Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

RoI,Space
by Barnali Basu 08 Jul '09

08 Jul '09

Experts, I have some snapshots of ROIs made in BrainVoyager (in non-TAL space on inflated brain, as well as ones projected onto TAL space). I need to take the above as reference and make near-exact ones (ROIs) using Freesurfer on inflated brains. Which one of the above do I use as my reference Barnali

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Fwd: [Freesurfer] mri_label2vol
by Natalia Sanchez 08 Jul '09

08 Jul '09

Hi FreeSurfer experts! I am kind of new to FreeSurfer and this is my first time using the software! I am using Freesurfer to create a corrtical mask for M1 for probabilistic Tracking in FSL. I am doing recon-all for segmentation, then in tksurfer I am selecting a label for the precentral gyrus for the left hemisphere for the subject of interest. The label is selected in the same subject in which I am planning on doing the mask, so I think it is not necessary to do label2label. Afterwards, I am doing vol2roi which gives me a .nii output. When plotting this in FSL, I have a complete misalignment of the ROI, which is not corrected by swapping the image. Obviously this means I am having problems with the registration. How can I improve this? I have been using the mni152register.dat for the registration, and I also tried doing fslregister before running vol2roi. I have also tried using label2vol but the output has given me the same problem. Which of the tools is better for this type of process label2vol or vol2roi? I attached a snapshot of the way the mask looks, (which is really bad) Am I following an adequate procedure, does this make any sense at all, is this a good approach to integrating FreeSurfer with FSL? Is there a more efficient way to do cortical masks? I would really appreciate any help! Thank you -- Natalia Sanchez -- Natalia Sanchez

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recon-all qcache
by Victoria Williams 08 Jul '09

08 Jul '09

Hello, I was hoping to get some more information about the qcache option. Would running all my subjects with qcache save me any time if I plan on using mri_glmfit instead of qdec? The GLMs I am running have to be sent through mris_preproc and mri_surf2surf each time since some inputs are #'d out due to missing variables in the fsgd file and each GLM differs. I was wondering if somehow mri_glmfit could use the fsgd file inputs to concatenate the already smoothed data outputted by qcache. Thus, saving me having to concatenate and smooth over and over again due to slight differences. Also, where is the output directory for qcahce? Is it in the average subject's directory or individual subject directories?? Thanks! Tori

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reconstructing .mnc file with freesurfer
by Jesse Bledsoe 08 Jul '09

08 Jul '09

Hi Everyone, What is the process for reconstructing a .mnc file with freesurfer? Do I just run the recon-all -s *.mncfile* -autorecon-all ? Thanks in advance, jesse ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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dimension mismatch error
by Markus Donix 08 Jul '09

08 Jul '09

Hi all, after running a group comparison using qdec I wanted to use mc-z instead of FDR for multiple comparison correction I tried to run mri_glmfit-sim-mc-z.abs.2 and got an error... ERROR: dimension mismatch between X and contrast /Users/..../subjects/ qdec/Untitled/tmp.mri_glmfit-sim-5637/lh-Avg-Intercept-area.pial.mtx X has 8 cols, C has 4 cols what does this mean and how to fix it? thanks, Mark

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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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Freesurfer July 2009