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Dear Mark, Thanks for your kind response. Intensities were high (if original intensity =145 the final undistorted image has intensity of 19500) all over the brain in undistorted final image when compared with the original distorted image.I checked in some of the white matter areas as per your guidelines they are very high. I will give you the details about my field map image and how i went step by step. Field maps were acquired with Gradient echo sequence i have two magnitude images and a single field map image which the physicist told me is the phase difference image. The intensity range of this phase difference image is from -4096 to +4096 so in my first step i scaled this range to -pi to +pi then i did phase unwrapping using PRELUDE and then i converted this image to rad/sec dividing by difference in TEs. Then i submitted this image to FUGUE GUI and fed in appropriate parameters. Thanks again for you information on FWHM and other questions. Regards venkateswaran -----Original Message----- From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson Sent: Fri 1/2/2009 9:13 AM To: [log in to unmask] Subject: Re: [FSL] Fugue -field map correction Hi, I'm concerned about the change in intensity range. A small change I would expect but nothing like this magnitude. Do you see this kind of change in many voxels or is there just one outlier peak voxel somewhere pushing up the range? Have a look at the typical intensities in an area of white matter (with FSLView) before and after the correction. If there is a big change in intensity here then we need to figure out why. If it doesn't seem to change then maybe it is only an outlier voxel. In that case, look at the 99th percentile (with fslstats) and see how that changes. If you do have any large changes it will certainly affect your FA, etc. As for FWHM, we have implemented an alternative in the FEAT GUI which only regularises at the boundary. We have found that this gives the desired benefits (suppressing noise in the voxels that are most affected by it) without having to smooth areas where the SNR is good. So there is no FWHM equivalent when doing it via the FEAT GUI. However, if you find that your fieldmaps benefit from smoothing then you can do some smoothing (via the command line fugue, or with fslmaths) before using it with the FEAT GUI. All the best, Mark On 29 Dec 2008, at 15:38, Rajagopalan, Venkateswaran wrote: > Dear Mark, > > Thanks for your kind help. I followed your guidelines and got good > results i.e my dti images are undistorted. Your advise to use report > page and FSL's course material on FUGUE was very helpful to find out > my mistakes. I made the following mistake that is i didn't use > PRELUDE to unwrap the phase in the preliminary processing stage as > mentioned in the FSL's FUGUE course material that solved the > problem, i thought the PRELUDE step is also included in the FUGUE > GUI option. There is only one problem which i would like to clarify > with you, before that, i would like to mention that i followed > exactly the same steps as mentioned in FSL's FUGUE course website > where i first converted my phase image to -pi to +pi range then > applied PRELUDE to unwrap it, then converted to rad/sec and then fed > the field map to pre stats part of FUGUE GUI and set the settings > there as per your guidelines. My final result image > filtered_func_data has intensities which range from 0 to 271021 > whereas my original DTI image before field map correction has > intensities from 0 to 2825 i understand that intensities will be > modified in my fieldmap corrected image due to so many processing > steps but my question is; is this high intensity value changes > common after field map correction or am i making any mistake and > will this high intensity values affect DTI parameters like FA, RA > and other DTI metrics which i would like to calculate after this > distortion correction step. > One other question is, in FUGUE GUI i didn't choose a value for FWHM > explicitly as i fed values for dwell time and % signal threshold > values, how is this FWHM value chosen whether the algorithm > calculates the appropriate value by using some kind of iterative > procedure. > If i have not given you enough information kindly inform me, i will > get back to you with details. > > Thanks a lot for your kind help. Wishing you a Very Happy New Year. I > > Thanks > > Regards > venkateswaran > > > > -----Original Message----- > From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson > Sent: Tue 12/23/2008 5:48 PM > To: [log in to unmask] > Subject: Re: [FSL] Fugue -field map correction > > Hi, > > You are right about the units of dwell time - in the GUI they are in > ms, so 0.85 should be OK. > What you are doing sounds generally right, although I would turn off > spatial smoothing as well. > You don't need to specify a TR or a highpass filter cutoff for this > application (you do need to > turn the filtering off on the pre-stats tab). > > For signal loss you could go down to 0% for spin-echo EPI, but it > won't really hurt > to have it at 10%. You shouldn't need to do registration either. So > basically it all sounds > fine except for a bit of extra/unnecessary smoothing. I would expect > you to get reasonable > results and don't understand why you get excessively large > intensities. What other things > go wrong? Does it apply too strong a change, or not enough, or the > wrong direction, or what? > > Are you also looking at the FEAT output report (the report.html page > and the pre-stats output)? > This will help diagnose whether there is a problem in registration or > field-map preparation or > direction of warping. Look at the fsl course practical on FUGUE > (under registration) for more help. > http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html#fugue > > If you still cannot figure out what is going wrong then let us know. > All the best, > Mark > > > > On 23 Dec 2008, at 21:06, Rajagopalan, Venkateswaran wrote: > >> Dear Matt, >> >> Thanks, i followed exactly the commands you described when i used >> command line approach that is yours i divided my dwell time = 0.85 >> msec by 1000 as you showed, whereas in GUI mode i have to enter them >> in msec only. Thanks for your kind infromation. >> >> Regards >> venkateswaran >> >> ________________________________ >> >> From: FSL - FMRIB's Software Library on behalf of Matt Glasser >> Sent: Tue 12/23/2008 3:47 PM >> To: [log in to unmask] >> Subject: Re: [FSL] Fugue -field map correction >> >> >> >> Your dwell time seems rather high compared to the one I used. >> Perhaps you >> need to divide it by 1000 and try again? I think it is measured in >> milliseconds but fugue takes it in seconds. >> >> Peace, >> >> Matt. >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf >> Of Rajagopalan, Venkateswaran >> Sent: Tuesday, December 23, 2008 1:31 PM >> To: [log in to unmask] >> Subject: Re: [FSL] Fugue -field map correction >> >> Dear Mark, >> >> Thanks for your kind information. I tried using Pre stats in FEAT >> GUI as per >> your guidelines but I didn't get good results. I would like clarify >> with you >> some of my doubts; 1) i chose only "pre-stats " from the top pull >> down menu >> as a result of this the icons in the bottom which were enabled to do >> pre >> stats operation are Misc, Data, Pres-stats and Registration, i >> unchecked the >> option Balloon help and progress watcher under the "Misc" option. >> Then under >> the data icon i loaded my DTI data set and chose an output folder to >> save my >> results, here under the "Data" icon do i need to give the value of >> TR for my >> EPI sequence and do i also need to specify the high pass filter >> cutoff >> value. Then under "Pres stats" icon i chose B0 unwarping option and >> unchecked all other options except FWHM like BET extraction , >> temporal >> filtering etc then gave my field map image and BET extracted >> magnitude >> image, dwell time and EPI TE time and chose my unwarp direction, i >> don't >> know how to choose the %signal loss threshold any criteria available >> for >> that currently i retained the default value of 10, then >> corresponding to >> sigma of 0.5 i chose FWHM =2.35*0.5 ~1.2. Then i unchecked the >> default >> checked Linear registration icon, is it correct to uncheck this >> registration >> option or i have to leave it checked as such. >> I tried Matt's command line approach also but didn't get good >> results. I >> repeated the above steps by changing the unwrap direction from y to - >> y but >> once again i didn't get good results. One more doubt i want to >> clarify is >> the end result "filtered_func_data" has intensity values which are >> very >> large when compared to the original DTI image intensity whereas i >> didn't see >> these large values in my final image when i followed Matt's approach. >> >> I am sorry to bother you, >> >> Thanks >> >> Regards >> venkateswaran >> >> >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson >> Sent: Mon 12/22/2008 5:28 PM >> To: [log in to unmask] >> Subject: Re: [FSL] Fugue -field map correction >> >> Hi, >> >> The pre-processing of the fieldmap sounds fine. >> >> The FEAT GUI is the best way to get fieldmap unwarping done as >> it will do all the necessary registration steps (and some extra >> cleanup >> of the fieldmap) for you automatically. All you need to do is give >> it >> your fieldmap in rad/s, the corresponding magnitude image (after >> running BET on it to remove the non-brain structures) and some >> parameter values (e.g. echo spacing). It is all contained under >> the "pre-stats" part and you can run it on your DTI images by >> just selecting pre-stats only as the main option (top left pull-down >> menu), using your DTI as the 4D input data, and turning off all the >> other pre-stats options. The output file will be called >> filtered_func_data >> but will represent your distortion corrected EPI data. >> >> That should work for you with your data. >> If you have any trouble then let us know. >> >> All the best, >> Mark >> >> >> >> On 22 Dec 2008, at 22:19, Rajagopalan, Venkateswaran wrote: >> >>> >>> Dear All, >>> >>> I am new to field map correction. My field map data acquisition is a >>> single real field map image, gradient echo sequence. I have the >>> following images 1) EPI (for DTI),2)single real field map image in >>> units rad/sec and 3) the corresponding gradient echo magnitude >>> images. I went through FUGUE instruction manual and also through >>> PRELUDE documentation. There are few things which i am not able to >>> understand. I went through the field map processing steps mentioned >>> here http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html and made >>> sure that my field map images meet the requirement for instance my >>> field map is a single real field map image registered with the >>> magnitude image (step 1b and c ), its units are in rad/sec >>> (confirmed with MR technician), i regularised them using gaussian >>> FWHM of 0.5 fugue --loadfmap=fieldmap_rads -s 1 -- >>> savefmap=fieldmap_regu. After this step i used the following FUGUE >>> command fugue -i epi --dwell=0.85 --loadfmap=fieldmap_regu -u >>> result. My first question is this approach correct. >>> >>> My Next question is, i have uploaded the screenshot of my "result" >>> image in the following link >> http://www.beetony.com/uploads/venk/FUGUE_result.jpg >>> where you can see the problem, i feel that this is due to the fact >>> that field map and EPI images are not registered. I don't know >>> whether FUGUE takes cares of the registration between the gradient >>> echo field map which is of dim 63*63*30 and epi (DTI) sequence dim >>> 127*127*30 or i have to register my fieldmap by distorting it using >>> FUGUE option "fugue -i undistortedimage -p unwrappedphase -- >>> dwell=dwelltime --asym=asymtime --nokspace -s 0.5 -w warpedimage" >>> and then register the two images together and then use the following >>> FUGUE option "fugue -i epi --dwell=0.85 --loadfmap=fieldmap_regu -u >>> result" where now epi and fieldmap_regu are brought into common >>> space. >>> >>> I am sorry this may be a stupid question or approach kindly help me >>> with this. >>> >>> Thanks in advance, >>> >>> venkateswaran >>> >>> >>> P Please consider the environment before printing this e-mail >>> >>> >>> >>> Cleveland Clinic is ranked one of the top hospitals >>> in America by U.S. News & World Report (2008). >>> Visit us online at http://www.clevelandclinic.org <http://www.clevelandclinic.org/ >>>> for >>> a complete listing of our services, staff and >>> locations. >>> >>> >>> Confidentiality Note: This message is intended for use >>> only by the individual or entity to which it is addressed >>> and may contain information that is privileged, >>> confidential, and exempt from disclosure under applicable >>> law. If the reader of this message is not the intended >>> recipient or the employee or agent responsible for >>> delivering the message to the intended recipient, you are >>> hereby notified that any dissemination, distribution or >>> copying of this communication is strictly prohibited. If >>> you have received this communication in error, please >>> contact the sender immediately and destroy the material in >>> its entirety, whether electronic or hard copy. Thank you. >>> >> >> >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S. News & World Report (2008). >> Visit us online at http://www.clevelandclinic.org <http://www.clevelandclinic.org/ >>> for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> >> >> >> >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S. News & World Report (2008). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.