Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

question about curv.mgh
by Raffaele Dubbioso 21 Jan '20

21 Jan '20

External Email - Use Caution Hello FS team, can you please tell me what is the measurement scale of the curv.mg file? Is it a mean curvature (mm-1) or a gaussian curvature (mm-2)? I got values between 0.02 and -0.08 and it seems they are gaussian curvature. Thanks a lot for your help Best regards Rafael

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Re: [Freesurfer] freesurfer fornix
by Annink, K.V. 20 Jan '20

20 Jan '20

External Email - Use Caution Dear all, I have a question about the fornix segmentation. First I have used the comment mri_cc -f to create fornix.mgz. After all files were created, I have used mri_segstats to create the stats file. Is this correct? In the output file the nvoxes and volume are the same. Thank you for your help. Kind regards, Kim # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # NRows 1 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 250 465 465.0 Fornix ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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20 Jan '20

Hi everyone, This is a reminder that registration for the Spring 2020 FreeSurfer course will open TOMORROW (Tuesday, January 21st) at 10:30am EST! At that time, the link to the registration page will appear on the course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription The four-day course will run from March 30th through April 2nd, 2020 at the Massachusetts General Hospital Martinos Center for Biomedical Imaging in Charlestown, Massachusetts. The schedule for this course has not been finalized but an example schedule can be found on the course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription How to get a spot in the course -Easy! Register on the day we open registration & submit an accepted form of payment by the deadline. Some reasons why people are unable to attend the course: -Waiting too long to register. The 50 seats in the course usually fill up within a day or two. -Waiting too long before requesting a check from their institution. (Make sure you put in the request for a check immediately *after* you register.) -Not realizing cash payments must also be made by the deadline. (MoneyGram or Western Union transfers are accepted as well as personal deliveries.) -Booking flights, sending in payment, and/or just showing up without registering for the course or moving up from the waiting list! For questions about the course, you'll likely find answers on the course website. If you don't find what you're looking for, feel free to email the course organizers at freesurferlab(a)gmail.com. If you would like to hear about future course dates, sign up for the course mailing list here<http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi>. ------------------ FreeSurfer Course Organizers Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street Charlestown, MA 02129 Phone: (617) 726-6598

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Re: [Freesurfer] Unable to run recon all
by Greve, Douglas N.,Ph.D. 20 Jan '20

20 Jan '20

It is not clear why it failed for these subjects (always happens at the same place). Can you upload one of them for me to take a look at? here are the instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 1/6/20 11:49 AM, Sahil Bajaj wrote: > > External Email - Use Caution > > Hi Dough, > > I finished recon -all on about 515 subjects and I get error in 11 out > of 515 subjects. Here I am attaching recon-all.log files of all those > 11 subjects. I would really appreciate your help in fixing these errors. > > Thanks, > Sahil > > On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D. > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: > > Can you send the recon-all.log file? You sent the .error file > > On 12/20/2019 10:13 AM, Sahil Bajaj wrote: >> >> External Email - Use Caution >> >> Hello FS experts, >> >> I am trying to run recon all on about 100 subjects. But one out >> of 100 subjects finishes recon all with error, and doesn't >> complete the process. Here I am attaching recon all log for your >> reference. Also, before installing freesurfer on MAC Catalina, I >> ran sudo spctl - -master -disable >> >> I would really appreciate any help in resolving this. >> >> Thanks, >> Sahil >> 1) FreeSurfer version: >> >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c >> >> 2) Platform: MACOS Catalina >> 3) recon-all.log: see attached >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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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Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29
by Devika K 19 Jan '20

19 Jan '20

External Email - Use Caution I tried by specicying the subjects name, by following the below command. aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl But still I got the same error. On Sun, Jan 19, 2020, 10:30 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. RES: Re: freesurfer container - freeview error > (marcosm(a)hucff.ufrj.br) > 2. registration of dwi images (Sam W) > 3. Re: registration of dwi images (Yendiki, Anastasia) > 4. Project hippocampus to inflated 3D model? (Mohammad Rashid) > 5. Re: aparcstats2table error (Devika K) > 6. Re: Project hippocampus to inflated 3D model? (Bruce Fischl) > 7. Re: aparcstats2table error (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Jan 2020 15:05:15 -0300 > From: <marcosm(a)hucff.ufrj.br> > Subject: [Freesurfer] RES: Re: freesurfer container - freeview error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5e2383f1.1c69fb81.cfdf5.57cf(a)mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200118/f… > > ------------------------------ > > Message: 2 > Date: Sun, 19 Jan 2020 00:52:10 +0100 > From: Sam W <samfmri(a)gmail.com> > Subject: [Freesurfer] registration of dwi images > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > CAFYEHVvrxw-P0VWvqeiA_fMnUrMavmSb9wts3zDhLGFVZHC2ow(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello! > I have run eddy on all my dwi images and then run bbregister using the > first b0 image as the source image. > The b0 image is now well aligned with the anatomical image but how can I > apply the same transformation to all other dwi images in my dataset? > > After eddy correction I extracted the first b0 image (nodif.nii.gz) and run > the bbregister command: > bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg > /home/samm/nodiffb2orig.dat --dti --init-fsl --o > /home/samm/registered_b0.nii.gz > > Thanks! > Sam >

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Project hippocampus to inflated 3D model?
by Mohammad Rashid 19 Jan '20

19 Jan '20

External Email - Use Caution Hello, I have had success projecting regions such as the entorhinal region to an inflated 3D model. But I can't seem to do the same for hippocampi. I wouldn't need any hippocampal subfields, just projecting the hippocampus as a whole would be useful. Is there perhaps a particular file used for this that I am missing? Any help is appreciated, Mohammad Rashid

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registration of dwi images
by Sam W 18 Jan '20

18 Jan '20

External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my dataset? After eddy correction I extracted the first b0 image (nodif.nii.gz) and run the bbregister command: bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg /home/samm/nodiffb2orig.dat --dti --init-fsl --o /home/samm/registered_b0.nii.gz Thanks! Sam

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RES: Re: freesurfer container - freeview error
by marcosm＠hucff.ufrj.br 18 Jan '20

18 Jan '20

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Results in different size
by Marina Fernández 17 Jan '20

17 Jan '20

External Email - Use Caution Dear Freesurfer team, I run statistical analysis with the files in the average subject of a dataset (created with 5th order icosahedron tesselation). In order to visualize the results, I open the inflated-surface and the pial-surface with tksurfer and I realize that inflated-surface of the average subject is smaller than the pial-surface. Is it normal? In the fsaverage5 subject these surfaces have a very similar size. Even, when I load the results as an overlay in the inflated-surface, the results are shown smaller (more than the proportional size) than if I load the results in the pial surface (see attached image). What can I do to generate an inflated figure with the results in the same size than in the pial surface? Thank you in advance. Best regards, Marina.

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Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines
by Swati Rane 17 Jan '20

17 Jan '20

External Email - Use Caution Hello, I was wondering if someone could answer my question below Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files. Are there any set of parameters that should be set differently when using pc1 instead of thickness files? Thanks! Swati ____________________________________________ Swati Rane Levendovszky, PhD Interim Director, Diagnostic Imaging Sciences Center Assistant Professor, Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srleven(a)uw.edu<mailto:srleven@uw.edu> | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Swati Rane <srleven(a)uw.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, January 10, 2020 at 10:06 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the multiple comparisons corrections that come with it but does not comment on using the mri_glmfit-sim option. I just want to confirm whether there is anything prohibiting me from using mri_glmfit-sim. Are there any set of parameters that should be set differently when using pc-1 instead of thickness files? Also, would you do a stricter correction and stick to the longitudinal model or prefer the linear mixed effects model and do a FDR? How do you decide between the two? Thanks! Swati

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Freesurfer January 2020