Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

DODS/DOSS
by Iris Frankenberg 10 Oct '13

10 Oct '13

Hi mailinglist, I have a question regarding DOSS/DODS. In the mailinglist I read that if you do a group analysis, you have to check for interaction between your continuous variable and categorical variable in DODS, and if there's no interaction, you can use DOSS. This however leaves a few questions regarding my analysis: I want to look at the correlation between cognitive performance and cortical thickness, accounting for gender, age and IQ. In a sense, this is not a 'real' group analysis, since gender is merely a covariate. Do I have to check for interactions, and if so, for which ones? "Does the cogn perf-thickness correlation differ between male and female?" "Does the age-thickness correlation differ between male and female?" (age = demeaned) Last but not least, at which Monte Carlo settings would you usually check for an interaction? As far as I understood from reading the mailinglist, I would think vertexwise threshold at 2, absolute (2 way), clusterwise threshold 1.3. Is this correct? Or would it for example make more sense to test 1 way (positive for cogn perf-thickness, negative for age-thickness)? Thank you very much, Iris

1 0

Processing Freesurfer thickness files in SPM for ANOVA
by Muhammad Naveed Iqbal Qureshi 10 Oct '13

10 Oct '13

Dear Experts, Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM for ANOVA testing? Waiting for a precise reply. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi(a)gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to

1 0

suggestion for wiki
by Ruth Carper 10 Oct '13

10 Oct '13

It would be really helpful if your Wiki had a page that collected all of the available commands (e.g. contents of /bin) and listed them with brief descriptions of their functions. Something like part 4 of the page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands (Might reduce the number of forum questions you get too). There are other commands listed on that page but without brief descriptions, you're forced to do quite a lot of additional navigation to determine what each command might do or else scan the contents of /bin for something that sounds like it might apply and then check the help output. If you could just collect the descriptions from the individual wiki pages or from the help sections of the code itself that would be great. There also seem to be a number of useful commands that aren't listed anywhere in the Wiki (mni152reg, fslregister, etc) so that a typical user has no idea they exist. --Ruth

1 0

Re: [Freesurfer] V1 Labels (fwd)
by krista kelly 09 Oct '13

09 Oct '13

Thanks Allison, So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that? Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch? Thanks so much for looking into this for me! Best, Krista On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < astevens(a)nmr.mgh.harvard.edu> wrote: > Hi Krista, > I took a look at your subject and think I have determined the problem. > Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the > talairach registration step failed. If you look at the talairach.xfm, > you'll see it is way off: > tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig > > But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm > to talairach.xfm and rerun from the -normalization step. > > You might also want to look at these instructions: > https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon> > > They might not all apply to you but could potentially. > Allison > > > > ---------- Forwarded message ---------- >> Date: Thu, 03 Oct 13 22:55:12 -0400 >> From: krista.kelly16(a)gmail.com >> To: fischl(a)nmr.mgh.harvard.edu >> Subject: V1 Labels >> >> Hey! >> >> Krista (krista.kelly16(a)gmail.com) has uploaded some files for you at >> the Martinos Center FileDrop: >> >> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** >> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4> >> > >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here is a zipped file of one of the subjects that I'm having label >> troubles with. The lh.v1.label isn't mapping correctly. I find the same >> goes for the aparc atlas as well (I haven't checked out anything else). If >> you could help me figure out why this is happening, that would be great! >> >> Thanks, >> Krista >> >> Please be aware, your upload will expire on December 31st. If you'd like >> to download these files, feel free to use the link below: >> >> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf> >> >> Cheers, >> The NMR Team >> >> >> >> >> > > 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 at > http://www.partners.org/**complianceline<http://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. > >

1 2

A function to write mgh files from R
by Heath Pardoe 09 Oct '13

09 Oct '13

Hi all, I've written a function that can write mgh files from R ( http://www.r-project.org/) Hopefully some of you will find it useful. It's more or less a translation of save_mgh.m. If you're looking for a function that can read mgh files into R, load.mgh.R is included in a package I wrote which can be found here: http://www.nitrc.org/frs/download.php/4629/cortex_0.1.tar.gz I recommend using load.mgh.R to read data in, only because save.mgh.R follows the same scheme within R for storing data. I'll include save.mgh.R in this package at some stage. If you run into problems with either of these let me know & I'll do my best to help. Code is pasted below between the lines below, copy this into a text file and save as "save.mgh.R" Example usage (in R): >my.surface <- load.mgh("hpardoe.lh.thickness.fsaverage.mgh") >my.surface$x <- rnorm(163842, mean = 3, sd = 0.3) # replaces thickness values with random noise >save.mgh(vol = my.surface, fname = "test.lh.mgh") you can then open "test.lh.mgh" in freeview. Best wishes Heath ---------------------------------------------- save.mgh <-function(vol,fname) { # R translation of save_mgh.m # written by Heath Pardoe, heath.pardoe(a)nyumc.org, 09/12/2013 MRI.UCHAR <- 0 MRI.INT <- 1 MRI.LONG <- 2 MRI.FLOAT <- 3 MRI.SHORT <- 4 MRI.BITMAP <- 5 MRI.TENSOR <- 6 slices <- c(1:256) fid <- file(fname,open = "wb", blocking = TRUE) width <- vol$ndim1 height <- vol$ndim2 depth <- vol$ndim3 writeBin(as.integer(1),fid,size = 4, endian = "big") writeBin(as.integer(width),fid,size = 4, endian = "big") writeBin(as.integer(height),fid,size = 4, endian = "big") writeBin(as.integer(depth),fid,size = 4, endian = "big") writeBin(as.integer(1),fid,size = 4, endian = "big") # HP note: I've ignored all the diffusion tensor stuff writeBin(as.integer(MRI.FLOAT),fid,size = 4, endian = "big") writeBin(as.integer(1),fid,size = 4, endian = "big") # dof = fread(fid, 1, 'int'); ## HP note: ignored ^this line^ from save_mgh.m UNUSED.SPACE.SIZE <- 256 USED.SPACE.SIZE <- (3*4+4*3*4) # space for ras transform unused.space.size <- UNUSED.SPACE.SIZE - 2 # ignored all the stuff about "M" - could probably do it if necessary so let me know #if (nargin > 2) ## fwrite(fid, 1, 'short') # ras.good.flag <- 0 # writeBin(1,fid,size = 2, endian = "big") # unused.space.size <- unused.space.size - USED.SPACE.SIZE ## fwrite(fid, sizes(1), 'float32') # xsize ## fwrite(fid, sizes(2), 'float32') # ysize ## fwrite(fid, sizes(3), 'float32') # zsize # # fwrite(fid, M(1,1), 'float32') # x.r # fwrite(fid, M(2,1), 'float32') # x.a # fwrite(fid, M(3,1), 'float32') # x.s # fwrite(fid, M(1,2), 'float32') # y.r # fwrite(fid, M(2,2), 'float32') # y.a # fwrite(fid, M(3,2), 'float32') # y.s # fwrite(fid, M(1,3), 'float32') # z.r # fwrite(fid, M(2,3), 'float32') # z.a # fwrite(fid, M(3,3), 'float32') # z.s # fwrite(fid, M(1,4), 'float32') # c.r # fwrite(fid, M(2,4), 'float32') # c.a # fwrite(fid, M(3,4), 'float32') # c.s #else # fwrite(fid, 0, 'short') # ras.good.flag <- 0 writeBin(as.integer(0),fid,size = 2, endian = "big") # } # writeBin(as.integer(rep.int(0,unused.space.size)),fid,size = 1) bpv <- 4 # bytes/voxel nelts <- width * height # bytes per slice writeBin(vol$x,fid, size = 4, endian = "big") close(fid) } --------------------------------------------- -- Heath Pardoe, PhD Research Scientist School of Medicine New York University 223 East 34th Street New York, NY 10016 Office: +1-646-754-5320 Cell: +1-347-285-1126 Skype: hpardoe https://sites.google.com/site/hpardoe/

1 0

Freesurfer Confidence Index
by Daniel Moadel 09 Oct '13

09 Oct '13

Dear Freesurfer friends, I am wondering if there is a confidence value or correction index for the volumetric data in aseg.stats. Thanks for your help! Daniel Moadel

2 3

Repost: pcc maps and mri_glmfit
by Caspar M. Schwiedrzik 09 Oct '13

09 Oct '13

Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? *Is the average r-value or z-value saved somewhere? *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar

2 18

sim ocn clusters mean effect size
by Kayle Sawyer 09 Oct '13

09 Oct '13

Hi, Using FS 5.3, I ran a group analysis with mri_glmfit-sim to identify clusters where my two groups differed (along with many other analyses, e.g. age slope for each group). For each cluster, I would like to see what the mean group difference is, in mm. So, I used this command: mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --annot fsaverage rh ./mc-z.th1.3.pos.sig.ocn.annot Unfortunately, mri_segstats looks in the wrong place for the annot file, prepending "$SUBJECTS_DIR/fsaverage/label/rh." instead of looking in my present GLM directory that I typed the command from. In comparison, if I manually create a label for one of the clusters from the ocn.annot, and use the label, mri_segstats works: mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --slabel fsaverage rh ./label.th1.3.neg/rh.cluster-001.label This time, it doesn't try to look under fsaverage, but uses the present GLM directory. Is there a way to override the SUBJECTS_DIR issue with --annot? I tried without the "./", and with specifying the absolute path, but it still pre-pended the "$SUBJECTS_DIR/fsaverage/label/rh." before the path. Or, should I just create labels for each analysis, run mris_segstats for each cluster, and then combine them all back together with grep? Thanks, -Kayle

2 1

Error with bbregister (using T2 to refine pial surface)
by Sophie Maingault 09 Oct '13

09 Oct '13

Dear FS experts, I'm trying to use T2 weighted image to refine the pail surface. I have this error message : ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation In release notes, I saw that in "known issues" : fslregister (and so bbregister with --init-fsl) requires that FSL be installed. This has been fixed. The fix will be in the next version. Ask for a patch if you need it before then. Could you send me this "patch" to perform my analyzes ? Thank you by advance. Sophie

2 1

Missing geometry information when converting lh.white using mris_convert
by Clive Wong 09 Oct '13

09 Oct '13

Dear Surfers, I am trying to create a ROI in freesurfer, and export surface ROI for FSL/ProbtrackX. I have successfully created label in the template, and use mri_label2label to map the label to different subjects. As suggested by FSL, I use mris_convert to convert the lh.white to Gifti mris_convert lh.white lh.white.gii echo LMOG.label > listOfAreas.txt label2surf -s lh.white.gii -o lh.LMOG.gii -l listOfAreas.txt After I failed to do ProbtrackX, I tried to visualize the gii surface in freesurfer, and it tells me: "Did not find any volume geometry information in the surface" So, I tried to check the mailing list and tried: mris_convert -t subj1 lh.white lh.white2.gii However, it's even worse... [image: Inline image 2] Red: original lh.white Green: mris_convert -t subj1 lh.white lh.white2.gii Blue: mris_convert lh.white lh.white2.gii Does anyone successfully used freesurfer surface to do FSL/ProbtrackX？ Any suggestions? Thanks, Clive

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