Hi Matt,
Here is my bedpostx_datacheck output. I do not understand why they cannot
find all these files.
b-all.nii.gz b5.nii.gz bvecs.txt
b0.nii.gz b6.nii.gz data.ecclog
b1.nii.gz bedpostcom_log.tcl data.nii.gz
b2.nii.gz bvals nodif.nii.gz
b3.nii.gz bvals.txt nodif_brain.nii.gz
b4.nii.gz bvecs nodif_brain_mask.nii.gz
These are my files in the folder.
/Users/macadmin/se5-nex16/data does not exist
/Users/macadmin/se5-nex16/nodif_brain_mask does not exist
num lines in /Users/macadmin/se5-nex16/bvals
cat: /Users/macadmin/se5-nex16/bvals: No such file or directory
0
num words in /Users/macadmin/se5-nex16/bvals
cat: /Users/macadmin/se5-nex16/bvals: No such file or directory
0
num lines in /Users/macadmin/se5-nex16/bvecs
cat: /Users/macadmin/se5-nex16/bvecs: No such file or directory
0
num words in /Users/macadmin/se5-nex16/bvecs
cat: /Users/macadmin/se5-nex16/bvecs: No such file or directory
0
Sincerely,
Mi Jung
On Tue, Mar 10, 2009 at 7:40 AM, Mi Jung Kim <[log in to unmask]> 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]> 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]] *On
>> Behalf Of *Mi Jung Kim
>> *Sent:* Monday, March 09, 2009 11:31 PM
>>
>> *To:* [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]> 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]] *On
>> Behalf Of *Mi Jung Kim
>> *Sent:* Monday, March 09, 2009 9:45 PM
>>
>>
>> *To:* [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]> 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]] On
>> Behalf
>> Of Mi Jung Kim
>> Sent: Monday, March 09, 2009 6:43 PM
>> To: [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
>>
>>
>>
>>
>>
>
>
