Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

BUG in multiple comparisons correction for ABS
by Douglas N Greve 08 Jul '09

08 Jul '09

Nasim and Judith (and everyone else), I've found and fixed a bug that was causing the surfcluster results for the mc and perm simulations of absolute "abs" contrasts. To implement the fix, get Linux 64bit versions of these files and copy them to $FREESURFER_HOME/bin (make backups of the originals:). ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfclust… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit You can then run something like: mri_glmfit-sim --glmdir yourglmdir --no-sim mc-z.abs The "--no-sim" option tells it NOT to do the full simulation again, just use the CSDs that are there to recompute the cluster results for each contrast, so it should be done in a matter of minutes. If you've used a permutation, then run mri_glmfit-sim --glmdir yourglmdir --no-sim perm.abs Please let me know if this fixes the problem. doug

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Re: [Freesurfer] make_average_subject error about limit
by Feng-Xian 08 Jul '09

08 Jul '09

Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh The terminal shows: ERROR: flag -- not recognized Now, I have two problems want to ask. 1) What's wrong about the commands that I type? And, how to solve the problem? 2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them. Thank you in advance! Feng-Xian On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote > in general, it is not necessary to run make_average_subject prior to > performing an analysis. using the default average subject that > freesurfer provides, named 'fsaverage', is sufficient for most cases, > because it doesnt affect the analysis, its only used as a target upon > which to project results. the 'fsaverage' subject is in the > $FREESURFER_HOME/subjects dir, and you should copy it to your own > SUBJECTS_DIR prior to performing any group analysis. > > Nick > > On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: > > Hi, > > > > I know I wont to do QDEC now, so I want to change the method of group > > analysis from QDEC to the web you tell me. But, I did QDEC before. > > > > Before I do DODS, should I do make_average_subject to view the result of my > > subjects? Or, I have another method to view the results?? > > > > Thank you in advance! > > > > Feng-Xian > > > > > > > > > > On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote > > > Feng-xian, > > > > > > I should also mention that i dont think creating your own average > > > subject will solve the problem you describe, where you need to work with > > > three levels in your group. for that, you wont be able to use qdec, > > > but will need to run things manually. these pages give examples: > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > > > > > and note one of them is 1 Factor, 3 Levels. > > > > > > Nick > > > > > > On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: > > > > Feng-Xian, > > > > > > > > It appears that you do not have permission on your system to change the > > > > limits. So you will have to edit the scripts make_average_volume, > > > > make_average_surface and make_average_subject to comment out the 'limit' > > > > line, so that it looks like this: > > > > > > > > #limit descriptors unlimited > > > > > > > > > > > > Nick > > > > > > > > On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: > > > > > Hi, > > > > > > > > > > I have a problem with make_average_subject. > > > > > > > > > > After running all commands (including ln -s > > > > > $FREESURFER_HOME/subjects/fsaverage > > > > > and recon-all -s <subjid> -qcache for all my subjects) about running > > QDEC, I > > > > > found that QDEC could not analysis my group. > > > > > > > > > > Because the group have 1 factor and three levels, QDEC can't run. > > > > > > > > > > So, I want to change the method of analysis from QDEC to DODS. > > > > > > > > > > > > > > > I had a fsaverage file when I running QDEC, but the fsaverage did not > > use my > > > > > subjects to make. > > > > > > > > > > So, can I use the fsaverage file to run DODS? > > > > > > > > > > If not, I should make a new fsaverage with my subjects. > > > > > > > > > > But, I encounter the problem about make_average_subject. > > > > > > > > > > > > > > > When I type: > > > > > > > > > > make_average_subject --subects <subjid1> <subjid2> ... > > > > > > > > > > the terminal show that: > > > > > > > > > > limit: descriptors: Can't remove limit > > > > > > > > > > > > > > > What's wrong about the command I type? And, how to solve the problem? > > > > > > > > > > > > > > > > > > > > > > > > > Thank you in advance! > > > > > > > > > > Feng-Xian > > > > > > > > > > > > > > > ------------------------------------------------- > > > > > Chang Gung University Mail Server Web Mail system > > > > > By Chang-Gung University Information Center > > > > > (http://www.cgu.edu.tw/ic/) > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > ------------------------------------------------- > > Chang Gung University Mail Server Web Mail system > > By Chang-Gung University Information Center > > (http://www.cgu.edu.tw/ic/) > > > > ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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mri_label2vol
by Natalia Sanchez 08 Jul '09

08 Jul '09

Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?) Thank you -- Natalia Sanchez

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How to remove defects from inflated surface
by pcraisan＠cc.hut.fi 08 Jul '09

08 Jul '09

Hello, I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for. Is there an automatic way to smooth the inflated surface? I have tried using mris_smooth but it also messed up my .curv-file in the process. Best regards, Paula Räisänen Helsinki University of Technology, Department of Biomedical Engineering and Computational Science

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How to threshold an input mutli-volume?
by 李猛 08 Jul '09

08 Jul '09

Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the first volume are set to zero. In addition, the help for mri_threshold options is very limited. There is nothing about the options. Usage: mri_threshold [options] <in vol> <thresh> <out_vol> This program will threshold an input volume Where do I get more detailed description? Best Regards.

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restarting after edits to brainmask.mgz and wm.mgz
by Mira Michelle Raman 07 Jul '09

07 Jul '09

Hi, I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after making adjustments to both the brainmask.mgz and wm.mgz when restarting freesurfer. -Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 940305 (650)498-4538 http://cibsr.stanford.edu

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Citing QDEC
by nmaleki＠mclean.harvard.edu 07 Jul '09

07 Jul '09

Hello, Could you advise me on how to cite QDEC please? Thank you, Nasim

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Within group analysis
by Muhammad Ayaz 07 Jul '09

07 Jul '09

I am trying to run glm for two different scans of same subjects, ie first year scan vs second year scan. I ran the mris_prepoc and mri_surf2surf and it completed without error. When i run mri_glmfit it gives me error ERROR: gdfReadV1: Input line 1, subjid = 0049_05102006 Found 1 variables, expected. 0 FSGDF Format Error: file = CAA_1stScan_VS_2ndScan_Control_thickness.fsgd, tag=Input Ayaz

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How to "Fitting Tensors" in dt_recon?
by 李猛 07 Jul '09

07 Jul '09

Hi, All. The related item of "Fitting Tensors" is listed from the dt_recon. # Fit tensors echo "#@#-------------------------------" | tee -a $LF echo "Fitting Tensors" | tee -a $LF date | tee -a $LF set cmd = (mri_glmfit --y $fec --glmdir $OutDir); if($#bvals == 0) then set cmd = ($cmd --dti $infodump) else set cmd = ($cmd --dti $bvals $bvecs) endif However, I can't find any description about this argument(--dti) in mri_glmfit. Did the mri_glmfit call the dtifit to fit the tensor from fsl?If not, what is it? -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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citation for appropriateness of using freesurfer with children
by Anthony Dick 07 Jul '09

07 Jul '09

Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11 years) and adults. A reviewer asked for evidence that the parcellation works equally well in children and adults. Has this been tested empirically and published anywhere? I found a post saying not too worry about it for this age range (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06537.html) but reviewers tend to like references to published evidence :) The closest I get are papers by Burgund et al., 2002 and Kang et al., 2003 (http://tinyurl.com/m6v5s5; http://tinyurl.com/kwckol) but those papers do not use Freesurfer. Anything with Freesurfer? Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

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