Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

QDEC and ROI drawing
by Arnaud Boré 06 Apr '17

06 Apr '17

Dear Freesurfer's experts, I draw a specific region on fsaverage using QDEC, then I mapped this label on each subject using mri_label2label. I looked at these registered labels using freeview. Most of them are perfect but for some of them I would like to correct the segmentation. I would like to modify it using QDEC but when I overlay this label on the surface of my subject it has been shifted. I think this shift is because QDEC is using fsaverage as the standard space. I try opening QDEC using the "average" option and use the subject I want but I still get this shift. am I missing something ? Thank you in advance for your help. Arnaud Bore

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General QDEC clarification queastions
by Veggeberg, Rosanna 06 Apr '17

06 Apr '17

Hello, I am using QDEC to analyze cortical structural data and am looking for some clarification on some questions that have come up. 1. Design tab: In the "Measure" drop-down selection, I understand what we are getting when looking at thickness but the other measurements I am unclear on. Is there information or publications on the other 12 possible measures (how they are measured, what they mean, applications for using them). In particular, I am interested in learning more about area, area.pial, volume, sulc, and curv but would like to understand what the others mean as well to determine if they would be applicable to our study questions. 2. Design tab: I am a little unclear on why the model factors are labeled the way they are and wanted to see if I am using them correctly. -Discrete (Fixed Factors): this is pretty straight forward to be used as independent categorical variables, correct? -Continuous (Covariate): even though it says covariate, should these variables just be treated as independent continuous varaibles? -Nuisance Factors: should these just be treated as the covariates we wish to control for? 3. Results: When I am doing a group comparison (i.e. disease vs. control), does QDEC run the comparison based off of which order the labels appear in the table: disease vs. control, or does it run the comparison based off of which label comes first alphabetically: control vs. disease? 4. Results: When viewing the results in freeview, if I click on a significant cluster, in the bottom panel, does a negative value next to the mc-z.abs.th13.sig.cluster.mgh label indicate a decrease in cortical thickness (i.e. disease vs. control: negative value indicates control is greater than disease)? 5. Finally, once you have closed QDEC, is it possible to reopen the files again in the Gui? Or would you have to rerun the analysis? Thank you for help and please let me know if you need any further clarification.

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Custom color maps
by Senften, Peter 06 Apr '17

06 Apr '17

Hello, I am wondering if it is possible to create a custom color map that will be visible in freeview using the 3D viewer - not the coronal, axial, or sagital views. I created a copy of the LUT file and then replaced the RGB values the ones I wanted but haven't been able to get it to load at all. In the end I am trying to make pretty 3D pictures to see our regions of interest better for our data. I am open to other ways of doing this. Thanks, Peter

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ROI seed size
by ERIK JAHNER 06 Apr '17

06 Apr '17

What is the appropriate size for a surface based seed? I am referencing a study with volumetric based seeds with spheres with a radius of 3mm (in fMRI data). I would like to do a similar study using surface based representations. In a volumetric based analysis folding may actually increase the amount of cortical surface represented in a sphere. Using a circle on the surface with a 3 mm radius therefore would not be the same. But…. is the difference so minimal and variable across the cortex that it is not worth considering especially since the seeds are derived from published work and not using a localizer? Do you know of any published guidelines on generating seed sizes in surface based models, not based on a localizer. Or is this the completely wrong approach? Should I be using the tal coordinates to locate which parcellation of the available atlases that the seed was located in? (for example i have a fusiform face area seed which I have set as a circle 3mm radius) many thanks for your continued help Erik

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Selxavg3-sess Looking for (and can't find) "fmc.sm0"
by Taylor, Johnmark 06 Apr '17

06 Apr '17

Hello, I am getting an odd bug on selxavg3-sess. I am getting the error message, *ERROR: cannot find [rest of file path]/fmc.sm0* I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am confused because the output of preproc-sess for no smoothing is fmc.nii.gz, *NOT *fmc.sm0.nii.gz when doing analyses in native volume space, so I am not sure why selxavg-sess is looking for the wrong file path. For reference, here is my call to mkanalysis-sess: mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile runlist.txt -native -nuisreg mcextreg 3 -fwhm 0 -event-related -nconditions 8 -paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5 -polyfit 2 -nskip 8 I am using Freesurfer 5.3, if that helps. The analysis works fine when I apply 3mm smoothing (I've done preprocessing for both the 0mm and 3mm options). Thank you very much, and cheers, JohnMark

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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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Freesurfer April 2017