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Hi all,
I am computing volumetry using freesurfer using two different runs.
1. I just use recon-all -all, and then look at the aseg.stats file.
2. I ran recon-all only to the 12th step where gca labeling is done. It doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats.
I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these?
Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12?
Thank you!
Ruifeng
There is not enough information to understand what you did in #2
On 8/30/2022 3:56 PM, Ruifeng Dong wrote:
External Email - Use Caution
Hi all,
I am computing volumetry using freesurfer using two different runs.
I just use recon-all -all, and then look at the aseg.stats file.
I ran recon-all only to the 12th step where gca labeling is done.
It doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats.
I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these?
Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12?
Thank you!
Ruifeng
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for pointing that out. The step numbers are those from section 5 in https://secure-web.cisco.com/1MvjYJiIaIHWh8caycAJQMG2vD_09oIjJWD1kFpdpLGaLJq...
On Tue, Aug 30, 2022, 6:16 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is not enough information to understand what you did in #2
On 8/30/2022 3:56 PM, Ruifeng Dong wrote:
External Email - Use CautionHi all,
I am computing volumetry using freesurfer using two different runs.
I just use recon-all -all, and then look at the aseg.stats file.
I ran recon-all only to the 12th step where gca labeling is done. It
doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats.
I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these?
Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12?
Thank you!
Ruifeng
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1nbDpNGhlO8S2mJqYzslOHhceoHNXymcQ5InPEtzkoaBHTm... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/16W4w5rco4KczASit5D4JyFZruG-ABKPiMhwl1p6RWW53SG... < https://secure-web.cisco.com/16W4w5rco4KczASit5D4JyFZruG-ABKPiMhwl1p6RWW53SG... .
External Email - Use Caution
For clarification of the problem, here is the volumetry results from two methods. Thanks.
*Using recon-all -all* *Using recon-all -motioncor -nuintensitycor -talairach -normalization -skullstrip -gcareg -canorm -careg -rmneck -skull-lta -calabel, then copy aseg.auto.mgz to aseg.mgz, then recon-all -segstats* *% diff between two methods* StructName Nvoxels Volume_mm3 Nvoxels Volume_mm3 Left-Lateral-Ventricle 6108 6462.2 6044 6402 *-0.931571291510628* Left-Inf-Lat-Vent 362 407.9 383 434.2 *6.44765873988723* Left-Cerebellum-White-Matter 13750 14452.3 14084 14743.6 *2.01559613348741* Left-Cerebellum-Cortex 53088 52492.3 53277 52750.1 *0.4911196499296* Left-Thalamus-Proper 9099 8847.6 9070 8850.9 *0.0372982503729743* Left-Caudate 3720 3711.6 3724 3702.5 *-0.2451772820347* Left-Putamen 4796 4891.1 4389 4582.1 *-6.31759726850811* Left-Pallidum 2132 2093 2636 2487.7 *18.8580984233158* 3rd-Ventricle 815 847.6 800 864.2 *1.95847097687589* 4th-Ventricle 2420 2597.3 2448 2602.7 *0.207908212374375* Brain-Stem 22048 21733.5 21895 21613.2 *-0.553523362550897* Left-Hippocampus 4389 4269.4 4387 4295.7 *0.616011617557507* Left-Amygdala 1593 1598.9 1610 1609 *0.631684282944519* CSF 958 995.5 903 941.7 *-5.4043194374686* Left-Accumbens-area 390 434.3 401 438.8 *1.03615012664057* Left-VentralDC 4385 4218.8 4326 4143.3 *-1.78960841945577* Left-vessel 31 50.3 23 35.3 *-29.8210735586481* Left-choroid-plexus 627 523.1 578 481.7 *-7.9143567195565* Right-Lateral-Ventricle 6720 6886.1 6542 6750.9 *-1.96337549556354* Right-Inf-Lat-Vent 386 400.5 385 400.5 *0* Right-Cerebellum-White-Matter 17274 17314.7 18327 18388.2 *6.19993415999122* Right-Cerebellum-Cortex 53923 54008.8 53382 53457.4 *-1.02094473493209* Right-Thalamus-Proper 8675 8371 8476 8166.2 *-2.44654163182416* Right-Caudate 3921 3837.1 3892 3831.2 *-0.153761955643587* Right-Putamen 4846 4871.4 4892 4865.3 *-0.125220675781078* Right-Pallidum 1996 1930.2 1979 1943.3 *0.67868614651331* Right-Hippocampus 4392 4342.9 4432 4386.7 *1.00854267885515* Right-Amygdala 1634 1624.8 1648 1631.1 *0.387740029542095* Right-Accumbens-area 698 699.9 702 693.2 *-0.957279611373044* Right-VentralDC 4465 4175.2 4451 4191.3 *0.385610270166707* Right-vessel 21 34.9 7 13.1 *-62.4641833810888* Right-choroid-plexus 557 522.4 630 577.8 *10.6049004594181* 5th-Ventricle 0 0 0 0 WM-hypointensities 733 717.9 759 730.8 *1.79690764730464* Left-WM-hypointensities 0 0 0 0 Right-WM-hypointensities 0 0 0 0 non-WM-hypointensities 0 0 0 0 Left-non-WM-hypointensities 0 0 0 0 Right-non-WM-hypointensities 0 0 0 0 Optic-Chiasm 242 271.4 215 240.3 *-11.4591009579956* CC_Posterior 1087 986.8 1068 969.3 *-1.77340899878395* CC_Mid_Posterior 767 710.9 769 711.8 *0.126600084400053* CC_Central 574 536.1 565 521.7 *-2.68606603245663* CC_Mid_Anterior 621 579.5 629 576.1 *-0.58671268334771* CC_Anterior 1110 1022.8 1107 1010.9 *-1.1634728197106*
On Tue, Aug 30, 2022 at 6:28 PM Ruifeng Dong ruifeng14@gmail.com wrote:
Thanks for pointing that out. The step numbers are those from section 5 in https://secure-web.cisco.com/1cb81WIHjn9vzqtpw06azMhbd16PJB6Hm9anNcjMaa54lab...
On Tue, Aug 30, 2022, 6:16 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is not enough information to understand what you did in #2
On 8/30/2022 3:56 PM, Ruifeng Dong wrote:
External Email - Use CautionHi all,
I am computing volumetry using freesurfer using two different runs.
I just use recon-all -all, and then look at the aseg.stats file.
I ran recon-all only to the 12th step where gca labeling is done. It
doesn't generate the aseg.mgz file but only aseg.auto.mgz. I assumed that they are the same and ran the -asegstats step to get the output in aseg.stats.
I noticed there are differences between the above two runs on the same image. Firstly, the volumes of WM, GM and ICV are not there from the 2nd run. How does this happen? In which step does Freesurfer compute these?
Secondly, the volumes of some subcortical structures are also different between the two runs. Does Freesurfer make corrections to the volume segmentations after step 12?
Thank you!
Ruifeng
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1shIPXUVhNZG4T_PQySmg-Ei2WC8Uq1jLWB82lywpWh3hci... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1jnMUfv0vQdpDSuCYwJ7aP6zfumGPlulWCWp1Kl85Nt4XOL... < https://secure-web.cisco.com/1jnMUfv0vQdpDSuCYwJ7aP6zfumGPlulWCWp1Kl85Nt4XOL... .
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Ruifeng Dong