Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

LGI path problem
by Linn Mittlestein 05 Nov '13

05 Nov '13

Hi, I am trying to compute lgi measures, and I think my problem lies in the fact that the matlab path is not set correctly; it is calling an older version of matlab however I need it to point to matlab2013b. I have tried numerous things like changing the startup.m file, the .bashrc file and exporting the matlab path, however It keeps calling another version of Matlab. Can someone please tell me how exactly the path is set and where? Best Wishes and thank you, Linn

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mri_surf2vol questions
by Govindarajan, Koushik Athreya 05 Nov '13

05 Nov '13

Hello Freesurfers, I am trying to use mri_surf2vol to convert my thickness files into analyze/nifty format to use with a custom code. Is there a way I can write all output files from mri_surf2vol in axial format? Also, is there a way in FreeSurfer to combine these thickness files from both hemispheres? Thanks in advance Koushik

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glmfit for paired-diff on 2 groups
by Vivian R. Steiger 04 Nov '13

04 Nov '13

Dear FS-Experts, I would like to compare 2 Groups (Responder (N=19) vs. Non-Responder (N=11)) with longitudinal data. Participants from both groups had only 2 scan sessions in each case 10 weeks apart. So far is used the glmfit-variant with --paired-diff option in the first place. (based on http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis) The paired-fsgd contained then 2 classes (Responder, Non-Responder) which is used in glm-fit for comparison with the contrast (1 -1) for group diffs. This approach confirmed our hypothesized effects but I'm not sure whether I used the right strategy. Could you might help me with this issue? Thank in advance Best, Vivian

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mri_segstats url in 5.3.0 release notes does not exist
by Jonathan Harlap 04 Nov '13

04 Nov '13

The version of mri_segstats that fixes the issue where mri_segstats fails unless -autorecon3 is run returns a file not found at the url ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats. Is there a source that the release notes should refer to and which will not disappear, or can it be restored? Cheers, Jonathan

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Fwd: Qdec Questions
by Ashley Shurick 04 Nov '13

04 Nov '13

Great - and this would be true for all models? For example, in the attached graph, I'm looking at a region representing increased cortical thickness for one group compared to the other (orange blob, Q: "Does the average thickness differ between HC and SAD?" nuisance factor: mean thickness). From this plot it appears that SAD > HC, but based on your answer to the previous question I would think this region should represent HC > SAD. Can you please explain this? Thank you! On Wed, Oct 30, 2013 at 7:33 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > In your case you have HC listed first, so red/yellow means HC>SAD, blue > means SAD>HC > doug > > > > > > > On 10/29/2013 11:03 PM, Ashley Shurick wrote: > >> Hi Doug, >> >> Apologies, but I have a rather easy follow-up question that I can't >> figure out: >> >> How do you interpret the effect in each significant region? A previous >> post suggests using ctrl + left mouse click on a blob and examining the >> plot of the data. However, for the model I am looking at ("Does the >> thickness-ERQ correlation differ between HC and SAD?") I still can't >> determine if cortical thinning represents HC<SAD or SAD<HC. I'm attaching a >> representative plot here. >> >> Thank you, >> >> Ashley >> >> >> On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick < >> ashley.shurick(a)gmail.com <mailto:ashley.shurick@gmail.**com<ashley.shurick(a)gmail.com>>> >> wrote: >> >> Thank you! >> >> >> On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> >> On 10/29/2013 01:10 PM, Ashley Shurick wrote: >> > Hi all, >> > >> > I'm running analyses in Qdec and want to verify a few things: >> > >> > 1. When comparing two groups (HC vs patients) I am including >> mean >> > cortical thickness as a covariate, using the following equation: >> > >> > >> > bh.thickness = (lh.thickness*lh.surfarea + >> rh.thickness*rh.surfarea) / >> > (lh.surfarea + rh.surfarea) >> > >> > >> > Is this the best way to calculate global mean thickness? >> Yes >> > >> > >> > 2. I want to regress out any effects of age, therefore I need to >> > demean the ages for my groups as a whole, and not perform this >> > calculation on each group separately, correct? >> Yes, in which case the test of the difference between groups >> will be >> done at an age equal to the mean of the ages. >> > >> > 3. I'm including questionnaires as a covariate of interest - >> do I need >> > to demean these values as well? >> When you do a test on a continuous covariate, that test will be >> unaffected by demeaning of the covariate. Demeaning will >> affect the >> difference between groups if you use a separate covariate for each >> group. If you have a single covariate across groups, demeaning >> will have >> no effect. >> >> doug >> > >> > >> > Thank you in advance for your help! >> > >> > >> > Ashley >> > >> > >> > -- >> > Ashley A. Shurick >> > Ph.D. Candidate >> > Department of Psychology >> > Stanford University >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

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Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
by Roderick McColl 04 Nov '13

04 Nov '13

Hmmm, Actually using aseg.mgz works just fine (just tried this now), displays correctly on fslview. What I was really trying to do was convert aparc+aseg.mgz which does not provide the expected orientation in fslview. Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow? For the aparc_aseg_mni152.nii.gz output, 1) the coronal image in fslview (top left) has the S/I labels upside down compared to the coronal slice, (or the coronal slice upside down compared to the S/I labels) 2) the sagittal image (top right) has the same S/I issue 3) the axial image (bottom left) has the A/P labels the opposite of the image slice. Thanks for any advice -roddy ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Roderick McColl [Roderick.McColl(a)utsouthwestern.edu] Sent: Monday, November 04, 2013 3:37 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target I am obviously using mri_vol2vol incorrectly but I'm stumped. Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 space to do some fslmaths. >From looking around it seemed the command to accomplish this is (inside $SUBJECTS/fsaverage/mri) mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o asegmni152.nii.gz which does execute but if I load asegmni152.nii.gz into fslview all of the orthogonal views are upside down. There is something missing regarding the co-ordinate system but I'm not sure what. Can anyone point me in the right direction? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today. _______________________________________________ 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.

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tkregister2 and mri_label2vol
by Zhao Jingjing 04 Nov '13

04 Nov '13

Hi Doug, I asked a question a couple days ago for how to convert .label files into .nii files in freesurfer. At the end of this email, you can see the original email from me and your response. I tried to run the function mri_label2vol by myself. However, it seems not working quite well. In order to run mri_label2vol, it seems that I have to have a registration.dat file. I search online for how to generate it and get an answer from maillinglist posted by you several years ago. That is, I need to run the function of tkregister2. Then I tried to find out how to run tkregister2 and I found out an example suggested by you, although I don't know how it works because there is no information online for this function. Your example is like this: *tkregister2 --mov rawavg.mgz --targ aseg.mgz --regheader --reg rawreg.dat --noedit* I ran it and it successfully generated a rawreg.dat file, but I don't know if it is a correct file that I should use. Below is the results that I got from the command window: *tkregister_tcl /opt/freesurfer/lib/tcl/tkregister2.tcl target volume aseg.mgzmovable volume rawavg.mgzreg file rawreg.datLoadVol 0ZeroCRAS 0$Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $Diagnostic Level -1INFO: loading target aseg.mgz Ttarg: ---------------------1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000;INFO: loading movable rawavg.mgzTmov: -------------------- -0.900 0.000 0.000 100.799; 0.000 0.000 0.898 -115.000; 0.000 -0.898 0.000 115.000; 0.000 0.000 0.000 1.000;mkheaderreg = 1, float2int = 0Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) ---------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;--------------------------------------- ---- Input registration matrix ---------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;Determinant -1subject = subject-unknown RegMat ----------------------------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;* Then I tried to run the function of mri_label2vol. I specifically referred to the example posted online in freesurfer website. It seems to me that this is a popular function that a lot of people have used. My command line is as below: *mri_label2vol --label lh.words10_10.label --temp T1.mgz --reg rawreg.dat --fillthresh .5 --o lh.words10_10.nii* However, my command line didn't run successfully to generate the nii file that I want. The error message is "segmentation flaut". Here I attached all the results from the command window after I run this function. *Number of labels: 1lh.words10_10.labelAnnot File: (null)Template Volume: T1.mgzOutut Volume: lh.words10_10.niiRegistration File: rawreg.datFill Threshold: 0.5Label Vox Vol: 1ProjType: (null) ProjTypeId: 0ProjStart: 0ProjStop: 0ProjDelta: 0.1Subject: (null)Hemi: (null)UseNewASeg2Vol: 1DoLabelStatVol 0$Id: mri_label2vol.c,v 1.32 2009/10/22 23:35:53 greve Exp $ Template RAS-to-Vox: ---------1.000 0.000 0.000 128.000;-0.000 -0.000 -1.000 128.000;-0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000;Template Voxel Volume: 1nHits Thresh: 0.5 Loading registration from rawreg.datRegMat: ---------1.000 -0.012 -0.025 -0.000;-0.025 0.069 0.997 0.000; 0.010 -0.998 0.070 -0.000; 0.000 0.000 0.000 1.000;Label RAS-to-Vox: -------- 1.000 0.012 0.025 128.000;-0.010 0.998 -0.070 128.000;-0.025 0.069 0.997 128.000; 0.000 0.000 0.000 1.000;Allocating Hit Volume (16777216) voxelsnlabels = 1Loading lh.words10_10.label Thesholding hit volume.Segmentation fault* I was surprised by this result, because it tells me that "the template voxel volume is 1". How strange! And finally, no nii file was generated. Can you help check whether I did something wrong? Attachment I put the files that might be used for running these two functions (I didn't put T1.mgz and rawavg.mgz in this email since it makes the file bigger than 500K, but if you need it please let me know and I will send you the link from my dropbox). I might need to specify more parameters in the functions, which I didn't how to either. If you can supervise me for how to write the functions correctly, that would be really appreciated. And after I generate nii file, how can I visualize it and see how it matches the ROI from the .label file? I tried tksurfer "subject name" lh inflated, but it doesn't work. If I can get some instructions for this command, that would be also helpful. Thanks. Best, Jingjing Date: Tue, 29 Oct 2013 10:21:59 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] how to transfer .label file to .nii file To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <526FC487.6020601(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed You can use mri_label2vol to create a nii mask from the label. To map the label to the DTI space, register your DTI (b=0) to the anatomical using bbregsiter. You can then use mri_label2vol to transfer the label. doug On 10/28/2013 06:14 AM, Zhao Jingjing wrote: > Hi, > > Our lab have managed to generate ROIs in T1 images using Freesurfer, > which led to .label files. We succesfully measured the cortical > thickness in these ROIs for each subject in Freesurfer. Now we are > aiming to track white matter fibers from these ROIs in a tractography > software Trackvis. However, .lable files seem not be readable in > Trackvis. Thus, we are wondering if .label files can be tranferred to > .nii files easily in Freesurfer so that we can use the converted .nii > ROI files to track fibers in Trackvis. Another related question is how > can we coregister the ROIs drawn in T1 images with DTI images and make > sure that those ROIs converted from T1 images are the still in the > same regions in the DTI images? > > Thanks. > Jingjing Zhao > > Postdoc scientist > > Laboratoire de Sciences Cognitives et Psycholinguistique > > Departement d?Etudes Cognitives > > Ecole Normale Superieure > > 29 rue d?Ulm, 75230, Paris Cedex 05, France > > Tel: +33 1 44 32 26 57 > > Fax: +33 1 44 32 26 30

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convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target
by Roderick McColl 04 Nov '13

04 Nov '13

I am obviously using mri_vol2vol incorrectly but I'm stumped. Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 space to do some fslmaths. >From looking around it seemed the command to accomplish this is (inside $SUBJECTS/fsaverage/mri) mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o asegmni152.nii.gz which does execute but if I load asegmni152.nii.gz into fslview all of the orthogonal views are upside down. There is something missing regarding the co-ordinate system but I'm not sure what. Can anyone point me in the right direction? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today.

3 2

new version of mri_segstats
by Matura, Silke 04 Nov '13

04 Nov '13

Dear Freesurfer community, we are doing cortical thickness analyses with Freesurfer version 5.3.0 in a Linux environment. In order to do the autorecon-1 and autorecon-2 steps, we need to download the new version of mri_segstats. Unfortunately, the link on the Freesurfer Release Notes Webpage does not work. Also, we could not find mri_segstats on the ftp server: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… Could you tell us, where we can download the new version of mri_segstats? Thank you, Silke Dr. Dipl.-Psych. Silke Matura Department of Psychiatry, Psychosomatic Medicine and Psychotherapy Laboratory of Neurophysiology and Neuroimaging Johann Wolfgang Goethe University of Frankfurt Heinrich-Hoffman-Str. 10 60528 Frankfurt Germany Tel: 069 6301 7655 email: Silke.Matura(a)kgu.de

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Which boost version is used in CVS, mris_resample
by Martin Kavec 04 Nov '13

04 Nov '13

Hi guys, When running mri_cvs_register on linux (5.3.0), I get into problem with mris_resample, which cannot find libboost_programs_options.so.5. I installed the latest version of boost-1.52.0 for my system, but there are unresolved symbols. Which version is suitable for mris_resample? Thanks, Martin Sent from my iPad

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Freesurfer November 2013