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 > 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>> 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>> >>> 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>> 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 > 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/ > > > -- 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
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