Are you sure that *all* are 0? By passing it FreeSurferColorLUT.txt, you force it to report hundreds (or thousands) of ROIs which are not represented in the aparc+aseg.mgz. Also, try removing --seg-erode.
On 09/18/2014 04:43 PM, Salil Soman wrote: > Dear Doug, > > Thank you for your email. > > The registration overlap looks reasonable. Thank you for considering > this question. > > Best wishes, > > Sal > > On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look > reasonable? Does it overlay correctly on the T1.mgz? > doug > > On 09/14/2014 11:40 PM, Salil Soman wrote: > > Thank you Doug. I am having trouble with extracting > statistics using this method. > > I am able to use bbregister to get a transformation that > registers the PD image of the ASL to the T1. I then used this > transformation matrix to register the CBF map for the ASL > study into the T1.mgz space. Checking the images, the > registration looked reasonable. However, when I try to extract > the values from the registered image using the vois from > aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. > > *The command I ran is:* > > mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz > --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i > SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 > > *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* > > mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp > nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat > --no-save-reg > > (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the > same folder). > > *for which SUBJECT_ID.dat was generated by running the code:* > > bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg > SUBJECT_ID.dat --t1 --init-fsl > > Thank you for your consideration of this question. > > Best wishes, > > Salil Soman, MD, MS > > > > > On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > yep, you can use it for anything. > doug > > > On 9/14/14 12:52 PM, Salil Soman wrote: > > Dear Doug, > > Thank you again for this email. Do you think it is > possible to > use this method for ASL images as well? If so, how > would you > change the options? > > Best wishes, > > Salil Soman, MD, MS > > On Sat, May 25, 2013 at 11:51 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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. > > > > > > > -- Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological > Sciences > Laboratory > Fellow - Palo Alto War Related Illness and Injury > Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo > Alto Health > Care System > > > > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences > Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto > Health Care System > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
