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30132 discussions

Re: [Freesurfer] Easiest way to resample a volume..?
by Rudolph Pienaar 16 Oct '13

16 Oct '13

Thanks, Jon -- although the '-ds' seems depreciated: [paris:x86_64-Linux-chb-fs-stable]...olphpienaar/tmp$>mri_convert -vs 1 1 1 -ds 0.25 0.25 0.25 BM05_recon.nii BM05_recon3.nii mri_convert -vs 1 1 1 -ds 0.25 0.25 0.25 BM05_recon.nii BM05_recon3.nii mri_convert: unknown flag "-ds" type mri_convert -u for usage On 10/16/13 16:07 , Jon Wieser wrote: > mri_convert can change the voxel resolution for you > > > mri_convert -vs 1 1 1 -ds 0.33 0.33 0.33 <filename> > > > see the help: > https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html > > Jon > > ----- Original Message ----- > From: "Rudolph Pienaar" <rudolph(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, October 16, 2013 2:36:37 PM > Subject: [Freesurfer] Easiest way to resample a volume..? > > Hi all -- > > I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to > 300x300x300 0.33mm^3. > > What's the easiest way to do this? Will 'mri_convert' do the trick? > > Best > -=R > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] Easiest way to resample a volume..?
by Rudolph Pienaar 16 Oct '13

16 Oct '13

Perfect! That worked :-) Thanks On 10/16/13 16:03 , Juan Eugenio Iglesias wrote: > Hi Rudolph, > yes, you can use mri_convert with the flag -vs 0.333333 0.333333 0.333333 > You might want to play with -rt as well to switch from linear to cubic > resampling. > Cheers, > /Eugenio > > > On 10/16/2013 03:36 PM, Rudolph Pienaar wrote: >> Hi all -- >> >> I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to >> 300x300x300 0.33mm^3. >> >> What's the easiest way to do this? Will 'mri_convert' do the trick? >> >> Best >> -=R >> > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Easiest way to resample a volume..?
by Rudolph Pienaar 16 Oct '13

16 Oct '13

Hi all -- I have a volume of say 100x100x100 1mm^3 and I'd like to resample it to 300x300x300 0.33mm^3. What's the easiest way to do this? Will 'mri_convert' do the trick? Best -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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2x2 repeated measures ANOVA?
by Caspar M. Schwiedrzik 16 Oct '13

16 Oct '13

Hi Freesurfer Experts, is it possible to run a 2x2 repeated measures ANOVA for functional data on the surface in Freesurfer (both factors have two levels and are fully within subjects)? If not, is there a way to use mri_glmfit-sim on results calculated in Matlab to correct for multiple comparisons? Thanks, Caspar

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gamma.mgh
by Rees, Elin 16 Oct '13

16 Oct '13

Sorry, I mean the gamma.mgh maps for the cross-sectional differences appear to be blank as no overlay is overlaid on the fsaverage when I do the same command as with the longitudinal gamma.mgh. The commands I am running for the cross-sectional group comparison are: mri_glmfit --glmdir lh_groupdiff.dir --fsgd fsgd.fsgd doss --y lh.thickness10.mgh --C groupdiff.mtx --surf fsaverage lh --cortex tksurfer fsaverage lh inflated -overlay /lh_groupdiff.dir/groupdiff/gamma.mgh Thanks Message: 8 Date: Wed, 16 Oct 2013 11:47:59 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] gamma.mgh To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <525EB52F.5000006(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed what do you mean they are "coming up blank" On 10/16/2013 05:15 AM, Rees, Elin wrote: > Dear FreeSurfers, > > I've been looking at between-group (controls and disease) differences > in cortical thickness cross-sectionally and longitudinally (PC1). I've > outputted sig.mgh maps and effect size maps (gamma.mgh) but the > cross-sectional gamma.mgh maps are coming up blank. Could you explain > why this is (and why it works for the longitudinal data) and how I can > create a cross-sectional effect size map? > > As the scans I am an analysing are from four different scanners I am > also looking at scanner differences in the controls only. No > significant differences are coming up but the effect size maps are > showing both positive and negative differences across the whole brain > and the gammavar.mgh maps are completely yellow (5 on the colour bar). > How do I interpret this? > > Any help would be much appreciated. Thanks, > Elin > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 9 Date: Wed, 16 Oct 2013 11:51:41 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] DOSS FS 5.3 To: amirhossein manzouri <a.h.manzouri(a)gmail.com> Cc: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <525EB60D.1010808(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed From the command line you will need to run mri_glmfit. The mri_glmfit.log file in the QDEC output folder will have a sample mri_glmfit command line. You will need to modify this by adding "doss" after the FSGD file. You will also need to create new contrast matrices to match the DOSS model. Search for fsgd on our wiki to get examples doug On 10/16/2013 03:19 AM, amirhossein manzouri wrote: > Dear Experts, > Hi, > I have already done my data analysis having group as fixed factor and > age as nuisance factor in QDEC FS 5.3. I also need to run it with > DOSS. Would you please advise how to run the same analysis with > DOSS from terminal and if it is possible to look at the results in > QDEC Display again. > > -- > Best regards, > Amirhossein Manzouri > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 116, Issue 29 *******************************************

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Confusion about dods
by Jürgen Hänggi 16 Oct '13

16 Oct '13

Dear FS experts I compared two groups wrt cortical thickness using total grey matter volume as a covariate. The results obtained without the covariate (first row in the attached figure) and with the covariate modeled across both groups (doss option, second row in the figure) differed only in quantity (clusters are smaller with the covariate). However, when using the covariate with dods, the results changed completely (third row in figure) compared to doss and compared without the covariate. Then I tested (using dods) the covariates itself (using 0 0 1 -1) and get almost identical clusters (although in the opposite direction, forth row in the figure) as found in the group comparison with the covariate (dods, third row). In my opinion, this is puzzling! Any idea? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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gamma.mgh
by Rees, Elin 16 Oct '13

16 Oct '13

Dear FreeSurfers, I've been looking at between-group (controls and disease) differences in cortical thickness cross-sectionally and longitudinally (PC1). I've outputted sig.mgh maps and effect size maps (gamma.mgh) but the cross-sectional gamma.mgh maps are coming up blank. Could you explain why this is (and why it works for the longitudinal data) and how I can create a cross-sectional effect size map? As the scans I am an analysing are from four different scanners I am also looking at scanner differences in the controls only. No significant differences are coming up but the effect size maps are showing both positive and negative differences across the whole brain and the gammavar.mgh maps are completely yellow (5 on the colour bar). How do I interpret this? Any help would be much appreciated. Thanks, Elin

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LGI radius
by Jon Wieser 15 Oct '13

15 Oct '13

Hi freesurfer experts is it possbile to change the radius for the LGI computation. ( it's normally set at 25 mm) we waned to try computing the LGI with a smaller radius. I looked the in the "compute_lgi.m" file, and it does not use radius, (even though radius is an input parameter for it) Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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Fwd: talairach registration troubles
by Robyn Migliorini 15 Oct '13

15 Oct '13

Dear freesurfer folks, My colleagues and I have been running into some troubles with our talairach registration. These are the steps that we run: 1. cd SUBJECT_DIR: 2. recon-all -all -subjid $SUBJECT 3. cd $SUBJECT/mri 4. mri_nu_correct.mni --i orig.mgz --o orig.mgz --n 3 5. recon-all -s $SUBJECT -talairach -clean-tal -tal-check 6. cd ../../ 7. recon-all -all -subjid $SUBJECT recon -all -version yields this: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Then we have been checking our talairach registration by following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach When we go to visually examine the talairach transformed volume (*file --> load transform--> load transform for main volume --> talairach.xfm*), we've found that many of the images look chunked, jagged, or striated, like pieces of a puzzle fit together poorly rather than a smooth whole brain (see attached images for examples). When we look at the talairach overlay using *tkregister2 --mgz --s subjectID --fstal --surf orig *on these same brains, they don't look particularly misaligned. We have tried doing some minor moving and stretching of the talairach volume to better fit our subject volume when it seems necessary, but when we compare the edited vs unedited talairach, the one we fixed still has the striation problem, though sometimes less so. What might be causing this? What might be some remedies? We are also particularly concerned because we know that the alignment of the corpus callosum is important for the talairach registration progress, and the population that we work with (children with fetal alcohol exposure) has know callosal abnormalities (e.g., some deviations in shape, placement, volume), although we are seeing problems even in ones that look perfectly aligned. Thank you very much for any advice you can offer! Best, Robyn Migliorini Center for Behavioral Teratology San Diego State University / University of California San Diego Joint Doctoral Program in Clinical Psychology

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labels coordinates from atlases
by maria estanqueiro 15 Oct '13

15 Oct '13

Dear all, I need the center coordinates of the anatomical labels from the desikan and destrieux atlases. I saw a similar post a while ago in which it was recommended the following: #1 Convert the annotation to a set of labels. This is for the Desikan atlas, but you can spec the destrieux instead mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc # For each label, run mri_surfcluster to get the centroid mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel lh.pericalcarine.label --sum sum.lh.pericalcarine --centroid --thmin 0 --hemi lh --subject fsaverage I did the last step step for 2 different labels, one in the temporal and the other in the occipital cortex. However, the coordinates that were generated in the sum files were the same. Does anyone know why? Is this the right procedure for what I want to do? Thanks!

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