Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Brining Freesurfer colomaps and/or lookup table to MRIcron
by Dorian P. 17 Jun '14

17 Jun '14

Dear Freesurfers, Is there a way to bring the colormaps of Freesurfer to MRIcron. Right now when I bring parcellations in MRIcron there is no good way to distinguish parcels, because the parcels are numerated 1000+ for left hemisphere, 2000+ for right, 3000+ for white matter left, etc. This makes MRIcron to color all 1000 with the same color, all 2000 with another, etc. Any suggestion would be welcome. Dorian TJU

1 0

Number of Slices
by Caroline Lewis 17 Jun '14

17 Jun '14

Hi, I want to perform recon-all on four different structural sequences for the same participant. Three of the sequences have the same number of slices, whereas the T1 has fewer slices, so when I input the different sequences with the recon-all command, I get the following error: ERROR: inputs have mismatched dimensions! Is there a way to bypass this or make each sequence have the same number of slices? And if so, will this affect data quality? Many thanks, Caroline

2 7

problem of Label file
by 王康程 17 Jun '14

17 Jun '14

Hi all, I create a label file according to my result using QDEC, does it correct? why some number is so large? #!ascii label , from subject vox2ras=TkReg 260 963 -9.181 41.343 -47.222 0.0000000000 1515 -9.022 44.425 -43.083 0.0000000000 1516 -7.070 45.386 -46.312 0.0000000000 3485 -8.162 46.694 -42.879 0.0000000000 3486 -8.111 44.955 -44.755 199456282314100703232.0000000000 3487 -7.235 47.186 -44.476 0.0000000000 6341 -10.194 40.795 -45.508 0.0000000000 6342 -11.386 38.884 -45.964 0.0000000000 6343 -10.382 39.516 -47.765 0.0000000000 7376 -9.101 42.821 -45.101 0.0000000000 7377 -8.073 43.300 -46.733 0.0000000000 7378 -6.918 43.647 -48.225 0.0000000000 9843 -6.168 47.599 -45.963 72719596043655881627927828234240.0000000000 9844 -5.895 45.704 -47.732 0.0000000000 9845 -5.637 43.852 -49.553 0.0000000000 11163 -7.843 48.753 -41.943 0.0000000000 11165 -7.775 47.849 -42.800 0.0000000000 11166 -7.714 46.949 -43.690 0.0000000000 11167 -7.323 48.099 -43.592 0.0000000000 14408 -9.705 41.086 -46.381 0.0000000000 14409 -10.290 40.137 -46.625 53662309296634309728540819456.0000000000 14410 -9.770 40.413 -47.487 0.0000000000 16216 -9.565 42.537 -44.238 0.0000000000 16218 -7.607 45.184 -45.549 0.0000000000 16219 -8.091 44.116 -45.733 0.0000000000 16220 -7.558 44.327 -46.514 0.0000000000 16221 -7.511 43.491 -47.498 0.0000000000 16222 -6.993 44.507 -47.260 0.0000000000 18751 -11.537 38.329 -47.146 0.0000000000 18752 -12.021 37.968 -46.208 0.0000000000 22043 -6.312 48.554 -45.102 0.0000000000 22048 -5.765 44.771 -48.637 0.0000000000 23621 -8.623 41.563 -48.026 0.0000000000 23622 -9.215 40.651 -48.313 0.0000000000 24705 -8.577 45.552 -42.973 0.0000000000 24706 -8.583 44.702 -43.932 0.0000000000 24707 -8.134 45.816 -43.803 0.0000006824 24708 -7.659 46.059 -44.607 0.0000000000 24709 -7.151 46.280 -45.383 0.0000000000 30157 -10.777 39.826 -45.730 0.0000000000 30158 -10.900 39.219 -46.881 0.0000000000 30159 -11.019 38.650 -48.053 0.0000000000 30160 -9.829 39.773 -48.612 0.0000000000 30161 -10.467 38.928 -48.923 0.0000000000 32636 -10.096 41.492 -44.414 0.0000000006 32637 -9.636 41.794 -45.297 0.0000000000 32638 -9.142 42.066 -46.150 0.0000000000 32639 -8.592 43.875 -44.920 0.0000000000 32640 -8.603 43.076 -45.933 0.0000000000 32641 -8.615 42.306 -46.970 0.0000000000 32642 -8.055 42.510 -47.754 0.0000000000 32643 -7.464 42.677 -48.499 0.0000000000 32644 -6.842 42.806 -49.203 70680060550261023833231196160.0000000000 39765 -6.836 48.334 -44.361 0.0000000000 39766 -6.720 47.403 -45.234 0.0000000000 39767 -6.608 46.477 -46.128 0.0000000000 39769 -6.030 46.648 -46.840 0.0000000000 39770 -6.500 45.560 -47.041 0.0000000000 39771 -6.395 44.656 -47.968 0.0000000000 39772 -6.292 43.768 -48.910 0.0000000000 39773 -6.191 42.896 -49.864 1198670724329189084508911654928384.0000000000 41883 -7.634 48.885 -42.342 0.0000000000 41884 -7.808 48.301 -42.368 0.0000000000 41885 -7.593 48.430 -42.767 0.0000000000 41886 -7.553 47.976 -43.199 0.0000000000 41887 -7.369 48.557 -43.161 0.0000000000 45128 -9.447 41.219 -46.806 0.0000000000 45129 -9.738 40.745 -46.932 0.0000000000 45130 -9.472 40.874 -47.353 16928685348014293778432.0000000000 46935 -9.255 43.868 -43.144 0.0000000000 46937 -9.041 44.013 -43.576 0.0000000000 46938 -7.343 45.288 -45.935 0.0000000000 46939 -7.582 44.753 -46.029 0.0000000000 46940 -7.311 44.852 -46.411 0.0000000000 46941 -7.280 44.421 -46.892 0.0000000000 46942 -7.031 44.945 -46.784 0.0000000000 54728 -8.332 41.659 -48.414 0.0000000000 54729 -8.626 41.203 -48.560 0.0000000000 56535 -8.366 46.121 -42.923 0.0000000000 56536 -8.360 45.686 -43.391 0.0000000000 56537 -8.147 46.253 -43.337 0.0000000000 56538 -7.479 47.070 -44.086 0.0000000000 56539 -7.686 46.502 -44.145 0.0000000000 56540 -7.443 46.620 -44.539 0.0000000000 56541 -7.409 46.172 -44.999 4742407148412851825182397956096.0000000000 56542 -7.192 46.732 -44.927 0.0000000000 66263 -10.427 40.638 -45.059 0.0000000000 66264 -10.714 40.144 -45.164 0.0000000000 66265 -10.483 40.307 -45.618 0.0000000000 66266 -10.337 39.822 -47.192 0.0000000000 66267 -10.592 39.675 -46.752 0.0000000000 66268 -10.645 39.373 -47.327 0.0000000000 66269 -10.960 38.930 -47.464 273757759681993900032.0000000000 66270 -10.697 39.079 -47.907 0.0000000000 Wang Kangcheng

2 1

Tracula preprocessing error ( set dob0 = 1 )
by Elia S. 17 Jun '14

17 Jun '14

Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line: trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config It stops, giving me errors like these: niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz While setting "dob0 = 0" everything runs smoothly. Can you help me please? I'll attach the log + dmrirc (tracula.config) Best,Elia. -------------------------------------------------------------------------------------------------------------- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

2 6

pial edits near cerebellum and problems in sagittal view
by Elissa McIntosh 16 Jun '14

16 Jun '14

Hi, I'm new to manual editing and I'm noticing some potential problems in my data. There are several sagittal slices that seem to be showing the dura as gray matter. Also, by the cerebellum, I cannot tell if non gray matter is being included. There are some dips by the cerebellum (especially on outer edges in screen shot) and I'm not sure if that area should be included. I have attached screen shots of these potential problems. Please let me know if you have advice on what to do in both cases. I want to avoid over editing. Thank you.

3 2

template registration and wm edits
by Walton, Matt 16 Jun '14

16 Jun '14

Hello Freesurfer experts, I have two separate questions. 1. I am doing an MRI study on young children (3-5 years old). I have read in a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template. 2. When I do white matter edits, they seem to be getting overwritten when I rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line recon-all -s subject -autorecon2 -autorecon3 I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this. Greatly appreciate any help with this Matt

2 3

Announcing PySurfer version 0.5
by Michael Waskom 16 Jun '14

16 Jun '14

Hello everyone, We are pleased to announce the release of PySurfer <http://pysurfer.github.io/> version 0.5. PySurfer is a Python library for making beautiful and reproducible visualizations of Freesurfer data. Changes in this version include - The statistical overlay functions can now use a wider variety of colormaps, with any matplotlib colormap <http://matplotlib.org/examples/color/colormaps_reference.html> (including the "_r" reversed versions) accepted. - Surface normals are used when rendering the cortex for a smoother visualization. - Changed the default colormap for some functions to more perceptually appropriate options. - Added control over the width of label and annotation borders. - Added 2D grids of images when saving a montage. Additionally, we have substantially improved the docs with a new example gallery <http://pysurfer.github.io/examples/index.html> and an updated installation guide <http://pysurfer.github.io/install.html> describing how to get over some hurdles that can be encountered on OSX. To install or upgrade, just run: pip install -U pysurfer We hope you find it useful. As always, contributions, suggestions, and bug reports are welcome on our github page <https://github.com/nipy/PySurfer/>. - PySurfer Devs

1 0

Re: [Freesurfer] Linear Mixed Models in FS‏
by jorge luis 16 Jun '14

16 Jun '14

Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age (might be a random effect too) + Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(random effect) + centered age + group + group x centered age + sex the fourth coefficient is the interaction term that represents the difference in slope between the patient and control groups. This is easy to see from your Question 1 equations. It's also easy to see from those equations that [0 1 0 0 0] tests the effect of time in the control group since the group-specific slope is only equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge >________________________________ > De: Lars M. Rimol <lmr1999(a)hotmail.com> >Para: jorge luis <jbernal0019(a)yahoo.es> >CC: Ørjan Bergmann <orjan.bergmann(a)gmail.com> >Enviado: Lunes 16 de junio de 2014 8:25 >Asunto: RE: Linear Mixed Models in FS‏ > > > > >Hi Jorge, > >I have a couple of questions which I hope you can assist us with. We have run some analyses with the model you kindly assisted us with in previous e-mails: > >intercept(random effect) + centered age + group + group x centered age + sex > >We have two groups in these analyses; one control group and one patient group (Case 1), denoted 0 and 1 respectively. > >1) If we have more than two groups (Controls, Case 1 and Case 2), in the context of GLM we would model it like this: >Group variable 1, Group variable 2 >0 0 <-- Control >1 0 <-- Case 1 >0 1 <-- Case 2 > >Would a scheme like this be appropriate in the context of lme? In other words, do we use two columns with three groups (with controls as implicit baseline), three columns with four groups etc. Or are we supposed to have just one group column in your lme software, where the groups would be denoted by labels, e.g. 'ctrl','case1','case2' etc. (or by 1,2,3,4....)? > >2) We are a little puzzled by the following contrast vectors and their interpretations. Given the model above, in a previous e-mail you wrote (in red): > >Question 1: Is there a significant interaction between time and group? >Slope group1 (group covariate=0): coefficient of centered age >Slope group2 (group covariate=1): coefficient of centered age + coefficient of group x centered age >Contrast: [0 0 0 1 0] > >This contrast would seem to ask the question: In which regions of the cortex is there an effect of centered age for Case 1 and no effect for controls? Is this the correct interpretation? > >If you want to test if the volume tend to increase within group1 then test the coefficient (slope) of centered age>0 >Contrast: [0 1 0 0 0] > >Why would this contrast yield only the effect of time for group 1 (which we assume is the control group == 0) and not for both groups? Since the second column of the design matrix contains centered age for all subjects, regardless of group, wouldn't this contrast yield the effect of time irrespective of group? > >And finally: If Question 1 not significant then both groups have the same slope otherwise you can test the coefficient of centered age + coefficient of group x centered age > 0 >Contrast: [0 1 0 1 0] > >I have tested both 0 1 0 0 0 and 0 1 0 1 0and I get very similar results for cortical surface area (figures attached). So the question is how do I interpret this. It seems to me, although I may have misunderstood, that you're saying that 0 1 0 0 0 tests the effect of time in the control group and 0 1 0 1 0 tests the effect of age in the patient group Case 1. But I don't understand why 0 1 0 0 0 doesn't test the effect of time in both groups. > >And also, if 0 1 0 0 0 is the effect of time only in the control group, wouldn't 0 -1 0 1 0 (or 0 1 0 -1 0) be a better test of interaction? > > >Thank you! > >yours, >LMR > > > > > >________________________________ >Date: Wed, 11 Jun 2014 19:09:51 +0100 >From: jbernal0019(a)yahoo.es >Subject: Re: Linear Mixed Models in FS‏ >To: lmr1999(a)hotmail.com > > >This is the standard linear mixed-effects statistical procedure, so yes it's valid and correct. Lme and SStat (a toolbox for survival data analysis) are now on github: > > >https://github.com/NeuroStats > > > >I'll update them when I have time. > > >Best >-Jorge > > > > > > > > > > >>________________________________ >> De: Lars M. Rimol <lmr1999(a)hotmail.com> >>Para: jorge luis <jbernal0019(a)yahoo.es> >>Enviado: Miércoles 11 de junio de 2014 13:40 >>Asunto: RE: Linear Mixed Models in FS‏ >> >> >> >>Hi Jorge, >> >>I just wanted to check with you whether this procedure is OK for analyses of cortical data. I use: >> >>lme_mass_fit_vw.m >> >>and then >> >>lme_mass_F.m >> >> >>I do not use any of the Regrowth functions. I know regrowth is more advanced but is the procedure I have used here valid? >> >> >>Thank you! >> >>LMR >> >> >> >> >> >>________________________________ >>Date: Mon, 28 Apr 2014 20:30:47 +0100 >>From: jbernal0019(a)yahoo.es >>Subject: Re: Linear Mixed Models in FS‏ >>To: lmr1999(a)hotmail.com >> >> >>Hi LMR >> >> >>1- The effect size is usually equivalent to the absolute value of the Beta coefficient you test in your contrast for being different from zero. >> >> >>2- The residual vector r at each vertex/voxel can be computed as: >> >> >>r = y - X*Beta >> >> >>where y is the vertex/voxel data, X is the design matrix and Beta is the estimated population regresion coefficients at that vertex/voxel. >> >> >> >>Best >>-Jorge >> >>El Lunes 28 de abril de 2014 9:32, Lars M. Rimol <lmr1999(a)hotmail.com> escribió: >> >> >>>Hi Jorge, >>> >>> >>>1) I'm looking for a way to obtain effect size estimates from the lme longitudinal analyses. So for instance, for the effect of time in a model that is: >>> >>>intercept(random effect) + centered age + group + group x centered age + sex >>> >>>With a contrast vector that is [0 1 0 0 0] I would like to obtain a corresponding effect size measure. >>> >>>2) I would like to calculate the residuals from a linear mixed model. The residuals are part of the output from lme_fit_FS but it doesn't seem to be part of the output from lme_FSfit, lme_mass_fit_vw, or lme_mass_fit_Rgw. Could you please explain how I can calculate the residuals using values in the stat struct output from lme_mass_fit_vw? >>> >>> >>>Thank you! >>> >>> >>>LMR >>> >>> >>> >> >> > >

1 0

Vol stats of precentral gyrus
by Hugh Pemberton 16 Jun '14

16 Jun '14

Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh

3 5

registration of functional data to inflated brain
by Sherryse Corrow 16 Jun '14

16 Jun '14

Hi Douglas, This worked. Thank you so much! Just in the knick of time as the presentation is Wednesday! For anyone having issues of reg-feat2anat not producing register.dat or anat2exf.register.dat . . . The link below should solve your problem! Best, Sherryse Message: 19 Date: Mon, 16 Jun 2014 12:42:54 +0200 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Messages not appearing on Mail Archive To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <539ECA2E.8020709(a)nmr.mgh.harvard.edu<mailto:539ECA2E.8020709@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-1" Hi Sherryse, sorry for the delay, I've been traveling. I think the problem may be with your version of reg-feat2anat. I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat Copy that into $FREESURFER_HOME/bin (after making a backup of the one that is there) let me know if that does not work doug -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer