I suppose this one is filled by now, but you could check.
See you!
On Jul 12 2010, FSL automatic digest system wrote:
>There are 22 messages totaling 1898 lines in this issue.
>
>Topics of the day:
>
> 1. ROI volumes
> 2. fslview's error: std::bad_alloc (2)
> 3. DICOM b values and b vectors, required format for FSL?
> 4. registration of downsampled images to MNI (2)
> 5. ICA
> 6. Set two different coordinates
> 7. Melodic
> 8. AW: [FSL] AW: [FSL] FSL 4.1.6 released (2)
> 9. evaluation error (2)
> 10. FEEDS/FIRST error (2)
> 11. Research Assistant Position for Imaging Studies of Aging
> 12. fast std::logic_error
> 13. VBM
> 14. Re : [FSL] VBM
> 15. Feat, default settings change in the registeration step
> 16. Second level analysis error
> 17. Post-Doc Position at Princeton University
>
>----------------------------------------------------------------------
>
>Date: Sun, 11 Jul 2010 22:53:58 -0400
>From: William Hinkle <[log in to unmask]>
>Subject: Re: ROI volumes
>
>call when you are done
>On Jul 11, 2010, at 8:38 AM, Rolf Heckemann wrote:
>
>> Since you are sending this to the FSL list, even though you are
>> addressing us as "SPM users", I will assume you are looking for a
>> suggestion based on FSL.
>>
>> If you have a label image (i.e. an image volume that defines ROIs by
>> assigning nominal values to the voxels that belong to them) it is
>> straightforward to calculate the ROI volumes with fslstats. Example:
>> if you have three ROIs labelled 1, 2 and 3 on a background of zeros,
>> you can use the histogram feature:
>>
>> fslstats labelimage -h 4
>>
>> This lists the volume of each label in voxels, including background. Use
>>
>> fslstats labelimage -h 4 | nl -v 0
>>
>> to have the ROIs numbered in the output.
>>
>> To get the volume of an individual ROI in mm^3, use the volume option
>> with thresholding. For ROI 2, use
>>
>> fslstats labelimage -l 1 -u 3 -V
>>
>> Without thresholding, -V will work for images defining a single ROI,
>> independent of the values of the voxels within the ROI. That means you
>> can use it for MR images where an ROI has been masked.
>>
>> Hope that helps.
>>
>> Rolf
>>
>>
>> On 11 July 2010 12:04, Alexander Lebedev <[log in to unmask]> wrote:
>>> Dear SPM users,
>>>
>>> Sorry for disturbing. Could you please advice me the best way (software)
>>> to create and calculate ROI volumes?
>>>
>>> My task is to calculate volumes of
>>> several CSF spaces.
>>>
>>> My tactics:
>>>
>>> 1. Segmentation in SPM (getting data for CSF);
>>> 2. Starting MRICroN and combining my original (T1) data with segmented
>>> image (in order to perform adequate navigation);
>>> 3. Easily creating a VOI and...
>>> getting stuck with it... because I have no idea what should I do
>>> next (as far as I understood, all tools in MRICroN are for group
>>> analysis)...
>>>
>>> Please, help me if it is possible...
>>> Thank you beforehand!
>>> --
>>> Sincerely Yours,
>>> Alexander Lebedev,
>>>
>>> I.P. Pavlov State Medical University,
>>> 197022, Lev Tolstoy str. 6/8,
>>> Saint Petersburg, Russian Federation.
>>>
>
>------------------------------
>
>Date: Mon, 12 Jul 2010 12:28:24 +0800
>From: xuemei lei <[log in to unmask]>
>Subject: fslview's error: std::bad_alloc
>
>Hi all
> I have merged 126 3D images into a 4d image using fslmerge command
>without error. Then analysed the data use randomise field, but got an error
> report, said: " ERROR (nifiti_iamge_read):failed to find hrader file for
> the
>4d image ; ERROR: nifti_image_open:bad header info......"。
> I checked the 4d image cliking move mode in fslview。 It did ok
> at the
> first, but at the last , fslview crashed and found the error report,
> said:"
>std::bad_alloc, "
>
> I have checked the script and I used it to merge 40 3D images to a
>4d image, and it worked well。So I really have no idear.
> any help appreciated.
>
>
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