Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] nonlinear models in longitudinal analysis
by Jodie Davies-Thompson 13 May '14

13 May '14

Hi Martin, Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new to this!). Do you mean something like this? For examining an increase between timepoint 1 and 2, but the same between timepoint 2 and 3? fsid fsid-base years years-to-years Day1 base 0 0.4 Day2 base 0.4 0.4 Day3 base 0.8 0 All the best, Jodie Message: 6 Date: Fri, 09 May 2014 16:52:25 -0400 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] nonlinear models in longitudinal analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <536D4009.7030907(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Jodie, 'years' should contain the real time between time points (usually, unless you have test-retest where time is irrelevant, or different task that can be ordered as you like). For what you are trying to do you should use linear mixed effects models with a piecewise linear setup. This will allow you to estimate a slope before and after timepoint 2 and compare those slopes. Your design matrix would probably have the column of 1, years and a column with years-years(at tp2 of that subject) if that value is positive 0 otherwise Testing if the coef of the 3rd column is > 0 is asking if the slope increases in the second interval. Not exactly what you want, but close and of course you can test if the slope in interval 1 is different from zero (second column) and if the slope in interval 2 is different from zero ( 0 1 1, ie the sum of the last two columns). Best, Martin On 05/08/2014 03:48 PM, Jodie Davies-Thompson wrote: > Dear Freesurfer experts, > > I am attempting to do a longitudinal analysis of cortical thickness with 3 timepoints. So far, I have successfully completed the analysis for long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to timepoint 3, and a linear increase for timepoint 1 to 2 to 3. > > However, I am primarily interested in finding regions which show a) an increase between timepoint 1 and 2, but no difference between 2 and 3, and b) no difference between timepoint 1 and 2, but an increase between 2 and 3. > > Would the correct way of 'modelling' these two in the qdec file be: > > a) > fsid fsid-base years > day1 base 0 > day2 base 3 > day3 base 3 > > and b) > fsid fsid-base years > day1 base 0 > day2 base 0 > day3 base 3 > > All the best, > Jodie > > - > --- > Jodie Davies-Thompson, Postdoctoral Fellow > Department of Ophthalmology & Visual Sciences > UBC/VGH Eye Care Centre > 2550 Willow Street > Vancouver, BC, V5Z 3N9 > Canada > Tel: 604-875-4111 ext 69003 > - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003

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Re: [Freesurfer] Viewing functional data on the inflated brain
by Sherryse Corrow 13 May '14

13 May '14

Hi Douglas, I don’t receive any emails from anyone, I only receive the the digest which is what I “reply” to. So I am not sure what you mean by “try responding to the email that I sent.” This is why I attempted to email you directly as I thought that is what you were asking for. I hope to have straightened things out by finding each part of our conversation and pasting them below (in reverse order). If you have further questions, please let me know. Sincerely, Sherryse Message: 9 Date: Fri, 09 May 2014 17:36:36 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Viewing functional data on the inflated brain To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <536D4A64.5000400(a)nmr.mgh.harvard.edu<mailto:536D4A64.5000400@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed both of what? Sorry, it looks like the thread was garbled below or somehow the digest got into it. Try responding to the email that I sent to keep things in order On 05/09/2014 05:09 PM, Sherryse Corrow wrote: Thanks Douglas. Yes, both of those exist. Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 07 May 2014 12:51:02 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> It is looking for subject P143 in /usr/local/freesurfer/subjects Does it exist? If so, does /usr/local/freesurfer/subjects/P143/mri/brainmask.mgz Exist? Sherryse Corrow<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 07 May 2014 11:00:54 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Thanks Douglas. We tried that . . . The registration matrix that we need is not created. Here is the output log file (attached). I am a bit new to this so I am hoping it has the information you need. After taking a quick glance at the log file, we noticed there are errors in the log file. Step by step, this is what we did after we ran recon-all: Reg-feat2anat ‹feat OurFeatDirectory.feat ‹subject P143 When we open the folder experiment.feat/reg/freesurfer, there is no anat2exf.register.dat file. However, there is a file called: anat2exf.register.dat.init. Thanks, Sherryse Douglas Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 19:58:31 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Run reg-feat2anat. If that does not work, then send the command line and terminal output. Just saying that something does not work will not get you closer to a solution. We need to know what you did and what happened Doug Sherryse Corrow<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 16:56:58 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi all, Earlier today, I posted the message listed below. However, we discovered part of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat file created. Therefore, we have no registration matrix to use. Before, we were inadvertently using the anat2std file instead. Any suggestions on how to get the anat2exf.register.dat file created? Thanks, Sherryse Douglas Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 19:50:18 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Can you tell us specifically what you have done? I mean command lines … doug Sherryse Corrow<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 15:58:35 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Dear FreeSurfer community, We are having some issues registering our functional data (or masks) from FSL to an inflated brain in FreeSurfer. Some of our masks, when registered to the inflated brain and viewed in FreeSurfer, are not showing up on the cortical surface. We have followed web-tutorials for registration but are still having the issue. Any suggestions?

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mri_surf2surf
by Caka 13 May '14

13 May '14

Dear Doug and All, I want to register the individual subject surface into the fsaverage surface. I used mdi_surf2surf command. But one error occurred. Could you please help me with this. Here are the scripts: ————————————————————————————————————————————————————————— [root@localhost sub001]# mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.img srcsubject = sub001 srcval = thickness srctype = curv trgsubject = fsaverage trgval = ./sub001-thickness-lh.img trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /disk250/data_analysis/data_female_male_140/sub001/surf/lh.sphere.reg Loading source data Reading curvature file /disk250/data_analysis/data_female_male_140/sub001/surf/lh.thickness Reading target surface reg /disk250/data_analysis/data_female_male_140/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (132230) Reverse Loop had 21224 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 146822, nTrgMulti = 17020, MnTrgMultiHits = 2.247 nSrc121 = 93121, nSrcLost = 0, nSrcMulti = 39109, MnSrcMultiHits = 2.35099 Saving target data Saving to ./sub001-thickness-lh.img ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 ————————————————————————————————————————————————————————————— Thank you very much! Qiongmin

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Subcortical volume calculation from aparc+aseg.mgz?
by Schreiber, Stefanie 13 May '14

13 May '14

Dear all, For the evaluation of the subcortical volumes we executed ‘mri_segstats’ on ‘aseg.mgz’ and for comparison on ‘aparc+aseg.mgz’ in a number of individuals. Apparently the volume of subcortical structures, like the hippocampus, is calculated as the same values if calculated (without partial volume correction) from ‘aseg.mgz’ and ‘aparc+aseg.mgz’. However, when partial volume correction is applied, the resulting values for e.g. hippocampal volumes differ between the ‘mri_segstats’ calculation for ‘aseg.mgz’ and ‘aparc+aseg.mgz’. How could those differences resulting from the partial volume correction in these cases be explained? The command used to calculate the subcortical volumes with partial volume correction was: mri_segstats --seg ./mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum ./stats/my.test.stats --pv ./mri/norm.mgz Previously we have been using the subcortical volumes from ‘aseg.stats’, which, as I understand it, is generated by recon-all from ‘aseg.mgz’ via ‘mri_segstats’ (with partial volume correction). From your experience, would it be also valid to use subcortical volumes generated by applying ‘mri_segstats’ (with partial volume correction) on ‘aparc+aseg.mgz’, even though the resulting values might differ from the values in aseg.stats? Thank you very much in advance, Steffi Schreiber

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Fwd: extracting rois for connectivity analysis
by Jutta Ernst 13 May '14

13 May '14

Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta

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Re: [Freesurfer] LOOK FOR HELP
by 刘东博 13 May '14

13 May '14

Dear Greve Thank you for your reply I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?

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Quesion about lobar volumes
by pfotiad＠nmr.mgh.harvard.edu 13 May '14

13 May '14

Hi FS Community, I created a lobes annotation file with the --lobesStrict flag of the mri_annotation2label and then converted it to a volume with the mri_label2vol command and the --annot flag. However, the resulting volume is just overlapping on top of the white surface, and not on the whole cortex. Is there a way to create a volume for the lobes that covers the whole cerebral cortex? That is a volume that shows you which part of the cerebral cortex belongs to each of the 6 lobes individually? Thank you in advance, Panos

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Re: [Freesurfer] NHP surface reconstruction in FS5.3
by S.V.Shepherd [work] 13 May '14

13 May '14

I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough? Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint. stephen Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...(a)gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>

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bbregister surf2vol
by 刘东博 13 May '14

13 May '14

Dear Freesurfer I want to use surf2vol to get volume files of gray thickness.And the --volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. So I use bbregister.Why I need not invert the BBR registration matrix with surf2vol?I mean , the BBR registration matrix is functional to anatomial volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?

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how to save an intensity contour?
by Burke, Sarah 13 May '14

13 May '14

Hello, I am using the intensity contour tool for defining a white/gray matter border of my ROI. I can adjust my ROI according to this contour and save it. However, the contour itself is not saved (to the same layer as the ROI) and will not be loaded when opening the ROI layer again later. Is there a possibility to save the contour (maybe to an extra layer)? Thank you very much! Sarah

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