Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

longitudinal data processing
by Robby De Pauw 04 Nov '14

04 Nov '14

Dear FS-experts Is there any command that I can use for caching my preprocessed data in the recon-all longitudinal stream, since this is possible through adding the -qcache option in the cross-sectional pipeline. Or maybe this is already automatically done without adding any option to the command? Thank you Greeting Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Fwd: Underinclusion of Gray Matter
by Christina Chen 04 Nov '14

04 Nov '14

Hi, Are there any ways to fix underinclusion of gray matter cortical edges when the white matter is fine? Attached is a picture. Thanks, Christina

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permission denied
by Ali Radaideh 04 Nov '14

04 Nov '14

Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- *Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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mri_watershed -brain_atlas undocumented?
by tvg[fs] 03 Nov '14

03 Nov '14

Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for "-atlas". Does the "-brain_atlas" flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 > mri_watershed --version stable5

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registering coronal images
by Mahmoud 03 Nov '14

03 Nov '14

Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend to use for this case ? Does MIN152_T1_0.5mm work better or MIN152_T1_2mm ? Thank you, Mahmoud

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Re: [Freesurfer] Question
by Tanev, Kaloyan,M.D. 03 Nov '14

03 Nov '14

Hi, I just took the FreeSurfer course. I am using the command reconall -s <subj_ID> -i <t1w> -all. Frequently, because I log on remotely to the server and because of the time that it takes, the terminal disconnects and therefore the process is not complete entirely. Can you point me to a way to redo just the steps that have not been done yet. I give an example of the latest files generated, with just a few files missing. How do I direct it to pick up from where it left? Thank you. Here is the list of files generated: drwxrwsr-x 2 ktanev schiz 80 Oct 31 14:06 orig/ drwxrwsr-x 3 ktanev schiz 1.0K Oct 31 21:39 transforms/ -rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.auto.mgz -rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 21:31 aseg.auto_noCCseg.label_intensities.txt -rw-rw-r-- 1 ktanev schiz 257K Oct 31 21:38 aseg.auto_noCCseg.mgz -rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.finalsurfs.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.auto.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.mgz -rw-rw-r-- 1 ktanev schiz 395K Oct 31 15:33 ctrl_pts.mgz -rw-rw-r-- 1 ktanev schiz 145K Oct 31 21:49 filled.mgz -rw-rw-r-- 1 ktanev schiz 12K Oct 31 14:12 mri_nu_correct.mni.log -rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 mri_nu_correct.mni.log.bak -rw-rw-r-- 1 ktanev schiz 1.5M Oct 31 15:33 norm.mgz -rw-rw-r-- 1 ktanev schiz 5.6M Oct 31 14:12 nu.mgz -rw-rw-r-- 1 ktanev schiz 3.6M Oct 31 20:32 nu_noneck.mgz -rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:07 orig.mgz -rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 orig_nu.log -rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:08 orig_nu.mgz -rw-rw-r-- 1 ktanev schiz 19M Oct 31 14:07 rawavg.mgz -rw-rw-r-- 1 ktanev schiz 119 Oct 31 21:45 segment.dat -rw-rw-r-- 1 ktanev schiz 5.5M Oct 31 14:16 T1.mgz -rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 16:35 talairach.label_intensities.txt -rw-rw-r-- 1 ktanev schiz 214 Oct 31 15:30 talairach.log -rw-rw-r-- 1 ktanev schiz 214 Oct 31 21:08 talairach_with_skull_2.log -rw-rw-r-- 1 ktanev schiz 214 Oct 31 14:52 talairach_with_skull.log -rw-rw-r-- 1 ktanev schiz 463K Oct 31 21:48 wm.asegedit.mgz -rw-rw-r-- 1 ktanev schiz 464K Oct 31 21:48 wm.mgz -rw-rw-r-- 1 ktanev schiz 507K Oct 31 21:47 wm.seg.mgz

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correction for pial surface errors (not dura)
by Vincent Beliveau 03 Nov '14

03 Nov '14

Hi everyone, Now and then I see some pial errors where the pial surface is not pushed far enough or has some kind of dent in it (see attache figure). As far as I know, there's no way in FS to correct for this. It would be great to be able to specify some kind of control point to force FS to include identified voxels within the cortical ribbon. Is there something like this already existing or an alternative fix to this kind of problem? Thanks, Vincent.

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applying manual freesurfer edits to warped brain image
by David Grayson 02 Nov '14

02 Nov '14

Hi freesurfer experts, I have two T1 images from the same subject acquired at the same time point. One of the images is distortion corrected using a calibration phantom, put through the full freesurfer pipeline and then extensively manually edited. The uncorrected image has had zero processing. What I would like now is to have the freesurfer segmentations on the uncorrected image and preserve as much as possible the manual edits. In other words, I would like to warp the surface meshes already obtained on the distortion corrected image to the uncorrected image. Is there already a suggested method that is optimal for this purpose? Thanks in advance for any advice! -David

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Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
by Lars M. Rimol 02 Nov '14

02 Nov '14

Hi Bruce (and Jorge), Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface. To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that. In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample. Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface, and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects. On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area? As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer: I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model. Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are. Thank you! LMR yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway > Bruce Fischl > <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Sat, > 06 Sep 2014 07:00:14 -0700 > <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> > > Hi Lars > > > which surface are you using? If it's the white surface you might try looking > at white matter volume to see if it is decreasing > > cheers > Bruce > > On Sat, 6 Sep 2014, Lars M. Rimol wrote: > > > Hi, > > I have performed a longitudinal analysis using the lme module in FreeSurfer, > with this model: > > intercept(random effect) + centered age + group + group x centered age + sex > > I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. > Dependent variable is area. > > Here, mapping the second beta means mapping the effect size for (change > over) time. In the beta map, I find values from 0 to 0.004. I would > interpret that to mean that local area shrinks by at most 0.004 mm² per year > in the reference group. But I'm not 100% sure about the biological (or > geometrical) meaning of that. > > Can I interpret this literally as the mean yearly shrinkage of the three > triangles surrounding a given vertex, the average of whose area comprises > the area score of the vertex, being 4/1000 mm? Of course, these maps are > smoothed with 30mm, so the real spatial resolution is nowhere near this.... > > > Thank you! > > > -- > yours, > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > yours, > > Lars M. Rimol, PhD > Norwegian University of Science and Technology (NTNU) > Trondheim, > Norway > > On Mon, Oct 27, 2014 at 9:59 AM, Lars M. Rimol <larilin(a)gmail.com> wrote: > >> Hi Bruce (and Jorge), >> >> Yes, it's the wm surface. I have also done the analyses with the pial >> surface and the results are similar to wm surface (attached p-maps: >> lh_0-1000_wmarea_s30_log10p_inflated_lateral.tif vs. >> lh_0-1000_wmarea_s30_log10p_inflated_lateral.tif). >> >> To your second question: White matter volume increased over this time >> period (lme analysis; controls: logP = 8.49, patients: logP = 6.34). >> >> Since the cortical analyses were done using lme, which can handle missing >> data, some of the subjects have only one time point. So I created a >> difference map for >> those subjects for whom we have data on both time points, to see if area >> on the first time point is consistently larger than on the second time >> point. Almost all subjects >> showed larger values on tp1 than tp2 and the maps of average area change >> (across subjects) confirm that (attached file: >> lh_diff_vo-v2_rawdata_lateral.tif shows timepoint1 - timepoint2). >> In addition, I ran an lme analysis with the same subjects and found >> results very similar to those for the entire sample (attached file: >> lh_2tp_01000_pmap_lateral.tif ). >> >> Would you agree that this apparent reduction in cortical area seems >> plausible? There is a reduction over time in raw data, and pial surface >> area show the same trend as wm surface, >> and the lme analysis with only subjects that have data on both time >> points shows very similar results as the lme with all subjects. >> On the other hand, I suppose we wouldn't expect increased wm volume >> together with reduced area? >> >> As for the effect size maps, I have worked on finding a way to represent >> change in area over time that is intuitive for a reader not familiar with >> FreeSurfer: >> I figured one solution could be to log transform the dependent variable >> (wm or pial area). This way the significance tests are done with log >> transformed data and for purposes of illustration >> I do exp(beta)*100-100 on the beta for time, which ensures that if there >> is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I >> find this is a good way of demonstrating the >> effects (attached figure: >> lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think? >> >> I could of course also transform the dependent variable into percentages. >> That is, baseline == 100 and tp2 expressed in percent of baseline. However, >> I find this to be a less attractive solution because >> we basically lose the baseline values, and this makes the model less >> useful for all other purposes. For instance, we can't investigate group >> differences at the various time points within the model. >> Perhaps more importantly, it's unclear what assumptions we are making. >> The lme assumes a normal distribution and it's unclear to me what the >> distribution of such ratios are. >> >> >> Thank you! >> >> LMR >> >> >> --------------------------------------------------------------------------------------------------------------------------------------------------------- >> Douglas N Greve Tue, 09 Sep 2014 08:24:37 -0700 >> >> This is tough to interpret, but basically, yes it would be >> 0-.004mm2/year. It is not quite right to say that it is at that vertex >> because of smoothing, but in that area. It is also hard to say what the >> total change would be for a cluster. One could sum the changes over the >> cluster vertices, but that would probably over-estimate the change. >> doug >> >> Hi Lars >> >> which surface are you using? If it's the white surface you might try >> looking at white matter volume to see if it is decreasing >> >> cheers >> Bruce >> >> On Sat, 6 Sep 2014, Lars M. Rimol wrote: >> >> Hi, >> >> I have performed a longitudinal analysis using the lme module in >> FreeSurfer, >> with this model: >> >> intercept(random effect) + centered age + group + group x centered >> age + sex >> >> I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. >> Dependent variable is area. >> >> Here, mapping the second beta means mapping the effect size for >> (change >> over) time. In the beta map, I find values from 0 to 0.004. I would >> interpret that to mean that local area shrinks by at most 0.004 mm² >> per year >> in the reference group. But I'm not 100% sure about the biological (or >> geometrical) meaning of that. >> >> Can I interpret this literally as the mean yearly shrinkage of the >> three >> triangles surrounding a given vertex, the average of whose area >> comprises >> the area score of the vertex, being 4/1000 mm? Of course, these maps >> are >> smoothed with 30mm, so the real spatial resolution is nowhere near >> this.... >> >> >> Thank you! >> >> >> -- >> yours, >> Lars M. Rimol, PhD >> St. Olavs Hospital >> Trondheim, >> Norway >> >> _______________________________________________ >> >> yours, >> >> Lars M. Rimol, PhD >> Norwegian University of Science and Technology (NTNU) >> Trondheim, >> Norway >> > >

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White matter volume
by Alshikho, Mohamad J. 31 Oct '14

31 Oct '14

Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad

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