Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

mri_nu_correct.mni intensity correction problem
by Jeff Sadino 07 Oct '09

07 Oct '09

Hello, I asked this question a couple days ago, but never got an answer. Please excuse the double posting. I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right? Thank you! Jeff Sadino

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Smaller
by Jeff Sadino 07 Oct '09

07 Oct '09

Hello Surfers, I have a number of subjects that are displaying a large number of small holes in the superior region of their white matter. I believe the medical term for them is virchow-robin spaces. We would like to try to quantify the volume that these holes occupy. Is there any way to break down the Right-Cerebral-White-Matter and Left-Cerebral-White-Matter segmentation labels in aseg.mgz into finer regions so that we can quantify the volume of these holes? Or would it simply be easier to go through the volumes and manually label the holes as a label that is not being used? Thank you, Jeff Sadino

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watershed error...
by Gonzalo Rojas 07 Oct '09

07 Oct '09

Hi: I got the following error... How can I solve it ?... recon-all.log ----------------------------------------------------------------- mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=122 z=99 r=84 first estimation of the main basin volume: 2562881 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=103, y=120, z=70, Imax=255 CSF=17, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze main basin size=33359051 voxels, voxel volume =1.000 = 33359051 mmm3 = 33359.051 cm3 done PostAnalyze...Basin Prior 86 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=125, z=105, r=9959 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=52 , nb = 22212 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 1368 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1242 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=56 , nb = 9603 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=49 , nb = 9792 OTHER CSF_MIN=0, CSF_intensity=33, CSF_MAX=47 , nb = 207 mri_watershed Error: GLOBAL region of the brain empty ! Linux image 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 18:40:08 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Oct 7 15:29:31 CLT 2009 -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] How to calculate differences using the longitudinal data
by Martin Reuter 07 Oct '09

07 Oct '09

Hi Brian, when you use the longitudinal stream in FreeSurfer, it accounts for the 'relatedness' therefore the resulting information (e.g. segmentation labels, volume measures, thickness measures, surface locations etc. ) will be more accurate (on average) than if you'd just process the different time points independently (cross sectionally). Comparing the results after FreeSurfer is through will work exactly the same in both settings. You can compute what you are interested in (e.g. percent volume loss in left hippocampus by looking into the aseg.stats , or percent cortical thinning) per subject and then do a group analysis with your two groups. Best, Martin On Thu, 2009-10-01 at 14:39 -0400, Gogtay, Nitin (NIH/NIMH) [E] wrote: > Hi Martin + others, > > Thank you for your help on this. > > I am still a bit confused and maybe you can help me understand. So we have a sample of 12 patients + 12 controls and each with 2 scans (time 1 and time 2) thus total 48 scans. > > As suggested these have been processed using the longitudinal free surfer algorithm (Thanks for your help regarding troubleshooting during that as well) > > To compare the results between two time points (I assume slopes of subjects compared to those of controls? And intercepts?), how does one account for the 'relatedness' i.e. Same subject two time points? As it is now, wouldn't the free surfer treat the data as 'cross sectional' to calculate the slopes? > > Maybe i/we are missing something? > > Sorry for the bother and thank you again for the help! > > Nitin > > Nitin Gogtay, M.D. > Staff Clinician > Child Psychiatry Branch, NIMH > (301) 435 4494 > > ________________________________ > From: "Weisinger, Brian (NIH/OD) [E]" <Brian.Weisinger(a)nih.gov> > Date: Thu, 1 Oct 2009 14:26:23 -0400 > To: Nitin Gogtay <gogtayn(a)mail.nih.gov> > Subject: FW: [Freesurfer] How to calculate differences using the longitudinal data > > > ------ Forwarded Message > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Date: Wed, 30 Sep 2009 14:49:46 -0400 > To: "Weisinger, Brian (NIH/OD) [E]" <Brian.Weisinger(a)nih.gov> > Cc: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] How to calculate differences using the longitudinal data > > Hi Brian, > > after the longitudinal runs are through you have directories > tpN.long.base for each timepoint per subject. These contain the same > structure as the cross sectionally processed results, however the values > (e.g. thickness, volume etc. in the stat files) should be more > accurate. > > You can compare these results between timepoints in the same way you > would do that without the longitudinal stream. You just need to take the > more accurate information in the .long. directories instead. > > Best, Martin > > On Tue, 2009-09-29 at 14:59 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > > I have run the longitudinal stream on the scans I need, but now I am not sure what to use to compare the differences. > > If someone could clarify this for me I would really appreciate it. > > > > Thanks > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------ End of Forwarded Message > > >

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question about calculating total gray matter volume
by Mehul Sampat 07 Oct '09

07 Oct '09

Hi Folks, I was trying to compute the total gray matter volume and I wanted to check if I was using the correct procedure. I looked at the "Morphometry Stats" page for this issue (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats?highlight=%28gray…) The instructions say that: gm volume = pial volume - white volume My question is: to get the total pial volume, it is correct to use: mris_volume rh.pial and mris_volume lh.pial For the white matter volume I am using mris_wm_volume <subject> <hemi> Thanks Mehul

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cortical thickness estimation w/ grey matter segmentation apriori
by Elisa Dell'Oglio 07 Oct '09

07 Oct '09

Hi all, I have a question regarding cortical thickness estimation in freesurfer. I was wondering whether it is possible to input in freesurfer the gray matter segmentation as an a priori. Specifically, I run freesurfer on a set of cases on which I previously run spm and obtained a good discrimination between GM, WM and CSF. I would like to use these segmentation instead to proceed with manual edits on freesurfer segmentation output for gray matter segmentation, that sometimes was not segmented correctly. Would this be possible? Thanks a lot, Elisa

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show only thalamus segmentation
by asaf achiron 07 Oct '09

07 Oct '09

Hi group, i am using for visualisation this commend: tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt However, i would like to view *only* the thalamus. how can i do that? thank you, Asaf

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Binary files not executable
by Andrew Jahn 07 Oct '09

07 Oct '09

Hello, I recently installed FreeSurfer on one of my laptops running Ubuntu and get the following error when I attempt to run tkmedit: Exec format error. Binary file not executable. I thought I remembered something about setting a soft link for one of the libraries in Ubuntu. Am I on the right track here? Thank you, -Andrew

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tkmedit "save main volume as.." option...
by Gonzalo Rojas 07 Oct '09

07 Oct '09

Hi: I do all the steps of the "Manual Editing" process that appears in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, but the "save main volume as.." option appears in gray (off)... Why ?... I thought it might be a access permission related issue, but it was not... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Error message
by Weisinger, Brian (NIH/OD) [E] 07 Oct '09

07 Oct '09

This error message came up when running the base run with the notal check...any ideas how to fix this problem? imgrege: no voxels in register ERROR: 'imgreg_4dfp /Applications/freesurfer/average/711-2C_as_mni_average_305 /Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 3335' failed! status=254 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin CHP-MP2.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Tue Oct 6 17:33:24 EDT 2009

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