Hi Paul,
I have fixed all the issues now. Thank you so much Paul once again.
Regards,
Sahil
On Wed, Jan 20, 2016 at 1:56 PM, Sahil Bajaj <[log in to unmask]> wrote:
> Hi Paul,
>
> Perfect ! Thank you so much for the code, it's working now.
> I have one more question- so now the voxel dimensions for my reference
> image and input image are same (1x1x1) but for the ROI on which I am
> applying the transformation has different voxel dimensions 1.375x1.375x1.5
> and may be because of which I am unable to overlay resulted ROIs on my
> OUTPUT file. Could you please suggest any way to fix this ?
>
> Thanks,
> Sahil
>
> On Wed, Jan 20, 2016 at 1:12 PM, paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Sahil,
>>
>> Aah, this is an issue which affects older versions of FSL. I think it has
>> been fixed in the latest release (5.0.9). If not, it will be fixed in the
>> next release.
>>
>> As a workaround, you can create a script (called e.g. "fixmat.sh") with
>> the following contents:
>>
>> #!/bin/bash
>>
>> # Read from specified file, or from standard input
>> infile="${1:-/dev/stdin}"
>>
>> while read line; do
>>
>> for number in $line; do
>> printf "%f " "$number"
>> done
>> echo
>> done < $infile
>>
>> Then pass the NewDCE.mat file to this script to create a corrected
>> version, like so:
>>
>> ./fixmat.sh NewDCE.mat > corrected.mat
>>
>> Cheers,
>> Paul
>>
>>
>>
>> On 20 January 2016 at 18:58, Sahil Bajaj <[log in to unmask]> wrote:
>>
>>> Thanks a lot Paul. Yes, I can view this file now and also attaching here.
>>> There are some weird looking numbers in this file, which could be the
>>> reason I am unable to use this further in flirt.
>>>
>>>
>>> On Wed, Jan 20, 2016 at 12:37 PM, paul mccarthy <[log in to unmask]
>>> > wrote:
>>>
>>>> Hi Sahil,
>>>>
>>>> OUTPUT.mat should be a plain text file - you can view its contents by
>>>> entering 'cat OUTPUT.mat' into a terminal.
>>>>
>>>> Cheers,
>>>>
>>>> Paul
>>>>
>>>> On 20 January 2016 at 18:32, Sahil Bajaj <[log in to unmask]> wrote:
>>>>
>>>>> Thanks a lot Matthew and Rosalia.
>>>>>
>>>>> I checked OUT.mat file in matlab, it says- it's not a binary MAT-file.
>>>>> I tried to send you the files but FSL doesn't allow to send files > 2mb.
>>>>>
>>>>> On Wed, Jan 20, 2016 at 11:19 AM, Matthew Webster <
>>>>> [log in to unmask]> wrote:
>>>>>
>>>>>> Hello Sahil,
>>>>>> what is the contents of OUTPUT.mat?
>>>>>> Kind Regards
>>>>>> Matthew
>>>>>>
>>>>>> Dear FSL experts,
>>>>>>
>>>>>> I have an issue in using flirt command for FSL (5.0). I used flirt
>>>>>> and it works well to co-register an image, say INPUT using REFERENCE and
>>>>>> get final co-registered image as OUTPUT and transformation matrix
>>>>>> OUTPUT.mat.
>>>>>>
>>>>>> Now I have ROIs defined in the INPUT image space, so I tried to
>>>>>> transform these ROIs into OUTPUT image space using OUTPUT.mat matrix using
>>>>>> following command:
>>>>>>
>>>>>> flirt -in ROI.nii -ref REFERENCE.nii -applyxfm -init OUTPUT.mat -out
>>>>>> NewROI.nii
>>>>>>
>>>>>> But I get following error after I run this:
>>>>>> terminate called after throwing an instance of
>>>>>> 'NEWMAT::SingularException'
>>>>>> Aborted (core dumped)
>>>>>>
>>>>>> I would really appreciate if someone could help me in figuring this
>>>>>> out ?
>>>>>>
>>>>>> Thanks,
>>>>>> Sahil
>>>>>>
>>>>>> --
>>>>>> -------------------------------------------------
>>>>>> Sahil Bajaj
>>>>>> Post-doctoral Fellow
>>>>>> Nantz National Alzheimer's Center, Department of Neurology
>>>>>> The Houston Methodist Research Institute (THMRI)
>>>>>> Houston, TX, USA.
>>>>>> E-mail:[log in to unmask] <[log in to unmask]>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -------------------------------------------------
>>>>> Sahil Bajaj
>>>>> Post-doctoral Fellow
>>>>> Nantz National Alzheimer's Center, Department of Neurology
>>>>> The Houston Methodist Research Institute (THMRI)
>>>>> Houston, TX, USA.
>>>>> E-mail:[log in to unmask] <[log in to unmask]>
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> -------------------------------------------------
>>> Sahil Bajaj
>>> Post-doctoral Fellow
>>> Nantz National Alzheimer's Center, Department of Neurology
>>> The Houston Methodist Research Institute (THMRI)
>>> Houston, TX, USA.
>>> E-mail:[log in to unmask] <[log in to unmask]>
>>>
>>
>>
>
>
> --
> -------------------------------------------------
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:[log in to unmask] <[log in to unmask]>
>
--
-------------------------------------------------
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:[log in to unmask] <[log in to unmask]>
