Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

tracula failure
by Alena Piovar 21 Nov '14

21 Nov '14

Dear freesurfer experts, I am trying to run tracula but it fails on mri conversion of the data, it creates the nifty files from dicoms, but fails to produce bvec file where the problem could be? The terminal info as well as configuration file used for preprocessing is attached. Looking forward to your answer best regards Alena

2 1

prefrontal cortex label
by Anna Jonsson 17 Nov '14

17 Nov '14

Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna

3 5

Re: [Freesurfer] adding insula voxels
by Adam Mezher 06 Nov '14

06 Nov '14

I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks!

2 1

Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
by Matthew Riddle 06 Nov '14

06 Nov '14

Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo –E recon-all –s bert –all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. >From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt

4 11

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=>*

6 9

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 >> > >

3 3

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

3 8

Longitudinal prediction
by Alexandru Hanganu 31 Oct '14

31 Oct '14

Dear FreeSurfer Experts, How could the longitudinal analysis be performed in order to show whether a parameter at time 1 is predictive of changes in cortical thickness over time ? and can thecorresponding regions be shown in FreeSurfer ? In a statistical analysis, as we see it, we must perform the correlation between the parameter at time 1 and the cortical thickness difference (or ROI)time 2-time1, yet in this case we cannot see it on the cortex. Thank you, Alex

4 10

Re: [Freesurfer] adding insula voxels
by Adam Mezher 30 Oct '14

30 Oct '14

I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam

2 1

Converting lesion volume to surface area
by Timothy Meier 30 Oct '14

30 Oct '14

Hello, Previously we have used a lesion of 128 microliters and have filtered out anything smaller in volume than that for analyses (single subject "pothole" analysis). Now we want to do something similar on the surface. So we need to approximate the surface area of that 128 microliters when translated to group analysis surface (fsaverage). 128 microliters is 128 data points in 1x1x1 resolution. Let's say those data points only exist in the cortical ribbon volume. Question 1: How many of the 128 data points from cortical ribbon volume get translated into surface space? What is the volume to surface translation ratio? Question 2: Because we want to filter clusters with mri_surfcluster, we are interested in the resulting area of our original 128 lesion. Therefore, how much area is represented by each data point when translated onto the surface? Is this simply "AvgVtxArea" of the inflated surface multiplied by the number of data points that get translated from volume to surface? And what is the best way to answer these two questions from standard Freesurfer output: e.g. Should we calculate from the ("NumVert" "SurfArea" "GrayVol") columns of the lh.aparc.stats file, get the mean of all SurfArea/GrayVol from aparc.stats, and then multiple by our 128? Any thoughts or suggestions would be appreciated. Thanks, Tim

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Freesurfer October 2014