Re: [Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5
Hello All, We are interested in the ranges of eTIV values found by other Freesurfer users. As noted below, one research group reports a mean ICV of about 1560 cc for adults ranging from 20-90 years old. Our sample (n=40) including males and females (51 to 83 years old) has a mean eTIV of 1520 cc (standard deviation = 200 cc), and a median eTIV of 1511 cc. Do these values seem reasonable? Thanks, Paul [EMAIL PROTECTED] wrote: Hi, for those interested: we have correlated FS's ICV estimates and estimates from a procedure developed by Anders Dale (a deformable template procedure, similar to the “Shrink Wrapping” procedure previously described by Dale and colleagues (Dale et al, 1999; Dale and Sereno, 1993)). Mean ICV from FS: 1567690 (SD = 161247) Mean ICV from Dale: 1584008 (SD = 136979) The difference was not significant (p = .12, t = -1.596) The correlation was .84. A scatterplot is attached (FS on the y-axis, Dale's method on the x). Not too bad, but not perfect either. The sample was a life-span sample (20-90 years, n = 74). Hope this info was usefull. Best, Anders MF Hi Paul, Just as an aside, once you have a talairach_with_skull.lta file (whether from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), where the scale_factor employed is 2150. Incidentally, using the -eTIV option of mri_label_volume, you can also specify other transforms (e.g., talairach.xfm, talairach.lta) to be used used instead of the default talairach_with_skull.lta in computing "ICV". I've looked at the effect of using different transforms in a handful of brains, and "ICV" can vary a bit depending on transform you choose to use. I'm curious: Has anyone out there compared FS's ICV estimate to ICV estimated by another program? Best, Mike H. On Fri, 2008-06-20 at 14:35 -0700, Paul Greenberg wrote: Hello Freesurfers, I am interested in comparing eTIV calculated with version 3.0.5 to that calculated by version 4.0.5 (64 bit Cent OS). In order to compare eTIV for a single brain estimated in version 3.0.5 to version 4.0.5, I copied a subject's previous freesurfer output (v3.0.5) into the freesurfer version 4.0.5 folder, deleted all the files within the "transforms" folder and carried out the following procedures as outlined in the recon-all dev table: 1) Run the talairach procedure. Command = talairach_avi --i mysubject --xfm talairach.auto.xfm 2) cp talairach.auto.xfm talairach.xfm 3) Run automatic failure detection. Command= talairach_afd -T 0.005 -xfm talairach.xfm 4) Create talairach_with_skull.lta. Command = mri_em_register -skull nu.mgz $freesurferhome/average/RB_all_withskull_2007-08-08.gca talairach_with_skull.lta 5) Check the new eTIV. Command = mri_label_volume -eTIV talairach_with_skull.lta aseg.mgz 17 53 As the aseg.mgz file exists from previous processing (versio 3.0.5), and the talairach_with_skull.lta was re-created with the new processing (version 4.0.5), the output of this command should list the eTIV based on the new talairach transform? Are these procedures correct for generating new values of eTIV if that is all i want? Thanks! -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5
Hi yes, the FS ICVs mostly seem to work :-) I still think one should watch out for outliers. We had a sample of 28 kids aged 8-13 yrs, and the ICVs were quite a bit off and useless for two of those, so I would check all carefully especially if you have a group that may have smaller than normal adult ICV. Best, K > Hi, for those interested: we have correlated FS's ICV estimates and > estimates from a procedure developed by Anders Dale (a deformable template > procedure, similar to the Shrink Wrapping procedure previously described > by Dale and colleagues (Dale et al, 1999; Dale and Sereno, 1993)). > > Mean ICV from FS: 1567690 (SD = 161247) > Mean ICV from Dale: 1584008 (SD = 136979) > > The difference was not significant (p = .12, t = -1.596) > > The correlation was .84. A scatterplot is attached (FS on the y-axis, > Dale's method on the x). > > Not too bad, but not perfect either. > > The sample was a life-span sample (20-90 years, n = 74). > > Hope this info was usefull. > > Best, > Anders MF > > > > >> >> Hi Paul, >> Just as an aside, once you have a talairach_with_skull.lta file (whether >> from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), >> where the scale_factor employed is 2150. >> >> Incidentally, using the -eTIV option of mri_label_volume, you can also >> specify other transforms (e.g., talairach.xfm, talairach.lta) to be used >> used instead of the default talairach_with_skull.lta in computing "ICV". >> I've looked at the effect of using different transforms in a handful of >> brains, and "ICV" can vary a bit depending on transform you choose to >> use. >> >> I'm curious: Has anyone out there compared FS's ICV estimate to ICV >> estimated by another program? >> >> Best, >> Mike H. >> >> >> On Fri, 2008-06-20 at 14:35 -0700, Paul Greenberg wrote: >>> Hello Freesurfers, >>> >>> I am interested in comparing eTIV calculated with version 3.0.5 to >>> that calculated by version 4.0.5 (64 bit Cent OS). >>> >>> In order to compare eTIV for a single brain estimated in version 3.0.5 >>> to version 4.0.5, I copied a subject's previous freesurfer output >>> (v3.0.5) into the freesurfer version 4.0.5 folder, deleted all the >>> files within the "transforms" folder and carried out the following >>> procedures as outlined in the recon-all dev table: >>> >>> 1) Run the talairach procedure. Command = talairach_avi --i >>> mysubject --xfm talairach.auto.xfm >>> 2) cp talairach.auto.xfm talairach.xfm >>> 3) Run automatic failure detection. Command= talairach_afd -T 0.005 >>> -xfm talairach.xfm >>> 4) Create talairach_with_skull.lta. Command = >>> mri_em_register -skull nu.mgz >>> $freesurferhome/average/RB_all_withskull_2007-08-08.gca >>> talairach_with_skull.lta >>> 5) Check the new eTIV. Command = >>> mri_label_volume -eTIV talairach_with_skull.lta aseg.mgz 17 53 >>> As the aseg.mgz file exists from previous processing (versio >>> 3.0.5), and the talairach_with_skull.lta was re-created with the new >>> processing (version 4.0.5), the output of this command should list the >>> eTIV based on the new talairach transform? >>> >>> Are these procedures correct for generating new values of eTIV if that >>> is all i want? >>> >>> Thanks! >>> >>> -- >>> >>> Paul Greenberg, Ph.D. >>> Radiology Department, University of California, San Diego >>> VA San Diego Healthcare System (116A-13) >>> 3350 La Jolla Village Drive >>> San Diego, CA 92161 >>> Phone: (858) 552-8585 ext. 2903 >>> Fax: (858) 642-3836 >>> [EMAIL PROTECTED] >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5
Hi, for those interested: we have correlated FS's ICV estimates and estimates from a procedure developed by Anders Dale (a deformable template procedure, similar to the Shrink Wrapping procedure previously described by Dale and colleagues (Dale et al, 1999; Dale and Sereno, 1993)). Mean ICV from FS: 1567690 (SD = 161247) Mean ICV from Dale: 1584008 (SD = 136979) The difference was not significant (p = .12, t = -1.596) The correlation was .84. A scatterplot is attached (FS on the y-axis, Dale's method on the x). Not too bad, but not perfect either. The sample was a life-span sample (20-90 years, n = 74). Hope this info was usefull. Best, Anders MF > > Hi Paul, > Just as an aside, once you have a talairach_with_skull.lta file (whether > from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), > where the scale_factor employed is 2150. > > Incidentally, using the -eTIV option of mri_label_volume, you can also > specify other transforms (e.g., talairach.xfm, talairach.lta) to be used > used instead of the default talairach_with_skull.lta in computing "ICV". > I've looked at the effect of using different transforms in a handful of > brains, and "ICV" can vary a bit depending on transform you choose to > use. > > I'm curious: Has anyone out there compared FS's ICV estimate to ICV > estimated by another program? > > Best, > Mike H. > > > On Fri, 2008-06-20 at 14:35 -0700, Paul Greenberg wrote: >> Hello Freesurfers, >> >> I am interested in comparing eTIV calculated with version 3.0.5 to >> that calculated by version 4.0.5 (64 bit Cent OS). >> >> In order to compare eTIV for a single brain estimated in version 3.0.5 >> to version 4.0.5, I copied a subject's previous freesurfer output >> (v3.0.5) into the freesurfer version 4.0.5 folder, deleted all the >> files within the "transforms" folder and carried out the following >> procedures as outlined in the recon-all dev table: >> >> 1) Run the talairach procedure. Command = talairach_avi --i >> mysubject --xfm talairach.auto.xfm >> 2) cp talairach.auto.xfm talairach.xfm >> 3) Run automatic failure detection. Command= talairach_afd -T 0.005 >> -xfm talairach.xfm >> 4) Create talairach_with_skull.lta. Command = >> mri_em_register -skull nu.mgz >> $freesurferhome/average/RB_all_withskull_2007-08-08.gca >> talairach_with_skull.lta >> 5) Check the new eTIV. Command = >> mri_label_volume -eTIV talairach_with_skull.lta aseg.mgz 17 53 >> As the aseg.mgz file exists from previous processing (versio >> 3.0.5), and the talairach_with_skull.lta was re-created with the new >> processing (version 4.0.5), the output of this command should list the >> eTIV based on the new talairach transform? >> >> Are these procedures correct for generating new values of eTIV if that >> is all i want? >> >> Thanks! >> >> -- >> >> Paul Greenberg, Ph.D. >> Radiology Department, University of California, San Diego >> VA San Diego Healthcare System (116A-13) >> 3350 La Jolla Village Drive >> San Diego, CA 92161 >> Phone: (858) 552-8585 ext. 2903 >> Fax: (858) 642-3836 >> [EMAIL PROTECTED] >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ICV_scatters.pdf Description: Adobe PDF document ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5
Hi Paul, Just as an aside, once you have a talairach_with_skull.lta file (whether from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), where the scale_factor employed is 2150. Incidentally, using the -eTIV option of mri_label_volume, you can also specify other transforms (e.g., talairach.xfm, talairach.lta) to be used used instead of the default talairach_with_skull.lta in computing "ICV". I've looked at the effect of using different transforms in a handful of brains, and "ICV" can vary a bit depending on transform you choose to use. I'm curious: Has anyone out there compared FS's ICV estimate to ICV estimated by another program? Best, Mike H. On Fri, 2008-06-20 at 14:35 -0700, Paul Greenberg wrote: > Hello Freesurfers, > > I am interested in comparing eTIV calculated with version 3.0.5 to > that calculated by version 4.0.5 (64 bit Cent OS). > > In order to compare eTIV for a single brain estimated in version 3.0.5 > to version 4.0.5, I copied a subject's previous freesurfer output > (v3.0.5) into the freesurfer version 4.0.5 folder, deleted all the > files within the "transforms" folder and carried out the following > procedures as outlined in the recon-all dev table: > > 1) Run the talairach procedure. Command = talairach_avi --i > mysubject --xfm talairach.auto.xfm > 2) cp talairach.auto.xfm talairach.xfm > 3) Run automatic failure detection. Command= talairach_afd -T 0.005 > -xfm talairach.xfm > 4) Create talairach_with_skull.lta. Command = > mri_em_register -skull nu.mgz > $freesurferhome/average/RB_all_withskull_2007-08-08.gca > talairach_with_skull.lta > 5) Check the new eTIV. Command = > mri_label_volume -eTIV talairach_with_skull.lta aseg.mgz 17 53 > As the aseg.mgz file exists from previous processing (versio > 3.0.5), and the talairach_with_skull.lta was re-created with the new > processing (version 4.0.5), the output of this command should list the > eTIV based on the new talairach transform? > > Are these procedures correct for generating new values of eTIV if that > is all i want? > > Thanks! > > -- > > Paul Greenberg, Ph.D. > Radiology Department, University of California, San Diego > VA San Diego Healthcare System (116A-13) > 3350 La Jolla Village Drive > San Diego, CA 92161 > Phone: (858) 552-8585 ext. 2903 > Fax: (858) 642-3836 > [EMAIL PROTECTED] > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5
Hello Freesurfers, I am interested in comparing eTIV calculated with version 3.0.5 to that calculated by version 4.0.5 (64 bit Cent OS). In order to compare eTIV for a single brain estimated in version 3.0.5 to version 4.0.5, I copied a subject's previous freesurfer output (v3.0.5) into the freesurfer version 4.0.5 folder, deleted all the files within the "transforms" folder and carried out the following procedures as outlined in the recon-all dev table: 1) Run the talairach procedure. Command = talairach_avi --i mysubject --xfm talairach.auto.xfm 2) cp talairach.auto.xfm talairach.xfm 3) Run automatic failure detection. Command= talairach_afd -T 0.005 -xfm talairach.xfm 4) Create talairach_with_skull.lta. Command = mri_em_register -skull nu.mgz $freesurferhome/average/RB_all_withskull_2007-08-08.gca talairach_with_skull.lta 5) Check the new eTIV. Command = mri_label_volume -eTIV talairach_with_skull.lta aseg.mgz 17 53 As the aseg.mgz file exists from previous processing (versio 3.0.5), and the talairach_with_skull.lta was re-created with the new processing (version 4.0.5), the output of this command should list the eTIV based on the new talairach transform? Are these procedures correct for generating new values of eTIV if that is all i want? Thanks! -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
