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That's exactly right, and just to confirm that the -tr option for fslmerge is what you want for your other question. All the best, Mark On 1 Nov 2011, at 12:46, Jeanette Mumford wrote: > Hi, > > Using bet (the brain extraction tool) with the -m flag will create a new image with the skull removed and supply a binary brain mask. > > Jeanette > > > 2011/11/1 ·ëè´ <[log in to unmask]> > Dear Mark, > > > > So kind you are. I found your code was very useful. And using fslmerge, I can convert 3D files to one 4D file. Here is what I typed in the terminal. > > fslmerge -t 4D.nii 01.nii.gz 02.nii.gz > > Is it correct? Should I specify TR explicitly? Or should I use fslmerge ¨Ctr ¡¡.. instead? > > > > ANOTHER QUESTION may be not related to the one above. Can FSL create a mask for inside-brain voxels? How? > > > > Thank you very much! > > > > Best wishes! > > > > Lu FENG > > [log in to unmask] > > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson > Sent: 2011Äê11ÔÂ1ÈÕ 16:39 > To: [log in to unmask] > Subject: Re: [FSL] Can 'fslchfiletype' change a series of .img/.hdr files into one 4D NIFTI file? > > > > Dear Lu Feng, > > > > The second command is not for doing multiple images, it is for renaming > > an image at the same time as changing its type. If you did do: > > fslchfiletype NIFTI_GZ filename1 filename2 > > then you will have lost the contents of filename2 (if it existed before) and > > have replaced it with a version of the contents of filename1. So I think you > > need to avoid this in your case. > > > > If what you want to do is take a set of images and simply convert them > > from .hdr/.img pairs into .nii.gz format then you need to script this. A > > simple version is the following: > > > > for fn in *.img ; do fslchfiletype NIFTI_GZ $fn $fn ; done > > > > This will run it on all the files that match *.img in the present working > > directory. You can replace this *.img term with any other you prefer > > (e.g. control*.img would only do images that started with "control" in > > their filenames). > > > > Note that you only need to have the for loop find the .img files, as > > fslchfiletype will automatically find the matching .hdr file. It could > > also be rewritten to use .hdr instead of .img (it doesn't matter - it > > should just make sure that it only picks one and not both - as doing > > for fn in * ; do ... would be bad as it could do both .hdr and .img which > > would confuse things). > > > > I hope this is clear and helpful. > > > > All the best, > > Mark > > > > > > > > On 1 Nov 2011, at 08:20, ·ëè´ wrote: > > > > > Dear experts, > > > > Since I¡¯m new to FSL, please bear my questions which seem to be something silly to skilled ones. > > > > When I typed in the terminal > > fslchfiletype NIFTI_GZ filename1 > > it worked well and changed a pair of filename1.hdr and filename1.img into filename1.nii.gz. But when I typed in the terminal as the document suggested > > fslchfiletype NIFTI_GZ filename1 filename2 > > it only changed the latter pair into filename2.nii.gz. What I wondered is how to change a series of pairs into a 4D NIFTI file. > > > > I have tried a 3D to 4D convertor provided by SPM. But the final file can't be recognized by FSLView. > > > > ANOTHER QUESTION: Can FSL create a mask for inside-brain voxels? How? > > > > Thanks in advance~~~~ > > > > Best wishes! > > > > Lu FENG > > [log in to unmask] > > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature database 6532 (20111010) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature database 6532 (20111010) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com >