Freesurfer

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30087 discussions

Using mri_glmfit to regress out wm and ventricle signal
by Mcnorgan, Christopher 27 Mar '20

27 Mar '20

External Email - Use Caution I’ve been using mri_glmfit to regress out motion correction parameters and linear trends and saving residuals in surface space by first generating a QA matrix for the volume: mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/{hemi}.detrend \ --qa \ --surf ${SURFTOUSE} lh Then merging the QA and MC matrices into a single matrix of nuisance regressors: paste ${source_dir}/${r}/lh.detrend/Xg.dat mcprextreg > nuisance And finally, regressing out the nuisance values and saving the residuals mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/${hemi}.detrend \ --X nuisance \ --no-contrasts-ok --save-yhat --eres-save \ --surf ${SURFTOUSE} ${hemi} Is there a straightforward way of obtaining mean white matter and csf signal in my nuisance regressor matrix? I was unable to find any preprocessing step or application of mri_glmfit that will provide these values or regress out these values automatically. (Also note: the —qa flag is not documented in the mri_glmfit help; I must’ve learned of it from a previous email to this list) Thanks /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Re: [Freesurfer] PetSurfer reference region
by Dincer, Aylin 27 Mar '20

27 Mar '20

External Email - Use Caution Hello PetSurfer experts, We found the SUVR values for the reference region (lh/rh cerebellum cortex) does not equal 1 in the gtm.stat.dat file. We tried a few things: 1) leaving the PET image as multi-frames (ref region SUVR about 1.34) 2) concatenating the frames as suggested in the previous response (ref region SUVR about 1.34) 3) running with the SUV image (ref region SUVR about 1.003). I attached the terminal output and the gtm.stat.dat file from the concatenated image run. Here is the command we ran using v6: mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 8--seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 --rescale 8 47 -o regmean_gtmpvc_output Let me know if you have suggestions. Thanks so much, Aylin _______________________ Message: 11 Date: Fri, 6 Mar 2020 16:59:53 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] PetSurfer reference region To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8c262861-3272-151b-ae18-9068984084d4(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I think the issue is that your input has multiple frames (6). It will compute the scaling from all 6 whereas the gtm.stats file is only from the first frame. Try running it with a single frame. Note that the gtm.nii.gz will have all the frames for each ROI. On 3/6/2020 3:56 PM, Dincer, Aylin wrote: > External Email - Use Caution > > Thanks for the quick reply. I attached the terminal output to this email. We are running this on v6. > > Best, > Aylin > > _______________________ > Message: 9 > Date: Fri, 6 Mar 2020 11:50:51 -0500 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] PetSurfer reference region > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <64d6089e-f818-e30e-deff-98a812b72636(a)mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > I cannot replicate this in either v6 or v7beta. Can you send the > terminal output? > > On 3/5/2020 1:32 PM, Dincer, Aylin wrote: >> ????????External Email - Use Caution >> >> Hello PetSurfer experts, >> >> We are using the cerebellum cortex as our reference region, but >> noticed that the SUVR values for lh/rh cerebellum cortex do not have a >> value of 1 (which is what we were expecting). The actual SUVR values >> are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached >> the stats file (gtm.stats.dat) and below is the command we ran. >> >> mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf >> ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask >> PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output >> >> Let me know if you need any more details. >> >> Thanks so much, >> >> Aylin >> >> ???????????????????? >> >> _____________________________ >> >> Aylin Dincer >> >> Senior Research Technician >> >> NeuroImaging Laboratories >> >> Imaging Core, Benzinger Lab >> >> 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Density of the skull
by Pazuelo, Jeremy Raphael Judah 27 Mar '20

27 Mar '20

Hello FreeSurfer Developers, For my research on neurostimulation using ultrasound, I am trying to obtain a 3D matrix with the density values of a patient's skull. Is there a way with FreeSurfer to obtain a file containing the density of the skull. I could then transform this file on Matlab to obtain the matrix. Thank you for your help, Jeremy Pazuelo

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Run FreeSurfer recon-all on isoDWI
by Yixin Ma 27 Mar '20

27 Mar '20

External Email - Use Caution I was trying to use the average of DWI images (isoDWI) to run recon-all, and it didn't work. I understand that FreeSurfer can only take a T1-weighted image for now. But how hard would it be to modify the code by myself to make it work? If it works, how accurate do you think it would be to run FreeSurfer on isoDWI? All the best and thank you for your help, Yixin Message: 8 Date: Fri, 13 Mar 2020 18:44:18 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer Cortical Parcellation using isoDWI image only? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <14b89d9d-130f-08f0-d593-71f2cdef3107(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" you are trying to run a DWI image through recon-all? Sorry, it can only take T1w right now On 3/12/2020 3:28 PM, Yixin Ma wrote: > > ????????External Email - Use Caution > > Hi Freesurfer experts, > > I'm writing to ask if it's possible to run FreeSurfer Cortical > Parcellation by just using the isoDWI image. If it's possible, it will > reduce the scan time and avoid misregistration between T1 and DWI. > > I started from just input the masked isoDWI (mask generated from > MRtrix3) for -reconall command, and attached is a screenshot of the > image of NU.mgz, which shows a clear delineation of WM/GM matter. So I > think it's promising, although the recon-all stopped because of the > wrong contrast. > My ideas on tackling this problem are: > 1) generate a corresponding "fake" T1-weighted image by > either?adjusting the value directly or using a brain Atlas and > deformable registration to create one. > 2) Tweak some parameters in FreeSurfer. > > Any suggestions or comments on my ideas are appreciated. > > Thank you very much and all the best, > > Yixin Ma >

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mri_deface download link not found
by D'Silva, Hailey 27 Mar '20

27 Mar '20

External Email - Use Caution Hello Freesurfer Experts! I'm trying to anonymize a number of T1s by using mri_deface, but am getting a "Not Found" error when I try to download the tools for it. Thanks for your help, Hailey

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Re: [Freesurfer] Default GCA atlas FreeSurfer 6?
by Douglas N. Greve 27 Mar '20

27 Mar '20

Hi Andrei, in the future, please post to the FS list. On 3/23/2020 5:21 PM, Andrei Mouraviev wrote: > > External Email - Use Caution > > Hello, > > I’m trying to find the default atlas that was used to segment T1W > images(freesurfer v6.0.1). > > Is this the still the right file? > > $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca > Yes > > Is there a variable that points to the default atlas? > You mean an environment variable? No, just create it yourself > > Regards, > > Andrei >

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Convert cespct.nii to subject's own anatomy space (for ROI analysis)
by Star Xi 26 Mar '20

26 Mar '20

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Re: [Freesurfer] Hippocampal Volume Extraction
by Devika K 26 Mar '20

26 Mar '20

External Email - Use Caution Hi, I want to extract hippocampal volume from longitudinal samples. I am less aware of it. I ran recon-all-all with longitudinal pipeline for all those samples. How I need to process further (Commands that I need to follow). Would you please help me out? Thanks and Regards Devika K

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Misalignment of boundaries and T1 (Freesurfer/SamSrf)
by Mason Wells 26 Mar '20

26 Mar '20

External Email - Use Caution Hello Freesurfer developers, I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all command which finished without errors. However, the white/grey matter boundaries are significantly misaligned with the subjects T1 (images attached). Below are the steps I have taken to reach this point in the analysis: 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain. 2. Ran Feat · Distortion correction of the EPI · Motion correction · No smoothing · Highpass filter · No registration to whole brain · Register to T1_biascorr_brain · Register to standard space 1. Ran recon-all on T1_biascorr 2. Convert T1/T1_brain/orig(001) from mgz to nii 3. Check registration (using the SurfaceProjection command from the SamSrf package) which leads to the attached images named S1 and S1. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux 5.3.0-40-generic x86_64 Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux As you can see, the registration is significantly misaligned. Can anyone offer any advice on this/suggest a way to rectify it? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Freeview CLI feature request
by VINCENT KOPPELMANS 25 Mar '20

25 Mar '20

External Email - Use Caution Dear FreeSurfer team, I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39 Would it be possible to add the following features as command line flags to FreeView? 1) Set opacity for a surface It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself. 2) Set smoothing iterations for isosurfaces This can only be done in the GUI, not yet via the CLI. Thank you for your consideration. - Vincent

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