Dear Sir,
I was trying to convert DICOM images of DWI data through dcm2niigui. My output format was "Compressed FSL (4D NIfTI nii) and I have also checked 'Protocol name", "Acquisition series", "collapse folder", "recursive folder search depth=1"

I got the following message as I dragged and dropped all 308 images into the gui. Could you please help me resolving the error messages.

Converting 217/308 1
11145403->diffAPMPoptMB350b100050b200s012a1001.nii
151424 16
GZip...diffAPMPoptMB350b100050b200s012a1001.nii.gz
*Warning: Number of images in series (91) not divisible by number of volumes (14)
* Perhaps the selected folder only has some of the images
* Potential partial acquisition or improper segmentation of files
* Possible solution: check 'Collapse folders' in Help/Preferences and select directory that contains all images in subfolders
Converting 308/308 14
11161603->diffAPMPoptMB350b100050b200s013a1001.nii
1968512 16
GZip...diffAPMPoptMB350b100050b200s013a1001.nii.gz
Conversion completed in 206561 ms

Development of that tool ended 6 years ago. Even at that time, it recommended that you upgrade to dcm2niix. The DICOM standard has evolved a lot since that time, with vendors now supporting enhanced DICOM. I strongly suggest you use dcm2niix:
  https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage
If you prefer a graphical interface, get MRIcroGL (Import/ConvertDICOMtoNIfTI menu item):
  https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage

While I hope my legacy software is mature and robust, I am a full time scientist and instructor. I can not support old tools. It is an open source project, so you can always maintain and extend it as you wish.
  https://github.com/neurolabusc/MRIcron

Will you just tell me please what does the following message mean while converting dcm2niigui?

"Warning: for compatibility, converting UINT16->FLOAT32, range: 63064
If you prefer file size over compatibility, edit your preference named UINT 16 to FLOAT32"

DICOM images can store images as 16-bit unsigned integers (range 0...65535). However, several NIfTI tools only support 16-bit signed integers (-32768..32767) or 32-bit floating point data (e.g. AFNI). Therefore, while my tools attempt to convert DICOM data losslessly, it faces a dilemma with UINT16 data. There are two options:
 - Retain UINT16 datatype, and be aware that some tools may fail.
 - Promote UINT16 to FLOAT32, which requires twice the disk space and may be slower to process.

You can edit the preferences to choose between these two options.