Dear Doug, Thank you for your email. Following up on our previous discussions:
1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote: > > On 5/25/13 1:39 PM, Salil Soman wrote: > > Thank you Doug. > > Just so I am clear - is the anatomical the nifti T1.mgz or is it a > different file. From your email I gather should do the following: > > *1) Use bbregister to register the lowb image to the anatomical. This > creates a registration matrix.* > > bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat > > That is right, but add --t2 (since it is t2 weighted). > > > *2) Use mri_vol2vol and the registration to map the ADC map to the > anatomical* > > mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff > --reg $outdir/register.dat --no-save-reg > > Use the ADC as the moveable (not lowb, but use the lowb for > bbregister). The target volume should be the T1.mgz (or any conformed > volume). The output will be the adc in the anatomical space (not sure why > you call it vol2diff). > > *3) use mri_segstats to extract the values* > > *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats > > The input would be the adc volume mapped the anatomical space. I would > use WMParcStatsLUT.txt or else you'll get a billion different areas not > represented in wmparc. You may also want to add "--seg-erode 1" to erode > the segmentations by a voxel. This helps to prevent partial voluming. > > doug > > > > Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. > ADC), $vol2diff is the output image of the registration, and fa.stats will > be my output stats table? > > I suspect there is part of the syntax for these tools I do not > understand. Also, what input would $vol be? > > Best wishes, > > Sal > > > On Sat, May 25, 2013 at 10:06 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu > > wrote: > >> >> Hi Sal, yes you can. Use bbregister to register the lowb image to the >> anatomical. This creates a registration matrix. Use mri_vol2vol and the >> registration to map the ADC map to the anatomical, then use mri_segstats to >> extract the values >> doug >> >> ps. Please post questions to the FS list instead of us directly so that >> others can benefit and it gets archived. thanks! >> >> >> >> On 5/25/13 1:03 PM, Salil Soman wrote: >> >>> Dear Dr. Greve, >>> >>> Is it possible to register a nonstructural MR sequences (e.g. an ADC >>> map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using >>> the segmentation from the aseg (or aparc+aseg) file to output a mean ADC >>> value for each anatomic area segmented? >>> >>> Thank you for your time and consideration. >>> >>> Best wishes, >>> >>> Sal >>> >>> Salil Soman, MD, MS >>> >> >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > >
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