Dear Vinay -
It looks like this directory
/home/pkroy/Desktop/vinay/DTI/DTI.bedpostX/
is different from the directory that you got the error for probtrackx
in your previous email:
/home/vinay/DTI/DTI.bedpostX/
I have looked more closely at the error message you got from your
previous email, and I think the problem comes from the first two
lines fdt outputs to your shell. These are:
rm -rf /home/vinay/DTI/DTI.bedpostX
mkdir -p /home/vinay/DTI/DTI.bedpostX
It is not so surprising after these two lines of code, that
probtrackx is not able to find the following file:
/home/vinay/DTI/DTI.bedpostX/nodif_brain_mask
My suspicion is that this is because the directory has been deleted
and remade.
I am really struggling to imagine how this happened.
Did you, for example, go to the Fdt gui, change the mode to "seed
mask", select the bedpostX directory as your output directory, then
change your mind and go back to seed voxel before running?
The output directory is a new directory that will be made to contain
the outputs of fdt - if it is already there, it is first deleted and
then remade - hence you should not specify the bedpostx directory as
your output directory ever.
Could this have been the problem?
T
On 8 May 2008, at 07:46, Vinay Shukla wrote:
> Hi
> Thanks for your mail.
> As per your suggestion i checked bedpostx_datacheck and i got this
> message
>
> [root@image bin]# ./bedpostx_datacheck /home/pkroy/Desktop/vinay/
> DTI/DTI.bedpostX/
> /home/pkroy/Desktop/vinay/DTI/DTI.bedpostX//data does not exist
> /home/pkroy/Desktop/vinay/DTI/DTI.bedpostX//nodif_brain_mask
> data_type FLOAT32
> dim1 128
> dim2 128
> dim3 21
> dim4 1
> datatype 16
> pixdim1 1.7968750000
> pixdim2 1.7968750000
> pixdim3 5.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> num lines in /home/pkroy/Desktop/vinay/DTI/DTI.bedpostX//bvals
> 1
> num words in /home/pkroy/Desktop/vinay/DTI/DTI.bedpostX//bvals
> 16
> num lines in /home/pkroy/Desktop/vinay/DTI/DTI.bedpostX//bvecs
> 3
> num words in /home/pkroy/Desktop/vinay/DTI/DTI.bedpostX//bvecs
> 48
>
> Please if it possible suggest me what i can do after this .Waiting
> for your response.
> Thanks & Regards
> Vinay
> NBRC India
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Markus Gschwind
> Sent: Wed 5/7/2008 5:52 PM
> To: [log in to unmask]
> Cc:
> Subject: Re: [FSL] Please Reply -Error After Running Probtrackx in FSL
>
> Hi!
>
> Did you run bedpostx_datacheck on your DTI.bedpostX directory?
>
> sounds like your nodif_brain_mask
> - is not there
> - or has a differnt name
> - or was used by another process...
>
> Cheers,
> Markus
>
>
>
> Quoting Vinay Shukla <[log in to unmask]>:
>
>> Dear All,
>> This is the error i am getting after running Probtrackx in
>> FSL.Please post
>> comment on this.....
>> Regards
>> Vinay Shukla
>> NBRC India
>>
>>
>> [root@image bin]# ./fsl
>> rm -rf /home/vinay/DTI/DTI.bedpostX
>> mkdir -p /home/vinay/DTI/DTI.bedpostX
>> rm -rf /home/vinay/DTI/DTI.bedpostX
>> mkdir -p /home/vinay/DTI/DTI.bedpostX
>> rm -rf /home/vinay/DTI/DTI.bedpostX
>> mkdir -p /home/vinay/DTI/DTI.bedpostX
>> ---------------------------------------------------------------------
>> ------
>> ** ERROR (nifti_image_read): failed to find header file for
>> '/home/vinay/DTI/DTI.bedpostX/nodif_brain_mask'
>> ** ERROR: nifti_image_open(/home/vinay/DTI/DTI.bedpostX/
>> nodif_brain_mask):
>> bad header info
>> Error: failed to open file /home/vinay/DTI/DTI.bedpostX/
>> nodif_brain_mask
>> ERROR: Could not open image /home/vinay/DTI/DTI.bedpostX/
>> nodif_brain_mask
>> Image Exception : #22 :: Failed to read volume
>> /home/vinay/DTI/DTI.bedpostX/nodif_brain_mask
>> terminate called after throwing an instance of
>> 'RBD_COMMON::BaseException'
>> ** ERROR (nifti_image_read): failed to find header file for
>> '/home/vinay/DTI/DTI.bedpostX/nodif_brain_mask'
>> ** ERROR: nifti_image_open(/home/vinay/DTI/DTI.bedpostX/
>> nodif_brain_mask):
>> bad header info
>> Error: failed to open file /home/vinay/DTI/DTI.bedpostX/
>> nodif_brain_mask
>> ERROR: Could not open image /home/vinay/DTI/DTI.bedpostX/
>> nodif_brain_mask
>> Image Exception : #22 :: Failed to read volume
>> /home/vinay/DTI/DTI.bedpostX/nodif_brain_mask
>> terminate called after throwing an instance of
>> 'RBD_COMMON::BaseException'
>> while executing
>> "exec sh -c "echo $cX $cY $cZ | $FSLDIR/bin/std2imgcoord -img
>> $mask -vox - |
>> awk '{print \$1}'" "
>> (procedure "mm_to_voxels" line 10)
>> invoked from within
>> "mm_to_voxels x y z $probtrack(reference)"
>> ("simple" arm line 11)
>> invoked from within
>> "switch $probtrack(mode) {
>> simple {
>> set fd [ open "${filebase}_coordinates.txt" w ]
>> set x $probtrack(x)
>> set y $probtrack(y)
>> ..."
>> ("probtrackx" arm line 63)
>> invoked from within
>> "switch -- $probtrack(tool) {
>> eddy_current {
>> global eddy
>>
>> set errorStr ""
>> if { $eddy(input) == "" } { set errorStr "You need to
>> specify..."
>> (procedure "fdt:apply" line 5)
>> invoked from within
>> "fdt:apply .fdt keep"
>> invoked from within
>> ".fdt.apply invoke"
>> ("uplevel" body line 1)
>> invoked from within
>> "uplevel #0 [list $w invoke]"
>> (procedure "tk::ButtonUp" line 22)
>> invoked from within
>> "tk::ButtonUp .fdt.apply"
>> (command bound to event)
>>
>
>
>
> --
>
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
|