Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

Neuroimaging programmer job opening at Mayo Clinic
by Senjem, Matthew L., M.S. 10 Mar '20

10 Mar '20

External Email - Use Caution The Mayo Clinic Aging and Dementia Imaging Research Lab is an international leader in studies of Alzheimer's Disease and Related Dementias. IT staff from the Research Application Solutions (RAS) Unit provide data management and processing expertise in support of that role. RAS has an opening for a highly capable person to further advance image processing within the lab. This includes developing new, or improving existing, methods to extract quantitative biomarkers from medical images and the integration of those methods into robust automated pipelines. Development is done in a collaborative environment that includes physicians, PhD scientists, biostatisticians and medical physicists. Candidates interested in this position must have a background in image processing and mathematical computation. Clear communication skills, both oral and written, as well as demonstrated desire for continuous learning are essential. Ideally, candidates will have experience developing automated medical image processing pipelines and a fundamental understanding of medical imaging modalities including MRI and PET. Experience with both cross-sectional and longitudinal analyses is desired. Initial areas of work for the successful applicant will, depending on existing skills and interests, be improved functional MRI analysis or multi-modal PET/MRI fusion. Experience coding in Python and/or Matlab is required. Fluency in the DICOM imaging standard is desired. Applicants should have experience developing version-controlled software in a Linux-based environment. Experience with distributed computation using resource management systems such as slurm or open grid engine will be helpful. Linux system administration experience is considered a plus. For more information and to apply, please visit the following link: https://apply.mayoclinic.org/TGnewUI/Search/Home/Home?partnerid=25309&sitei…

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freeview failed to load Surface overlay
by Meike Hettwer 09 Mar '20

09 Mar '20

External Email - Use Caution Dear freesurfer experts, I am currently running a very basic correlation with two groups (gender, which I am not interested in), age and genetic scores (the latter of which I am interested in) included in the glm. Atm I am using a DODS model (0 0 0 0 0.5 0.5), however, as I am actually not at all interested in gender differences...would it be smarter to use a DOSS model? (0 0 1 ?). And a question regarding freeview: I always get "failed to load Surface overlay"/"could not open file" errors when trying to overlay calculated sig.mgh (or beta.mgh or pretty much anything) on the fsaverage.inflated surface. From these error messages I cannot really spot the issue- I guess it might be some kind of matrix dimension mismatch? Which confuses me, as I resampled the data to the fsaverage brain...? I ran: 1. mris_preproc --fsgd 1234.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.1234.10.mgh 2. mri_glmfit --y lh.1234.thickness.10.mgh --fsgd 1234.fsgd --C 1234.mtx --surf fsaverage lh --cortex --glmdir lh.1234.glmdir --> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh When I launch freeview and try to overlay sig.mgh manually, I get "Correlation data does not match with surface". Does this have something to do with the "apply registration option" and if so, what would I have to select here? (since the data should already be registered to fsaverage...?). Thanks a lot, Meike

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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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Freesurfer March 2020