Freesurfer

freesurfer@nmr.mgh.harvard.edu

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OHBM International Mentoring Programme Sign-up {Disarmed}
by Meena M. Makary 02 Sep '19

02 Sep '19

External Email - Use Caution Hi all, Between September 1st and September 31st 2019, registration for the fourth round of the Online International Mentoring Programme organized and coordinated by the OHBM Student and Postdoc Special Interest Group <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> will take place. In the programme, every OHBM member can become an (online) mentor or a mentee to another OHBM member(s) for a period of approximately one year (October-June). During this time, the mentor can support the mentee to grow in academia by providing advice on topics such as—but not limited to—personal development, grant writing, and work-life balance. In response to the feedback from previous participants and the increased interest of mentees in industry, we have also invited a number of mentors from industry to join us for this new round. If you are interested in being a mentor and/or mentee, please fill out this short registration form <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> and you will be contacted with further details. If you participated in any of the previous rounds and would like to further take part in the programme, you have two possible ways (It is possible to choose both options): 1. If you would like to continue being paired with your current mentors/mentees, please first discuss this with your mentoring partner. In this case, please do not re-subscribe for the programme and please delegate the mentee to fill in this feedback form <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> for us. 2. If you would like to apply for new mentors/mentees, you will be able to do so using the registration link above. Please feel free to forward this message to your colleagues. Please also forward this email to former researchers working in industry, if you know any, as we are still looking for more industry representatives to join the programme as mentors this year. We would like to thank all the OHBM mentors and mentees who participated in the previous three rounds of the programme! The third round of the programme is now ending. We hope that most of you had an opportunity to meet in person during the OHBM Annual Meeting in Rome. If you have feedback for us, please contact us at ohbmtrainees(a)gmail.com <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. Please share any comments which might help to further improve our programme! To find out more about the programme, please visit the OHBM Student and Postdoc SIG website <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> and check our previous publication <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. If you have any questions about the programme, please contact us at ohbmtrainees(a)gmail.com <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> . We hope to welcome you in the programme very soon! Best regards, — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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Two questions about flac_desmat.m for retinotopy analysis in fsfast
by Caspar M. Schwiedrzik 02 Sep '19

02 Sep '19

External Email - Use Caution Hi Doug, I have two quick questions about the analysis of polar angle maps: 1. Does the analysis take the HRF (lag etc.) into account? 2. Our stimulation starts at 12 for clockwise and counter clockwise. I found this older post https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-August/025241.ht… specifying changes to flac_desmat.m to account for that. I was wondering whether to change case {'fourier'} and/or case {'abret'}? This is using version 5.3. Thank you! Caspar

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syntax error near unexpected token 'newline'
by michele rizzi 31 Aug '19

31 Aug '19

External Email - Use Caution Dear All during freesurfer installation, I type export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh and I have this error syntax error near unexpected token 'newline' can you help me? thanks Mike

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Re: [Freesurfer] R: R: syntax error near unexpected token 'newline'
by fsbuild 31 Aug '19

31 Aug '19

External Email - Use Caution Yes, as Viviana said, you need to specify the path to the Applications folder by using a leading slash “/“ character. You can test that path /Applications/freesurfer/subjects is OK by opening the terminal application and then typing at the dollar sign prompt, $ ls /Applications/freesurfer/subjects ... which should not give you an error and show some files are there. Unless someone changed the shell preferences for your account on the Mac, then the default shell at the $ prompt in the terminal window is bash shell for Mac OS 10.14.  There should be no need to type “bash” again (and start another shell). So in the terminal window it should work for you to type the lines after the dollar sign prompt  (you could cut and paste the below), and then see if you get the same output. $ ls -d /Applications/freesurfer/Applications/freesurfer $ export FREESURFER_HOME=/Applications/freesurfer$ echo $FREESURFER_HOME/Applications/freesurfer $ ls $FREESURFER_HOME/SetUpFreeSurfer.sh/Applications/freesurfer/SetUpFreeSurfer.sh $ source $FREESURFER_HOME/SetUpFreeSurfer.sh If the “source" command results in an error, then you can try to see what failed by running the shell script with “sh -x” instead of “source”. $ sh -x $FREESURFER_HOME/SetUpFreeSurfer.sh If running the script with “sh -X” does not end with a “return 0” statement displayed on the terminal, then you cost cut and paste the last several lines before the error and email it back to us. - R. On Aug 31, 2019, at 00:04, Viviana Siless <viviana.siless(a)gmail.com> wrote:        External Email - Use Caution        Hi, I think you are just mistyping it, if the subjects dir is in "/Applications/freesurfer/subjects/ " the command  should be:export SUBJECTS_DIR=/Applications/freesurfer/subjects/ ( instead of  export SUBJECTS_DIR=<Applications/freesurfer/subjects>)Viv On Fri, Aug 30, 2019 at 4:35 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote:oh, the export command is failing? You mentioned you weren't running bash (which is the shell that knows what to do with an export command). Can you install bash? If not, you can use setenv instead of export and the .csh file instead of the .shOn Fri, 30 Aug 2019, michele rizzi wrote:> >         External Email - Use Caution        > > > I put > > > export SUBJECTS_DIR=<Applications/freesurfer/subjects>> > > > but again I get > > > > -bash: syntax error near unexpected token `newline'> > > > > > >_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Substancia-Nigra ROI
by Gwang-Won Kim 30 Aug '19

30 Aug '19

2 1

PETsurf kinetic modeling with MRTM
by Chanmi Kim 30 Aug '19

30 Aug '19

External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3 tau PET data for partial volume correction (PVC). So, I've tried to do a command line as below. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz The 'mri_glmfit' required 'time.dat' which is an information of the time activity curve (TAC), however, I don't know how to get this information. Can you please let me know how to get this information? Please share any examples of 'time.dat' If there is anyone who has experience in PetSurf PVC, Chan

2 1

Corresponding structures to an ROI
by Wang, Lily 30 Aug '19

30 Aug '19

Hi All, I have several white matter ROI masks unique to each subject that were made using the subjects' T2 scans and I would like to use wmparc to find out what brain structures those ROI's correspond to. I'm guessing that I will need to either register T1 to T2 or T2 to T1 at one point, which I have done by using mri_robust_register to register T1 to T2 (and it seemed to turn out ok, but how do I check other than by eye? And is there a better way to register?), and apply that transformation to wmparc. But other than figuring out the registration, what else do I do? Thank you, Lily

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recon_all cuda 9.1
by Dev vasu 30 Aug '19

30 Aug '19

External Email - Use Caution Dear all, Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1. Thanks Vasudev

1 0

I have a question for subthalamic nucleus ROI.
by Gwang-Won Kim 30 Aug '19

30 Aug '19

2 1

Problem with install freesurfer
by 余文豪 30 Aug '19

30 Aug '19

External Email - Use Caution Dear MR/MS: I have a problem with installation as the following. Could anyone help me with that. Thanks a lot

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