Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by Kathy Zhang 11 Nov '08

11 Nov '08

Hello, I've recently started a project that involves measuring the volume of the hippocampus and other subcortical structures, so I was also wondering whether aseg.stats was more accurate or wmparc.stats. So far the difference between them appears to be approximately a hundred voxels for each right/left hippocampus. Thank you, Kathy Zhang '09 On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi <nneyzi(a)gmail.com> wrote: Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats? On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Actually, the construction of aparc+aseg and wmparc do use info about where > the surface is to refine the aseg cortical boundaries. This information is > stored in ribbon.mgz (and it overrides the aseg definition). At some point, > we will use the surfaces to directly refine the aseg boundaries. > > doug > > > > > Michael Harms wrote: > > Hi Chris, > Doug, please correct me if I'm wrong, but the original gm/wm > segmentation contained in aseg.mgz is based on the 3D volume-based > tissue segmentation. This original segmentation then forms the basis > for all subsequent additional segmentations of either GM or WM in the 3D > volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the > surface based parcellation, but only to decide the most appropriate > label to assign to GM/WM as defined in the already existing volume-based > segmentation that is contained in aseg.mgz. > > Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on > the 3D volume segmentation, there is no apriori reason that their > spatial extent will correspond precisely to the more accurate gray and > white mattes surfaces that come out of the surface-based processing > stream. (Although certainly we would hope that the discrepancies don't > become too large). > > cheers, > Mike H. > > On Thu, 2008-07-17 at 12:00 -0500, bell0368(a)umn.edu <mailto:bell0368@umn.edu> wrote: > > > I have sent two images created with the following commands. > > tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white > -segmentation (aparc+aseg.mgz and wmparc.mgz) > $FREESURFER_HOME/FreesurferColorLUT.txt > > The wm segmenations go through the "main surface" and the "orig surface" > into the gray matter, for example in the rh-supramarginal and > rh-postcentral. From your last response I am unsure as to which pipeline > creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) or > the surface-based pipeline (i.e. ribbon.mgz) or some combination of the > two. It seems to me that the gm/wm parcellations are created using the > surface pipeline and then transferred to the closest class-matched voxels > from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg > segmentations. I guess the question is how are we getting from the surface > parcellations back to volume space; is there a binary? > In a related vein, the value from aseg.stats "surface-based-volume mm3 > lh-cerebral-white-matter" seems to be created with mri_segstats or is it > from mris_wm_volume? Thanks for all your help! > > Chris Bell > > > > > > On Jul 17 2008, Doug Greve wrote: > > > > When the volume is created, a decision has to be made at each voxel as > to what to classify it as. This is used when the aseg.mgz and > ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from > these files. When using mri_segstats with --pv, it will take the > volume of a 1mm3 voxel and divide it up so that it can contribute to > more than one region. But there's not a way to put the partial volume > information into the segmentation itself. Not sure why that do not > appear alingned, but we've been recently looking into this for other > reasons. Can you send a pic.? > > doug > > > > On Wed, 16 Jul 2008, bell0368(a)umn.edu <mailto:bell0368@umn.edu> wrote: > > > > I was wondering how the calculations of the wm volume were performed as > well. The six values below are volume values from aseg I believe. I > assume mris_wm_volume does more than sub-divide these regions into the > wm parcellations, but probably also includes partial volume estimations > along the wm/gm surface, is this correct? I basically have the same > question for the gm volume values in aparc.stats; do they include > partial volume calculations from the gm/pial and gm/white borders? Which > binary is used to create these values for gm in aparc.stats... is it > mri_segstats (with --pv)? I was assuming it would be an mris (surface) > calculation as well. I am asking because if you use tkmedit to view the > ?h.surface files and load the aparc+aseg or wmparc segmentation volumes > in also, the surfaces and the segmentations don't seem to line up. Is > there a way to create a segmentation volume that includes > partial-volumed voxels at the gray/white and gray/pial boundries? Thanks > for your help. > > Chris Bell > > > > > the interior voxels are only included in the volume if they are one of > the following in the aseg.mgz: > > case Left_Cerebral_Cortex: > case Right_Cerebral_Cortex: > case Left_Cerebral_White_Matter: > case Right_Cerebral_White_Matter: > case Left_WM_hypointensities: > case Right_WM_hypointensities: > > cheers, > Bruce > > > > On Tue, 15 Jul 2008, Marin Richardson wrote: > > OK, so aparc.stats is better for cortical gray matter. I want to look > at the > parcellated white matter volumes as well - is the only/best option to > use the > wm volumes from wmparc.stats? > > Also, when using mris_wm_volume to calculate total white matter, I > saw the > result defined as the volume within the white matter surface minus > non-WM > structures? Can you tell me which regions are and are not included? > > Marin > > > > > Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> > > It is better to use the aparc as it is derived from surface > measurements, which have sub-voxel resolution. The wmparc.stats are > generated by counting 1mm^3 voxels. > > doug > > Marin Richardson wrote: > > > Hi all, > > I noticed that the gray volumes for parcellated cortical regions > in > wmparc.stats are different from those for the same region in > aparc.stats (e.g. > ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = > 9466 in > lh.aparc.stats). Why are the values different and which one is a > better > measure to use? > > Thanks, > Marin > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Segmentation fault
by Nurunisa Neyzi 11 Nov '08

11 Nov '08

Hi I am getting the following error while running auto-recon2. ... Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Tue Nov 11 01:32:03 EST 2008 /localA/nneyzi/MLS2/PedBirnPipeline_20081103_014127/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 -- label_right_ribbon 42 --save_ribbon --save_distance PedBirnPipeline_20081103_01412 7 SUBJECTS_DIR is /localA/nneyzi/MLS2 Segmentation fault Linux ped-birn.med.cornell.edu 2.6.18-53.1.13.el5xen #1 SMP Mon Feb 11 13:41:50 ES T 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Nov 11 01:45:44 EST 2008 What does it mean?

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cortical and subcortical segmentation
by abel cruz vadell 11 Nov '08

11 Nov '08

Hi I have done the three recon-all process in my data and now I will check the thalamus segmentation. Can the changes in the thalamus boundaries that I will draw affect the cortical thickness measures generated in the recon-all steps? And changes in cortical boundaries structures like cuneus or precuneus? Thanks Abel

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Re: [Freesurfer] segmentation region export
by vin 10 Nov '08

10 Nov '08

thanx bruce, Now in the list, last time I didn't looked at To, and CC. FreeSurferColorLUT.txt file. I just tried, 1032 ctx-lh-frontalpole, this is also same, 0 voxel. FreeSurferColorLUT.txt ( 999 SUSPICIOUS 255 100 100 0) , so this means, after this entry.. all the listed regions are not yet included ? . Infact I wanted to use these segmented thalamas regions, and now when they are not there, I thought to take (frontal cortex, posterioparietal, occiptal, motor, temporal regions ) and put them in FSL diffusion based connectivity analysis, to segment thalamus according to connectivity. But I am not able to locate all these regions nicely, in FreeSurferColorLUT.txt file. sorry, just wana ask some very basic questions. Is aseg.mgz only source to get regions out ?, and FreeSurferColorLUT.txt for label info ? should I use anything else, to get these regions. regards, vin On Tue, Nov 11, 2008 at 12:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: no, the aparc+aseg.mgz has some as does the wmparc.mgz. You should send these questions to the list so Doug, Nick et al. can answer > > >> On Mon, Nov 10, 2008 at 11:46 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu>wrote: >> >> yes, they are in there because we intend to do them and have started >>> messing around, but nothing serious yet >>> >>> On Mon, 10 Nov 2008, vin wrote: >>> >>> Thank you for prompt reply. >>> >>>> >>>> I was looking this file, and there was listing of thalamic nuclei, so I >>>> thought it does. >>>> >>>> $FREESURFER_HOME/FreeSurferColorLUT.txt >>>> >>>> >>>> :) >>>> have a nice day !! >>>> vin >>>> >>>> On Mon, Nov 10, 2008 at 11:23 PM, Bruce Fischl >>>> <fischl(a)nmr.mgh.harvard.edu>wrote: >>>> >>>> Hi Vin, >>>> >>>>> >>>>> we don't currently segment any thalamic nuclei, although hope to do so >>>>> in >>>>> the future. >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> On Mon, 10 Nov 2008, vin wrote: >>>>> >>>>> *Hi Doug, * >>>>> >>>>> >>>>>> >>>>>> *Greetings!! * >>>>>> >>>>>> complete thalamus ROI extraction works, but when I tried segmented >>>>>> thalamic >>>>>> nuclei, than output file doesn't contain anything. >>>>>> >>>>>> *>mri_binarize --i aseg.mgz --match 8001 --o thalamus_nuclei_fs.nii* >>>>>> >>>>>> this how output looks like : >>>>>> >>>>>> input aseg.mgz >>>>>> frame 0 >>>>>> nErode3d 0 >>>>>> nErode2d 0 >>>>>> output thalamus_nuclei_fs.nii >>>>>> Binarizing based on matching values >>>>>> nMatch 1 >>>>>> 0 8001 >>>>>> binval 1 >>>>>> binvalnot 0 >>>>>> Found 0 values in range >>>>>> mri_binarize done >>>>>> >>>>>> >>>>>> should I choose some other file expect aseg.nii.gz ? to get thalamic >>>>>> nuclie >>>>>> . >>>>>> >>>>>> >>>>>> >>>>>> thank you very much !! >>>>>> >>>>>> vin >>>>>> >>>>>> * >>>>>> * >>>>>> >>>>>> >>>>>> On Tue, Nov 4, 2008 at 4:42 PM, Doug Greve <greve(a)nmr.mgh.harvard.edu >>>>>> >>>>>> wrote: >>>>>>> >>>>>>> >>>>>> They are in aseg.mgz, you can extract them into a nifti file with >>>>>> >>>>>> >>>>>>> mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii >>>>>>> >>>>>>> 251 is the code for CC Posterior (found in >>>>>>> $FREESURFER_HOME/FreeSurferColorLUT.txt) >>>>>>> >>>>>>> doug >>>>>>> >>>>>>> >>>>>>> vin wrote: >>>>>>> >>>>>>> hi, >>>>>>> >>>>>>> I am trying to export segmented regions as NIFTI, and it works for >>>>>>> the >>>>>>> regions like Thalamus whole. But when freesurfer finished autorecon, >>>>>>> than >>>>>>> it showed lot of sub regions for example : Thalamic sub regions and >>>>>>> also >>>>>>> CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum) >>>>>>> and...Mid >>>>>>> anterior and Anterior. >>>>>>> >>>>>>> How I can get these sub regions. In which files they are stored, and >>>>>>> How >>>>>>> I >>>>>>> can extract them as NIFTI format. >>>>>>> >>>>>>> any suggestion would be great !! >>>>>>> >>>>>>> thank you very much , >>>>>>> >>>>>>> vin >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps:// >>>>>>> mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Centergreve(a)nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> In order to help us help you, please follow the steps in: >>>>>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >>

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segmentation region export
by vin 10 Nov '08

10 Nov '08

hi, I am trying to export segmented regions as NIFTI, and it works for the regions like Thalamus whole. But when freesurfer finished autorecon, than it showed lot of sub regions for example : Thalamic sub regions and also CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum) and...Mid anterior and Anterior. How I can get these sub regions. In which files they are stored, and How I can extract them as NIFTI format. any suggestion would be great !! thank you very much , vin

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analysis
by b9403208 10 Nov '08

10 Nov '08

Hi, I have some problem about analysis with QDEC. 1) How can I get the information about analysis, like T value, cluster threshold, and so on? 2) What threshold setting (uncorrected or corrected) is Freesurfer used? Thanks a lot! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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analysis
by b9403208 10 Nov '08

10 Nov '08

Hi, I have some problem about analysis. 1) How can I get the information about analysis, like T value? 2) What threshold setting (uncorrected or corrected) is Freesurfer used? Thanks a lot! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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scan of 2.6 mm thicknes with overlap of 50-70 %
by asaf achiron 09 Nov '08

09 Nov '08

Dear Group we have acquired some MRI scan with an axial 3dfspgr with 2.6 mm thickness and an overlap of 50-70 %. thus the r reconstructed thickness is 1.3 mm. is the reconstructed scan suitable for analyses in freesurfer? can we use the scan with the 2.6 thickness and overlap also? thank you Asaf

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inflated surface
by Nurunisa Neyzi 08 Nov '08

08 Nov '08

Hello, I just wanted to ask what you think makes this inflated surface look somewhat wrong in the occipital lobe? (Or is it OK?) I attached the figure. Thanks a lot ! -Nurunisa-

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fslcalc.fsl
by Akram Bakkour 07 Nov '08

07 Nov '08

Hello, Thanks for adapting fslcal.fsl to work on surfaces Doug. This is very helpful. It was working for me until today. I'm working on thigpen. setenv SUBJECTS_DIR /space/brich_004/users/akram/HRDEV_processing mri_surf2surf --srcsubject 03222007_4TT_clindem47 --sval \ 03222007_4TT_clindem47/surf/rh.thickness --trgsubject HRDEV197_1mm \ --tval 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.mgh --hemi rh mri_surf2surf --s HRDEV197_1mm --sval \ 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.mgh --tval \ 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.fwhm15.mgh --fwhm 15 \ --hemi r mri_surf2surf --s HRDEV197_1mm --sval HRDEV197_1mm/surf/rh.thickness --tval HRDEV197_1mm/surf/rh.thickness.fwhm15.mgh --fwhm 15 --hemi rh fscalc.fsl HRDEV197_1mm/surf/rh.thickness.fwhm15.mgh -sub \ 03222007_4TT_clindem47/surf/rh.thickness_to_HRDEV197.fwhm15.mgh \ HRDEV197_1mm/surf/tp1_min_tp2.thickness.mgh --surf HRDEV197_1mm rh I get the following error: ** ERROR: nifti_convert_nhdr2nim: bad dim[1] ** ERROR (nifti_image_read): cannot create nifti image from header 'HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1.nii.gz' ** ERROR: nifti_image_open(HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1): bad header info Error: failed to open file HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1 Cannot open volume HRDEV197_1mm/surf/tmp.fscalc.fsl.23248/s1 for reading! It's weird, because I did exactly the same thing with a different subject tp1 and tp2 two days ago and it worked great! Thanks for the help! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

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Freesurfer November 2008