Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

Re: [Freesurfer] integrating FSL and Freesurfer
by noam Schneck 09 Oct '12

09 Oct '12

Hi Doug Here are more detailed versions of my first two questions. 1) I used tkmedit to look at the mean_func produced by a gfeat analysis of one subject's three functional runs overlayed onto the anatomical image produced by recon-all on that same subject(bert/mri/orig.mgz). The registration matrix I used was the anat2std.dat that was produced by running reg-feat2anat on all three of the feat analyses from the individual runs. When I did this I saw that the mean_func image was outside the boundaries of the anatomical image. Correspondingly, when I overlayed the zstat.nii.gz from the gfeat analysis onto the anatomical image I had activation outside of the anatomical image brain. 2) Originally, I ran BBR on a subject that I had run Recon-all for. I used BBR to register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat. I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto a T1 image that had been created by converting bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this time converting the orig.mgz to niftii. In both cases the example_func in T1 space image produced by ApplyXFM is rotated about 90 degrees and also inverted. This is viewed in fslview, The corresponding T1 images created by mri_convert are not. What can I do to allow me to use BBR's fsl.mat within ApplyXFM?

3 4

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://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 at >>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

3 5

Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15
by Sebastian Moeller 19 Jan '12

19 Jan '12

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it is set to 256 Colors you have your root cause, just switch to something higher and all should be fine. best Sebastian On May 9, 2010, at 9:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 May 2010 15:34:35 +0100 > From: Fred Dick <fdick(a)crl.ucsd.edu> > Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <873B33F2-3339-4871-9395-1EFEEC1EFAAB(a)crl.ucsd.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all > > This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] > > I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. > > Thanks, > Fred > > >

3 4

downsampling 4D volume
by ythomas 10 Jan '12

10 Jan '12

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

4 7

bug in surface-based area and volume
by Douglas N Greve 05 Oct '11

05 Oct '11

Hi Y'all, I recently found a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. I'm testing a fix now, but you should not use area or volume measures until I've posted the fix and you re-run either mris_preproc or qcache. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. I'll get back soon (next week) with the fix. Sorry for the inconvenience. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 2

thickness-age correlation
by Antonella Kis 22 Sep '11

22 Sep '11

Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age 2)what is the best iteration number for the simulation? Should be 5000 or 1000 or greater? 3)why when I run the simulation for 5 iterations I've got zero clusters? 4)can I derive the thickness from the significant clusters of glm analysis? Do I need to run QDEC after GLM? Thanks for any enlightenment. Antonella

2 18

recon-all steps necessary to get aseg.nii
by Jeff Eriksen 19 Sep '11

19 Sep '11

I would like to run FreeSurfer just up to the point it creates the aseg file, and no further. I believe this would be steps 1 through 11. Is there any way other than making a copy of the recon-all script and removing everything after step 11. Not sure I know exactly where this is. -Jeff

4 5

GLM or Qdec ?
by Antonella Kis 15 Sep '11

15 Sep '11

Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? 2). What sig.mgh represents? 3) What's the real significance of a cluster (how a cluster is formed)? 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? 8). Why when analysing with Qdec I get more clusters? Are this defining or representing the sig.mgh as in GLM? 9). When using Qdec were I can find as an output of results the number of clusters and the cortical thickness value? Thank you and have a great day! Antonella

3 13

hippo-subfield on longitudinally processed brains
by Wenger, Elisabeth 01 Sep '11

01 Sep '11

Dear freesurfer specialists, I am trying to run the very interesting hippocampus subfield segmentation on subjects that have already undergone the standard volumetric pipeline AND the longitudinal pipeline. I tried the command "recon-all –subjid <myid> -hippo-subfields". Unfortunately, i'm getting the following output message: "ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists." Can I just run the -hippo–subfields command on the already longitudinally processed brains, and simply include the flags "-long <tp1id> <templateid>" (without "-all") so freesurfer can use the long-directory as output (as it states in the error message)? Or do I have to run the -hippo–subfields command on the crosssectionally processed brains and include the flags "-long <tp1id> <templateid>"? Do I then also need to include the flag –all so that it will do the whole longitudinal processing again? Thank you very very much for your help! Cheers, Elisabeth ******************************* Dipl.-Psych. Elisabeth Wenger Predoctoral Research Fellow Center for Lifespan Psychology MPI for Human Development Lentzeallee 94, 14195 Berlin, Germany phone: +49-30-82406-427 web: http://www.mpib-berlin.mpg.de<http://www.mpib-berlin.mpg.de/>

2 2

Re: [Freesurfer] Paired analysis results into table?
by Braber, A. den 01 Sep '11

01 Sep '11

Hi, I just performed a paired analysis on my twin data. I am interested in the difference in cortical thickness between males and females, and have to run a paired analysis since the males and females in my sample are related (because they are twins). No covariate (such as age) has been included in the mri_glmfit yet, so I only have 1 contrast (mean.mtx = 1, meaning in my case males greater than females). After running the mri_glmfit I viewed my results using ' tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay $SUBJECTS_DIR/ sig.mgh'. Thereafter I corrected my results using FDR-correction, under View->Configure->Overlay->set threshold using FDR, rate 0.05 (so I did not perform a clusterwise correction for multiple comparison). Tksurfer than gives me a really nice overview of the significant results (FDR-corrected) of my paired analysis. I wondered whether there is a tool to export these results into a table (just like it's possible with aparc2table), so I get an overview of, for example, T-statistics, p-value and vertex number, for the observed significant clusters (or vertex with the highest T-value within an observed cluster). Is this possible? I have searched for a command to do this, but unfortunately I couldn't find it. Could you please help me? Thanks in advance. Anouk den Braber

2 2

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 August 2011