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30135 discussions

Input for mris_fwhm to generate fwhm.dat file
by Chung, Yoonho 03 Jun '16

03 Jun '16

Dear freesurfer experts, This is a follow up question from a previous post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47480.html I have created a sig.mgh from my own stats code and need to also generate fwhm.dat file to run the monte carlo sim, which is estimated from the residuals. What are the specifics and dimension of this residual file I need to generate for mris_fwhm? Is this a residual of model fit at each vertex across all subjects (so [number of subjects x number of verticies] matrix in .mgh file)? or variance or standard deviation of the residuals? Perhaps pointing to an example file in the glmdir directory (created when running glmfit) will help me understand the process (for example is rstd.mgh or rvar.mgh is being used for mris_fwhm --i or something else?). Thank you for your help!

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Re: [Freesurfer] recon-all segmentation error
by Jaiashre Sridhar 03 Jun '16

03 Jun '16

Bruce, The aseg looks fine to me. Is there anything in specific that I should be looking for in aseg? Thanks, Jaiashre.

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Re: [Freesurfer] recon-all segmentation error
by Jaiashre Sridhar 03 Jun '16

03 Jun '16

Bruce, The lh.inflated.nofix shows the brainstem and cerebellum are attached to the cortical surface. Also, the ventricles are not filled in the filled.mgz. Could you please tell me how to fix this manually? Thanks, Jaiashre.

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build fsaverage
by shi yao wang 03 Jun '16

03 Jun '16

Hello ! I work for the department of radiology, Emory University. We're planning to use the FreeSurfer software suite (or more precisely, the surface-based stream ) in a project that aims to compare cortical thickness between treatment and nontreatment patients. We have finished recon-all for all patients. And next will do group analysis. We need to rebuild fsaverage for data reconstruction. However, we cannot find any information about that process. Is anybody kindly provide some suggestions about that? Thank you very much! Lawrence Wang Radiology Department, Emory University

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Problem with FreeSurfer template and control subject
by Mahtab Farahbakhsh 03 Jun '16

03 Jun '16

Dear Freesurfer, The data that I'm using as a part of my study contains only the patients' T1 images and we have not collected any control subjects yet. I want to compare the cortical thickness of these subjects with a template (instead of a control subject), but I'm confused which volume I need to choose. When I run recon-all, does it transform the slices based on the fsaverage? Is fsaverage based on Talairach template or MNI or something else? Would you please guide me with the question and inform me what template volume is the best for me to use instead of my control subjects? Best Regards, Mahtab.

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Two functional connectivity methods
by Rodriguez-Thompson, Anais 02 Jun '16

02 Jun '16

Hi FreeSurfer experts, I have two different ways to do functional connectivity, and was wondering which one is optimal since they produce different results. The first is handed down to me from a previous coordinator. However a few of the steps seemed overly complicated, so I looked into a more direct method. Both methods use single vertex as a seed, so we smooth in order to include enough vertexes for fcseed-sess. Option 1 (the old version): Creating the mask, smoothing, and binarizing it: ~ mri_label2label --s fsaverage --regmethod surface --hemi lh --srclabel $SUBJECTS_DIR/$subject/label/$label.label --trglabel $SUBJECTS_DIR/$subject/label/junk.label--outmask $SUBJECTS_DIR/$subject/mri/{$label}_sm00.mgh ~ mris_fwhm --i $SUBJECTS_DIR/$subject/mri/{$label}_sm00.mgh --fwhm 4 --smooth-only --o $SUBJECTS_DIR/$subject/mri/{$label}_sm04.mgh --s fsaverage --hemi lh ~ mri_binarize --i $SUBJECTS_DIR/$subject/mri/${label}_sm04.mgh --min 10e-10 --o $SUBJECTS_DIR/$subject/mri/{$label}_sm04.10e-10.bin.mgh Switching to dev in order to convert the mask into a volume: ~ source /usr/local/freesurfer/nmr-dev-env ~ mri_surf2vol --so $SUBJECTS_DIR/fsaverage1/surf/lh.pial $SUBJECTS_DIR/$subject/mri/${label}_sm04.10e-10.bin.mgh --subject fsaverage --o $SUBJECTS_DIR/$subject/mri/{$label}_sm04.10e-10.bin.vol.mgz We then move back into 5.3 and use this volume as segmentation in fcseed-config and -sess Option 2: Turning label into a volume, smoothing it, and binarizing it: ~ mri_label2vol --label $SUBJECTS_DIR/fsaverage1/label/{$label} --temp $SUBJECTS_DIR/fsaverage1/orig.mgz --regheader $SUBJECTS_DIR/fsaverage1/orig.mgz --hemi lh --subject fsaverage --proj frac 0 1 .1 --o $SUBJECTS_DIR/{$subject}/{$label}.vol.mgz ~ mri_fwhm --i $SUBJECTS_DIR/{$subject}/{$label}.vol.mgz --fwhm 4 --smooth-only --o $SUBJECTS_DIR/{$subject}/{$label}.sm4.vol.mgz ~ mri_binarize --i $SUBJECTS_DIR/{$subject}/{$label}.sm4.vol.mgz --min 10e-10 --o $SUBJECTS_DIR/{$subject}/{$label}.sm4.bin.vol.mgz We then use this volume as segmentation in fcseed-config and -sess. I would prefer to use the second method since it is more straightforward, but I wanted to make sure that a) it is sound and b) it is more optimal than option 1. Thank you for your help! Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

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mri_convert segfault error
by Joshua Lee 02 Jun '16

02 Jun '16

On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 16.04 LTS mri_convert is seg faulting >>ls brain* > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz brain.mgz > > mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from ./brain.mgz... > Segmentation fault (core dumped) > Any ideas? Thanks Joshua

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Re: [Freesurfer] mri_glmfit-sim using custom stat outputs
by Chung, Yoonho 02 Jun '16

02 Jun '16

Thanks Doug - so the residual file would be [number of subjects x number of vertices] matrix? Does it have to be in special file format? > So you will generate the sig.mgh file? I would recommend just running > mri_glmfit using a design close to whatever you did to generate the > directory structure, then just replace the sig.mgh file with the file of > your choosing. The one snag may be the fwhm.dat file. This is a measure > of the spatial correlation in the residual. Since it works off the > residual, it depends on the actual design. If your analysis produces a > residual, you can run mris_fwhm to get the fwhm.dat file, and then just > run mri_glmfit-sim. > doug > On 06/02/2016 02:56 PM, Chung, Yoonho wrote: > > Dear experts, > > > This is a follow-up question from my previous post. > > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47287.html > > > If I am running stats with my own stats code to generate p-values and > other parameters, what other files > > do I need to generate in order to run 'mri_glmfit-sim'? I do not have > the glmdir file (since I am not running mri_glmfit) so I would like to > know which files need to be supplied with which flag/option, in place > of the '--glmdir', for mri_glmfit-sim to run the cluster-based > correction for my vector of p-values. An example command would be > extremely helpful. Thank you in advance! > > > Best, > > Yoon

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mri_glmfit-sim using custom stat outputs
by Chung, Yoonho 02 Jun '16

02 Jun '16

Dear experts, This is a follow-up question from my previous post. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47287.html If I am running stats with my own stats code to generate p-values and other parameters, what other files do I need to generate in order to run 'mri_glmfit-sim'? I do not have the glmdir file (since I am not running mri_glmfit) so I would like to know which files need to be supplied with which flag/option, in place of the '--glmdir', for mri_glmfit-sim to run the cluster-based correction for my vector of p-values. An example command would be extremely helpful. Thank you in advance! Best, Yoon

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glmdir question
by Clara Kühn 02 Jun '16

02 Jun '16

Dear FreeSurfer Experts, when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and create a new folder for this GLM I have to copy the mgh file into the glmdir to run the Monte Carlo correction. Is there a way to specify where that mgh is located so that I don't have a bunch of copies of it in all my glmdirs? Thanks for your help! Cheers Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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