Hi Mi Jung,
this is odd. Are you sure you are in the right folder?
bedpostx_datacheck is searching in /Users/macadmin/se5-nex16/
Is this the correct directory? Otheriwse try again. Open Terminal and
after prompt enter:
cd <path to where the files are>
pwd #this tells you where you are
ls # tells you the content of this directory
bedpostx_datacheck ./
If you are not sure, where the files are copy the complete path from finder starting with /.
HTH,
Mareike
Mi Jung Kim wrote:
> 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]
> <mailto:[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]
> <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] <mailto:[log in to unmask]>] *On
> Behalf Of *Mi Jung Kim
> *Sent:* Monday, March 09, 2009 11:31 PM
>
> *To:* [log in to unmask] <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]>> 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] <mailto:[log in to unmask]>] *On
> Behalf Of *Mi Jung Kim
> *Sent:* Monday, March 09, 2009 9:45 PM
>
>
> *To:* [log in to unmask] <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]>> 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]
> <mailto:[log in to unmask]>] On Behalf
> Of Mi Jung Kim
> Sent: Monday, March 09, 2009 6:43 PM
> To: [log in to unmask] <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
>
>
>
>
>
>
>
--
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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