Some Frequently Asked fMRI Related Questions
MRI Scanner Issues, Image Transfers and Conversions
Q1.1: I would like to test out a new protocol on the MRI Scanner. How can I
arrange development time on the scanner?
Q1.2: I have a CD/DVD of DICOM images from the BIC Siemens scanner. How can
I convert these DICOM images into MINC format?
Q1.3: Can I get a DICOM format version of my images acquired on the BIC Siemens
MR Scanner?
Q1.4: I need to convert an MRI scan from MINC to NIFTI (nii files).
Q1.5: Is it possible to have a variable scanning time interval?
Q1.6: Can I trigger the scanner, or tell it when to scan?
Q1.7: What is the trigger signal sent by the scanner for each time frame acquired
in an fMRI time series?
Q1.8: Is there a fast way to check my fMRI images for random
artefact spikes or noise?
Q1.9: What are the scanning parameters used in the standard T1 Weighted Global
sequence on the Siemens Sonata and Tim Trio MR Scanners?
Image Post-processing and Analysis
Q2.1: Can I find out at what time my fmri data series was acquired?
Q2.2: I have plotted the motion correction output from the log file of
fmr_preprocess and it does not look like the frames are ordered properly.
What is going on?
Q2.3: How can I batch my fmristat matlab scripts?
Q2.4: I have a bunch of 3D volumes from an fmri time series. How can I
stick them together to create a 4D MINC file?
Q2.5: I need to concatenate files from a proton density
and T2 sequence that are acquired in 8 separate volumes with a 1mm position
shift in each one. How can I do this?
Q2.6: How can I view the images on my DICOM CD or DVD and find out what all those numbered DICOM files correspond to?
Answers
MRI Scanner Issues, Image Transfers and Conversions
Q1.1: I would like to test out a new protocol on the MRI Scanner. How can I
arrange development time on the scanner?
A: Fill out and submit the MR Scan Request form available at the following
website:
BIC MR Scanner Request Form
In the "Other pertinent information..." field, include a note about how your
request is for Protocol Development time.
Currently development time can be arranged during the week from 8am to 5pm,
not including weekends.
Q1.2: I have a CD/DVD of DICOM images from the BIC Siemens scanner. How can I convert these DICOM images into MINC format?
A: You will most likely want to use Rick Hoge's dcm2mnc converter. Please refer to
the following webpage for complete details:
dcm2mnc help page
Q1.3: Can I get a DICOM format version of my images acquired on the BIC Siemens MR Scanner?
A: Yes, if you bring a blank CD-R or DVD-R disc (note that DVD-R are supported and not DVD+R), the MR technicians will gladly archive your imaging session to CD or DVD.
However, you can also find your images in DICOM format on the BIC network
after they have been transferred off the scanner console. These images are available on the BIC servers and
are erased 7 days after they are transferred.
You can find them in the following directory on any BIC network computer:
/data/transfer/dicom
Please keep in mind that these DICOM images occupy significantly more disk space than the respective MINC images.
Q1.4: I need to convert an MRI scan from MINC to NIFTI (nii files).
A: You could try the Java
LONI Debabeler.
But if you are working in the BIC computing environment, you should first
try mnc2nii. This is a NIFTI-1 image
converter that can produce IMG/HDR file pairs or 4D NIFTI files. Type in the following to run the command
and obtain a help message on how to use it:
mnc2nii -help
Please note that if you use this command, you should verify the output for correct coordinate information. This type of image conversion can sometimes result in Left-Right image flipping, so please be careful. We've also had better results with setting the NIFTI output to float, so try running the mnc2nii command with the -float option.
Q1.5: Is it possible to have a variable scanning time interval?
A: No. The scanning interval, or repetition time, TR, is fixed for BOLD EPI scans. The
scanner can only acquire an image once every X seconds, where X can be anything from
1 second to greater than 15 seconds.
Q1.6: Can I trigger the scanner, or tell it when to scan?
A: The scanner is equipped for cardiac or respiratory gated scanning and this is possible.
However, any other external triggering is not possible.
Q1.7: What is the trigger signal sent by the scanner for each time frame acquired in an fMRI time series?
A: The trigger signal from the scanner is available in a couple of different formats. It can be a standard TTL signal on a BNC cable.
Q1.8: Is there a fast way to check my fMRI images for random
artefact spikes or noise?
A: Yes, there are several methods to quickly get an idea if something went
really wrong with any of your slices during your fMRI run. Please refer to
the following webpage for an explanation of three different methods of
checking for spike artefacts.
Q1.9: What are the scanning parameters used in the standard T1 Weighted Global sequence on the Siemens Sonata and Tim Trio MR Scanners?
A: For the 1.5T Sonata:
3D Gradient Echo FLASH
Te = 9.2ms
Tr = 22ms
Slice Thickness = 1mm
FOV = 256mm
Image Matrix = 256 x 256
Phase Encode Dir = A -> P
160 slices (this could vary)
Flip Angle = 30 degrees
Interleaved Excitation
Sagittal Slice Acquisition
For the 3T Tim Trio:
3D Magnetization Prepared Rapid Gradient Echo (MP-RAGE)*
Te = 2.98ms
Tr = 23ms
Slice Thickness = 1mm
FOV = 256mm
Image Matrix = 256 x 256
Phase Encode Dir = A -> P
176 slices (this could vary)
Flip Angle = 9 degrees
Interleaved Excitation
Sagittal Slice Acquisition
*Note: these are the ADNI suggested parameters for the MPRAGE scan.
Image Post-processing and Analysis
Q2.1: Can I find out at what time my fmri data series was acquired?
A: You sure can. There are DICOM header fields that you will
find inside your minc header that contain this information. In
dicom header section 0x0008, the fields 0x0030 to 0x0033 are as follows:
dicom_0x0008:el_0x0030 = Study Time
dicom_0x0008:el_0x0031 = Series Time
dicom_0x0008:el_0x0032 = Acquisition Time
dicom_0x0008:el_0x0033 = Image Time
As an example, the output of the 'mincheader' command might show something
like this (use 'mincheader input_file.mnc |less' to scroll through the
output):
dicom_0x0008:el_0x0030 = "170805.765000 "
dicom_0x0008:el_0x0031 = "172823.359000 "
dicom_0x0008:el_0x0032 = "172513.194984 "
dicom_0x0008:el_0x0033 = "172823.390000 "
In this particular case, the session began at 5:08pm, and this particular
fmri series began at 5:28pm.
If you are curious about all those other DICOM headers, there is plenty of
documentation available online, including the DICOM Standard homepage.
Q2.2: I have plotted the motion correction output from the log file of fmr_preprocess and it does not look like the frames are ordered properly.
What is going on?
A: This was a bug with a previous version of fmr_preprocess that has since
been fixed. If your motion correction plots look weird, it is most likely because
the line ordering inside the log file is not sequential. The ordering is
not numerical in the 1, 2, 3 sense, but in a character based method of
0, 100, 101, ..., 10, 110, ..., 2, 21, ...
Edit the log file and rearrange the lines with this in mind. The plots may
make more sense after this correction.
Q2.3: How can I batch my fmristat matlab scripts?
A: Use the 'qbatch' command in conjunction with a shell script version of your usual matlab
script. For example, say you have saved all of your fmristat commands to a
file called 'fmristat_script.m', you would first convert the script into a shell executable
one by adding the following lines to the beginning of the file:
#!/bin/csh
matlab -nojvm -nodisplay <<EOF
then at the end of your matlab script, you would add:
EOF
You would then save the script with a '.sh' extension and on the command line, turn
on the script's execute permission:
chmod u+x fmristat_script.sh
Once this is done, you can batch it with the following command:
/usr/local/mni/bin/qbatch fmristat_script.sh
This will run the fmristat script on one of the many BIC Linux workstations. If you wish to restrict
fmristat's execution to yorick, you would type in the following:
/usr/local/mni/bin/qbatch -q irix.q fmristat_script.sh
You will obtain an output log file in the directory where the script is saved. Type "qbatch -help" for more options.
Q2.4: I have a bunch of 3D volumes from an fmri time series.
How can I stick them together to create a 4D MINC file?
A: mincconcat is the answer. There are 2 scenarios depending on
dimensionality of your individual files (which you can verify with
'mincinfo').
1) If the individual frames have a properly specified time dimension (with
the correct time 'start' and 'step' attributes):
mincconcat -concat_dimension time <input_files> <output_file>
The output will be sorted according to the time starts, stored inside the
individual minc file headers.
2) If they are 3D volumes with no time information, then you have to be
sure that the filenames are numbered properly (something like vol000.mnc,
vol001.mnc, vol002.mnc ...). Then you can run the command like this:
mincconcat -concat_dimension time -sequential <input_files> <output_file>
But be careful about the ordering of the individual frames. If the files
are not numbered with leading zeroes, you may get an incorrectly ordered file
listing.
If this is the case, you have to (a) rename the files, or (b) save the
directory contents to a text file, and then put them in the right order.
2a) To rename the files, you could use a file renaming script, something
like the following:
~mferre/bin/renamer 's/vol/vol00/' vol?.mnc
~mferre/bin/renamer 's/vol/vol0/' vol??.mnc
These commands will pad all single digit volume filenames with 2 leading
zeroes, and all double digit volume names with 1 leading zeroe.Once this is done
you can run the minconcat command specified above.
2b) To obtain a text file with the filenames so that you can arrange
the ordering in an editor or spreadsheet application (like Excel, Matlab,
or gnumeric), use 'ls' on the command line and redirect the output to a
file with the greater than '>' operator.
\ls -1 vol* > filenames.log
At this point, you can edit filenames.log and re-arrange the ordering of
the volumes. Once this is done, you would call mincconcat with the
'-filelist' option:
mincconcat -concat_dimension time -filelist <filenames.log> <output_file>
Q2.5: I need to concatenate files from a proton density
and T2 sequence that are acquired in 8 separate volumes with a 1mm position
shift in each one. How can I do this?
A: For sagittal images, varying along the xspace dimension (as the above example
illustrates):
mincconcat -nocheck_dimensions -concat_dimension xspace <input> <output>
The list of input files here should be listed according to echo time. For
axample, you would pass all the *e0* files, and then the *e1* files.
Q2.6: How can I view the images on my DICOM CD/DVD and find out what all those numbered DICOM files correspond to?
A: There are many freely available DICOM viewing tools available online. Try a Google, Bing, or DuckDuckGo
search for it. You could also try the Finder function available at idoimaging.com
If there is a question which you feel should be added to this page, please feel free to contact Mike Ferreira at the following e-mail address: 
Thank you.
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