Freesurfer

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30091 discussions

First-level GLM on externally-preprocessed functionals
by Christopher Markiewicz 06 Apr '17

06 Apr '17

Hi list, We're working on making a preprocessing stream that will be generally accessible to different analysis streams, including FreeSurfer. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM in FreeSurfer. I've always done this through the FSFAST pipeline, but that may be a bit much, given that I'm starting from surface time series (the equivalent of `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`, but as a GIFTI file). Supposing I have a paradigm file and the files described above, what's the best way to do a basic GLM? Would it be to `mri_surf2surf` our GIFTI surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST directory structure, and pick up at `mkanalysis-sess`? Or is there a more straightforward way to just get a simple set of contrasts to compare with a volumetric analysis? Thanks in advance, Chris Markiewicz

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Help on "mris_anatomical_stats"
by Lim, Lena 06 Apr '17

06 Apr '17

Dear Experts, I ran a group analysis in Qdec for the left volume and found a region of significant group difference. I wanted to extract this ROI. I defined this label and used the "map label to subjects" option in Qdec and ran the following but encountered the following error. Please kindly help... [spjwker@nanlnx2 FSL]1% mris_anatomical_stats -l lh.HCA_vol.label \-b -f PAC07/stats/lh.HCA_vol.stats PAC07 lh limiting computations to label lh.HCA_vol.label. reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz... reading input surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... reading input pial surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial... reading input white surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... Segmentation fault Many thanks, Lena

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postdoctoral Research Fellow position at Mayo Clinic
by Senjem, Matthew L., M.S. 06 Apr '17

06 Apr '17

The Mayo Clinic Departments of Neurology and Diagnostic Radiology in Rochester, Minnesota are seeking applications for a fully-funded, two-year postdoctoral Research Fellow position to begin in July of 2017. The Research Fellow position will primarily work on developing advanced multi-modal molecular and high-field (3T and 7T) neuroimaging to study connectomics in pre-clinical and clinical Alzheimer’s disease. The resulting data will be acquired and analyzed as part of a unique collaboration between investigators at Mayo Clinic Alzheimer’s Disease Research Center and the Center for Magnetic Resonance Research at the University of Minnesota. Basic programing skills and familiarity with widely used neuroimaging software platforms are required for successful applicants. Familiarity with the Human Connectome Project imaging and analyses protocols is preferred but not required. No clinical or Alzheimer’s specific background is required. Salary will be commensurate with postdoctoral experience. The position will remain open until filled by a successful candidate. Please send CV, three letters of recommendation, and any inquiries to: David T. Jones, M.D. Mayo Clinic Department of Neurology Email: Jones.David(a)mayo.edu<mailto:Jones.David@mayo.edu> A Research Fellow at Mayo Clinic is a temporary position intended to provide training and education in research. Individuals will train in the research program of a Mayo Clinic principal investigator. Qualified individuals will demonstrate the potential for research as evidenced by their training and peer-reviewed publications and should become competitive for national research grants. Proof of English proficiency is required for J-1 Short-Term Scholars, Research Scholars, Professors, Specialists, and Student Interns sponsored by Mayo Clinic. Why Mayo Clinic? Learn and grow among the best in your field at the nation’s top hospital (U.S. News & World Report, 2016-2017), ranked No. 1 in more specialties than any other care provider. Mayo Clinic is committed to sustaining and growing research, believes in research-driven care and establishes a well-defined integration between the clinical practice and research. At Mayo Clinic, you’ll use the power of collaboration to achieve the highest standards for medical care and health improvement, working in the largest integrated, not-for-profit medical group practice in the world with over 60,000 employees. You’re invited to contribute to a unique environment that brings together the best in patient care, groundbreaking research and innovative medical education. We offer exceptional benefits, and have been recognized by FORTUNE magazine as one of the top 100 “Best Companies to Work For”. Mayo Clinic is an equal opportunity educator and employer (including veterans and persons with disabilities). -------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis
by stdp82＠virgilio.it 06 Apr '17

06 Apr '17

Furthermore, the res-001.nii which is produce in produced in the res folder in not the same dimension of f.nii.I would do the whole FAST preprocessing on f.nii., maintaining the same dimension and open it with FSL.ThanksStefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 5-apr-2017 23.39 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis Hi, as you advise I have run selxavg3-sess with the -svres option.I found a folder called "res" which contain "res-001.nii". Is it the f.nii fully processed?ThanksStefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 17.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST without to perform a seed based analysis You can't on either occasion just using preproc-sess. You can create an analysis with those components, then run selxavg3-sess with the -svres option. This will create a folder called eres with volumes that have had all the nuisance variables and low freqeuncies regressed out On 3/14/17 12:32 PM, stdp82(a)virgilio.it wrote: Thanks. 1- By using only preproc-sess, how can I perform "band pass filtering"? 2- And how can I take in account the nuisance variables: the CSF from which the top 5 principle components, the white matter from which the top 5 principle components, motion correction parameters (-mcextreg), 5th order polynomial. How can I eliminate the first 4 time points? Regards Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 16.14 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis just use preproc-sess On 3/14/17 10:45 AM, stdp82(a)virgilio.it wrote: Hi list, in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option? I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re. display SPM results on inflated surface?
by Schoot, Lotte 06 Apr '17

06 Apr '17

Thanks so much, I appreciate the help. However, I am not sure what I am supposed to do with the output of the recon-all process. Can I simply use the .dat file that is outputted there in MRI_vol2surf? Lotte Date: Wed, 22 Mar 2017 13:01:42 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] display SPM results on inflated surface? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <41134c50-bb0b-792c-c52b-b6850bcecf3c(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" If you have the T1 for the mni152 (which is somewhere in the bowels of the spm distribution), then you just run recon-all on it. I've done this for myself, so you can just download the result (which I have not checked thoroughly) from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mni152.tar.gz On 3/21/17 1:27 PM, Schoot, Lotte wrote: > Hi Doug and others, > > A while ago, I got this reply to my question below (thanks!). I tried to look in to it, but I am a bit confused (probably because I am very new to Freesurfer). > My results are on the MNI 152, but I don't understand what you mean with 'run the mni152 through freesurfer'. Is this the process to get the register.dat file that is required in mri_vol2surf? > What would you recommend to get the register.dat file? Is it possible to use bbregister for that? I have tried this, but I don't know whether it is correct: > > bbregister --s fsaverage --mov con_0001.nii --init-spm --reg > register.dat --bold > > > Thanks! > Lotte > > > >If your results are on the MNI152, you can run the mni152 through > >freesurfer, then use mri_vol2surf to map the data to the surface then > >view it with freeview (or tksurfer). You should not confuse this with > >doing the fMRI analysis on the surface. You will not have the > >benefits of surface-based analysis > > > On 02/15/2017 03:37 PM, Schoot, Lotte wrote: > >/Hi all, />//>/I was wondering if you knew of a way to display SPM > >results onto the />/inflated surface in Freesurfer. />//>/I have > >tried using SurfRend but there seem to be problems which might />/be > >due to the fact the results are obtained with SPM12 and SurfRend > >/>/was designed to work with SPM5. />//>/Thanks, />/Lotte > >/>//>//>/_______________________________________________ > >/>/Freesurfer mailing list />/Freesurfer at 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 at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis
by stdp82＠virgilio.it 06 Apr '17

06 Apr '17

Hi, as you advise I have run selxavg3-sess with the -svres option.I found a folder called "res" which contain "res-001.nii". Is it the f.nii fully processed?ThanksStefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 17.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST without to perform a seed based analysis You can't on either occasion just using preproc-sess. You can create an analysis with those components, then run selxavg3-sess with the -svres option. This will create a folder called eres with volumes that have had all the nuisance variables and low freqeuncies regressed out On 3/14/17 12:32 PM, stdp82(a)virgilio.it wrote: Thanks. 1- By using only preproc-sess, how can I perform "band pass filtering"? 2- And how can I take in account the nuisance variables: the CSF from which the top 5 principle components, the white matter from which the top 5 principle components, motion correction parameters (-mcextreg), 5th order polynomial. How can I eliminate the first 4 time points? Regards Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 14-mar-2017 16.14 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis just use preproc-sess On 3/14/17 10:45 AM, stdp82(a)virgilio.it wrote: Hi list, in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option? I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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How to generate binary mask image using FreeSurfer's “mri_volsynth”?
by Karan Vahi 06 Apr '17

06 Apr '17

Dear Freesurfers, I am trying to implement the methods mentioned in this paper to deal with partial volume effects when quantifying metabolites: https://www.ncbi. nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title The first step it mentions is: A binary mask must first be created, which represents the 3D SVS voxel. A binary mask is an image where each voxel contains either 1 or 0; in this case, the SVS voxel would be represented by a value of 1 and all other voxels 0. There are multiple ways to create a binary mask; one example, which was used successfully in this work, is the “mask()” function within Matlab9 and the FreeSurfer (Fischl)10 application “mri_volsynth.” When I am trying the following command in FreeSurfer: mri_volsynth --dim 3 4 5 2 --vol try.IMA I am getting this output: [image: Inline image 1] But, I don’t know where it is saving the output file. And, I am also not sure whether I am using mri_volsynth correctly. What is --dim nc nr ns nf in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_volsynth? Also which pixels suppose to be 1's and which 0's? Any help is appreciated.

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Error during recon-all
by Das S. 06 Apr '17

06 Apr '17

Dear FreeSurfer Developers, I was trying to use the command recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 When I executed the command separately I got below error message: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani

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Re: [Freesurfer] Fwd: recon-all error
by Antonin Skoch 06 Apr '17

06 Apr '17

Dear Patricia, this is I suppose the last issue concerning symbolic links, related with part of code starting with following comment: # if fsaverage is not in subjects dir, put it there I think that the most straightforward solution of this issue is to manually copy the fsaverage subject to $SUBJECTS_DIR before invocation of recon-all. Antonin forgot to attach the printscreen 2017-04-06 9:49 GMT+02:00 Patr?cia Klobu?iakov? < patricia.klobusiakova(a)gmail.com>: > Hi Antonin, > > I edited recon-all file, but another error was reported. This error > concerns symbolic links, too. Is there any way I could make it work on this > virtual machine? I coud try to substitute all ln commands with cp or > something like that. > > Thanks. > > Patricia > > 2017-04-04 13:43 GMT+02:00 Antonin Skoch <ansk(a)ikem.cz>: > >> Dear Patricia, >> >> see this thread: >> >> freesurfer(a)nmr.mgh.harvard.edu/msg51797.html" title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html" target="_blank">http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html >> >> Your working directory probably resides on the filesystem which does not >> support symbolic links. You probably could workaround this by editing your >> recon-all and replace line >> >> set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) >> by >> >> set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix) >> >> Antonin Skoch >> >> >> >> Hello FreeSurfer Developers, I have installed Freesurfer on Windows >> using VMware - CentOS 64-bit (the one from FSLuser Linux installation). >> Everytime I run recon-all, there is an error. >> The same error occurs when I try to rum mri2mesh command in SIMNIBS >> toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and >> logfile attached. >> Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64 #1 >> SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> Thanks for your help. >> >> Best, Patricia

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Re: [Freesurfer] Fwd: recon-all error
by Antonin Skoch 06 Apr '17

06 Apr '17

Dear Patricia, see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html Your working directory probably resides on the filesystem which does not support symbolic links. You probably could workaround this by editing your recon-all and replace line set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) by set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix) Antonin Skoch Hello FreeSurfer Developers, I have installed Freesurfer on Windows using VMware - CentOS 64-bit (the one from FSLuser Linux installation). Everytime I run recon-all, there is an error. The same error occurs when I try to rum mri2mesh command in SIMNIBS toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and logfile attached. Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help. Best, Patricia

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