Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Query regarding FA quantification in ROI
by Puneet Talwar 09 Mar '20

09 Mar '20

External Email - Use Caution Dear Freesurfer team, I have done FA quantification in brainstem substructures using two ways and got slightly different results. First, I used dMRI Data Analysis Processing Stream with the following steps (after brainstem segmentation followed by dt_recon) - (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0) dt_recon - mri_vol2vol - masking - mri_segstats using FreeSurferColorLUT.txt In the second approach, I used vol2subfield after brainstem segmentation followed by dt_recon. dt_recon - vol2subfield Which one is more accurate for FA quantification? Thanks and Regards, Puneet -- Puneet Talwar, PhD Postdoctoral Fellow Seep and Chronobiology Lab B30 - Research Center Du Cyclotron University department in Liège, Belgium Email: ptalwar(a)uliege.be <agitude(a)uliege.be>

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fMRI resting state on mice
by Mohamed Ali Bahri 08 Mar '20

08 Mar '20

External Email - Use Caution Dear Experts, I would like to do some resting state and DWI (tractography) on mice and I am wondering if there is a detailed procedure for the processing of these small sized data? Any suggestion, advice will be very welcome, Best regards, Bahri -- Dr. Mohamed Ali Bahri, Logisticien de recherche principal, GIGA-Cyclotron Research Centre: In Vivo Imaging, Quartier Agora Université de Liège Bât B30 Allée du 6 Août n°8 4000 Liège, Belgique m.bahri(a)uliege.be 04 366 23 04

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field inhomogeneities and eddy current correction evaluation
by Adam Rytina 08 Mar '20

08 Mar '20

External Email - Use Caution Hello all, how can I evaluate the field inhomogeneities and eddy current correction I performed on my DWI images? Does any metric exist to do so? Thanks a lot in advance Regards Adam

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Re: [Freesurfer] sphere.reg file
by Marina Fernández 06 Mar '20

06 Mar '20

External Email - Use Caution These are the previous emails: 1 » » » » » » » » » » » » Dear freesurfer experts, I run the following commands to perform analysis with projected surfaces on my average subject: make_average_subject --out my_avg_subject --fsgd fsgd.txt surfreg --s s_001 --t my_avg_subject --o my_avg_subject.sphere.reg mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness --srcfmt curv --hemi [l/r]h --out [l/r]h.fsgd.mgh Theoretically, the mri_preproc function will automatically use the my_avg_subject.sphere.reg file because I specify my_avg_subject as the target subject. The problem is that in the output that comes out in the terminal while this function is running, it is specified that the file [l/r]h.sphere.reg is selected instead of [l/r]h.my_avg_subject.sphere.reg. Additionally, I did a test specifying the flag "--surfreg my_avg_subject.sphere.reg" in mris_preproc and the values of the output surface are different from the output that I have when I don't specify the flag --surfreg in mris_preproc (so, If I don't specify it, I think that definitely the function doesn't automatically use the file generated in surfreg, I think the default sphere.reg is used). What should I do? Is it better to specify the “--surfreg my_avg_subject.sphere.reg” flag in the mris_preproc function? Thanks in advance. Best regards, Marina. 2 » » » » » » » » » » » » what version of freesurfer are you running? 3 » » » » » » » » » » » » We are using Freesurfer v6.0 4 » » » » » » » » » » » » can you include the previous emails? __________________________

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Re: [Freesurfer] PetSurfer reference region
by Dincer, Aylin 06 Mar '20

06 Mar '20

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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] sphere.reg file
by Marina Fernández 06 Mar '20

06 Mar '20

External Email - Use Caution We are using Freesurfer v6.0

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Tracula Inquiry
by Ledesma, Jason 06 Mar '20

06 Mar '20

External Email - Use Caution Hello, I am having trouble carrying out Tracula on Freesurfer. See the following script (for confidentiality, patient's name has been replaced by XXX): Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer Admins-iMac:~ neurology$ Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Admins-iMac:~ neurology$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile FSLDIR: Undefined variable. Admins-iMac:XXX neurology$ My Config text file has the following info: setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri set subjlist = (XXX7.24.14) set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI set dcmlist = ( MR0001.dcm ) set bvecfile = (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt) set bvalfile = (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set threat = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Please advise. Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ___________________________________________________________________________________ LUNDQUIST Institute Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ___________________________________________________________________________________

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samseg permissions error
by Russo, Andrew William 06 Mar '20

06 Mar '20

Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew ____________ Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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Re: [Freesurfer] Apply transformation
by Adam Rytina 06 Mar '20

06 Mar '20

External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam ________________________________ Od: Adam Rytina <adam.rytina(a)outlook.cz> Odesláno: středa 19. února 2020 8:11 Komu: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Předmět: Fw: [Freesurfer] Apply transformation Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> za uživatele Adam Rytina <adam.rytina(a)outlook.cz> Odesláno: sobota 15. února 2020 19:52 Komu: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Předmět: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> za uživatele Douglas Greve <dgreve(a)mgh.harvard.edu> Odesláno: sobota 15. února 2020 17:15 Komu: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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questions about vertex information
by Jedy 06 Mar '20

06 Mar '20

External Email - Use Caution Dear FreeSurfer friends, Does anybody know how to extract vertex information of lh.white and lh.pial?  I would like to extract normal vector and other information of each vetex. I would be very appreciated if someone can give me some suggestions. Thank you very much! Best -jedy

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