.0 0.0 0.895 0.275 -0.723 -0.724 -0.277
0.0 0.0 0.0 0.851 -0.525 0.526 0.850}-bvecs
And your bvals to be:
{0 500 500 500 500 500 500}-bvals
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library
[mailto:
[log in to unmask]
Subject: [FSL] capillary phantom for muscle dti
Hi All,
I am trying to use probabilistic tractograph with my
phantom
data. I have
problem with running 'dtifit'. Below are my bvecs and
bvals.
{1.0 0.446 0.447 0.448 0.447 -0.449
0.0 0.895 0.275 -0.723 -0.724 -0.277
0.0 0.0 0.851 -0.525 0.526 0.850}-bvecs
{500 500 500 500 500 500]-bvals
But I see some error message so that I suspect that
my vectors
and values
are not matched with my dwi images. My images
actually scaled
images from
dicom.Would it be a problem?
Is there anybody who can help me?
Thanks,
Mi Jung
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad <
http://www.fmrib.ox.ac.uk/%7Esaad>
<
http://www.fmrib.ox.ac.uk/%7Esaad>
------------------------------------------------------------------------
-- Mareike Menz
NeuroImage Nord Lübeck
University Medical Center Hamburg-Eppendorf, Bldg. S10
Martinistr. 52
20246 Hamburg
Germany
+49 40 7410 53683
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--
Mareike Menz
NeuroImage Nord Lübeck
University Medical Center Hamburg-Eppendorf, Bldg. S10
Martinistr. 52
20246 Hamburg
Germany
+49 40 7410 53683
[log in to unmask]
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() ascii ribbon campaign
/\ - against html mail
--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg
Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Ricarda Klein
Prof. Dr. Dr. Uwe Koch-Gromus
