Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Freesurfer's last version installation
by Barletta, Valeria 03 Oct '19

03 Oct '19

Dear Freesurfers, We need to install the last version of Freesurfer, but we need to keep the wm edits that we made with version 5.3 How can this be done? Is there any specific command? Thanks a lot, Vale

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Freesurfer - issue after installation in Linux
by Theotonio Pauliquevis 03 Oct '19

03 Oct '19

External Email - Use Caution Hi, I just installed freesurfer in Linux Ubuntu 14.04, and I got a critical (and strange) problem in the earlier tests of freesurfer (Example 2). Any help would be appreciated. Basically, when trying example 2 in instructions homepage I got the following error: theo@theo-Inspiron-5457:~$ recon-all -i sample-001.nii.gz -s bert -all bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory But the fact is that recon-all is there and apparently it is well configured, because 1) the recon-all does exist, and 2) permissions are ok: theo@theo-Inspiron-5457:~$ ls -l /usr/local/freesurfer/bin/recon-all -rwxrwxr-x 1 8481 1590 327555 Jan 18 2017 /usr/local/freesurfer/bin/recon-all and the command is promptly recognized : theo@theo-Inspiron-5457:~$ which recon-all /usr/local/freesurfer/bin/recon-all/ Any ideas? Anybody got this issue before? It seems to be some (not obvious) permission problem. Below I type the whole procedure to install, so one can see that I followed all installation instructions. History: 1) Successfully downloaded and unzipped the files at /usr/loca/freesurfer 2) Successful set up of environment variables after including the following lines in .bashrc: ############################################## #Software FREESURFER - Enviroment variables # export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/theo/freesurfer/subjects ############################################## BTW, "theo" is my userID 3) File license.txt copied to /usr/local/freesurfer 4) message after open a terminal window confirms that Enviroment variables were correctly set: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni (base) theo@theo-Inspiron-5457:~$ echo $SUBJECTS_DIR /home/theo/freesurfer/subjects (base) theo@theo-Inspiron-5457:~$ Any help is welcome Regards Theotonio

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Curvature estimation from Hessian
by LOSKE, PHILIPP (PGR) 03 Oct '19

03 Oct '19

External Email - Use Caution Hi, I am trying to understand how exactly FreeSurfer estimates the curvature values from the white surface. From the mailing lists I understood that the white surface is modeled by fitting a second-order polynomial function and curvatures are estimated from the Hessian matrix at each vertex (thank you Bruce). However, I still have trouble to understand how this works in detail. First, as I understand it, curvature can only be derived from the Hessian if the gradient vanishes (why is this the case?), and from differential geometry, shouldn't instead the shape operator be calculated at each vertex on the surface? Second, are the Gaussian and mean curvatures then directly calculated from Hessian/Shape operator or first principle curvatures (and are they saved somewhere?). I tried to find a detailed explanation in some of the FreeSurfer papers, but couldn't find anything really. Thank you very much in advance! Cheers Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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selxavg3-sess
by Sanati Monfared, Shamsi 02 Oct '19

02 Oct '19

External Email - Use Caution Hi all, I am running the functional analyses (selxavg3_sess) and stuck at the following error, which I have no idea what to do (apparently the analyses have been OK up until run 010 and the error happened in run 012). I received the same errors in my all subjects (at run 012) 'gunzip -c /Users/smonfared6/Desktop/WheelerChess_dcm/Chess_Functional/chess001/bold/010/fmcpr.up.sm5.fsaverage.lh.nii.gz > /var/folders/v3/yznj9t351dbgs1093rr12wrh010dv3/T/tp7da06091_16b6_41ba_8283_005c005b5dd3.load_nifti.m.nii' cmd = 'gunzip -c /Users/smonfared6/Desktop/WheelerChess_dcm/Chess_Functional/chess001/bold/012/fmcpr.up.sm5.fsaverage.lh.nii.gz > /var/folders/v3/yznj9t351dbgs1093rr12wrh010dv3/T/tpc5683b1b_4f0b_4593_ab5d_82233348f546.load_nifti.m.nii' ERROR: fast_st2fir: two or more presentations are simultaneous ERROR: creating FIR design matrix for Condition03 Dot indexing is not supported for variables of this type. Error in flac_customize (line 358) if(~isempty(flacnew.TFmtx)) Error in fast_selxavg3b (line 184) flac = flac_customize(flac); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Any advice would be highly appreciated! Thanks, -Shamsi --- [cid:fdf9e808-3a33-4fda-a4f9-de06f4fae657] Wheeler Lab<http://wheelerlab.gatech.edu/> | Center for Advanced Brain Imaging<http://wheelerlab.gatech.edu/> 831 Marietta St NW, Atlanta, GA 30318 Email: smonfared6(a)gatech.edu Phone: 205-607-1656

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Freesurfer three groups: group A vs C power.
by cody samth 02 Oct '19

02 Oct '19

External Email - Use Caution Hi I have a question regarding how freesurfer calculates the degrees of freedom when you have three groups in the FSGD/contrast files but are running analyses on group A vs C. For example I have an analysis with 3 groups and 2 covariates. My primary question is: is there a difference between any groups. Which I have the contrast: 1 -1 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 When I write a contrast for A vs C: (1 0 -1 0 0 0 0 0 0) Does freesurfer consider this model as 9 regressors? Or 6 regressors; which would be present in a typical group 1 vs group 2 analysis that could be modeled by (1 -1 0 0 0 0) if group B didn't exist?

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Re: [Freesurfer] username and password
by fsbuild 02 Oct '19

02 Oct '19

External Email - Use Caution Hello Takashi, Did you create a login to the list on this page, http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - and then receive the email notification, and then did you do the confirmation step? - R. On Oct 1, 2019, at 11:03, Yamada, Takashi <takashi_yamada(a)brown.edu> wrote:        External Email - Use Caution        Hi,I'm subscribers of freesurfer.However, I am about to reading the mail exchange about the Q&A of freesurfer,I was asked to input the username and password, then I cannot read them.How should I proceed for that?Best,Takashi Yamada--------------------------------------------------------------------------------------------------------------------------------Takashi Yamada, MD & PhDPostdoctorial Research AssociateDepartment of Cognitive, Linguistic and Psychological Sciences (CLPS)Brown UniversityBox 1821  190 Thayer Street  Providence, RI 02912TEL : +1 401 863 9488  FAX : +1 401 863 2255Email: takashi_yamada@brown.edu--------------------------------------------------------------------------------------------------------------------------------_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"
by Caspar M. Schwiedrzik 02 Oct '19

02 Oct '19

External Email - Use Caution Hi! I am following up on this thread trying to understand how to make the color wheel visible in rtview, or, if necessary, in freeview. Thank you! Caspar

3 10

bad segmentation in the occipital pole
by Xiaoqian Yan 02 Oct '19

02 Oct '19

External Email - Use Caution Dear Freesurfer experts, I am trying to do the segmentation on a patient's T1 image. I did not get error messages running the 'recon-all' (recon-all -i T1.nii -subjid PatientName -all), but the segmentation over the right occipital pole was inaccurate. I tried to manually edit the wm.mgz several times, but the output did not change a lot (please see the attached image). The patient had depth EEG electrodes implanted in this region before, so there is a thermal lesion which I thought could have caused the bad segmentation over there. Do you have any ideas about what I can do next? Thanks in advance, best wishes Xiaoqian

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BIDS Governance and Steering Group voting has opened!
by Franklin Feingold 01 Oct '19

01 Oct '19

External Email - Use Caution The time has come to vote on our BIDS Governance document (https://docs.google.com/document/d/1R-J2lL9V_wIkYhye4zH-feyl4P4J8NyO40rIYyY…) and for the inaugural Steering Group (https://docs.google.com/document/d/1yb6j3a90serWbtab7ukSMyecs16sGfYTSGftH-4…) Voting opens today (October 1) and runs through October 15, 2019, closing at 11:59pm Pacific Daylight Time (UTC -7). Votes will be recorded using a Google Form (https://docs.google.com/forms/d/e/1FAIpQLSfG76N3dnazONsfCsWAXccgrizmb1gm233…) and a separate form for email validation (https://docs.google.com/forms/d/1zr-w3M2K7ApaW3yePXNRc1zYMhIiDsOVnG15nJ1sgx…) to make sure the vote is confirmed. The forms have been created separately to dissociate contact information from voting information, and no attempt will be made to re-associate these data. Contact information will be used to ensure that the number of votes matches the number of voters, making fraudulent voting easier to detect. The verification form allows voters to opt-in to having their email retained for this purpose. All email addresses will be deleted immediately once the election results have been verified, with the exception of voters who opt to have their email address retained. Ratification of the Governance Document is a mandatory vote, with “Yes” indicating approval of the document, and “No” indicating rejection. A simple majority of “Yes” votes will ratify the document. Failure to achieve a majority will nullify the election. Steering Group candidates are organized into slates of five candidates, and the winning slate will form the inaugural Steering Group. Slates are voted on according to a ranked ballot, with the preferred slate ranked as “1”, second choice as “2”, and so on. Votes will be tabulated according to the instant-runoff (https://en.wikipedia.org/wiki/Instant-runoff_voting) method. A ballot will be considered invalid if multiple slates receive the same rank. In addition, we are getting very close to finalizing our BIDS-Derivatives extension! We are looking for more feedback from community! The relevant conversations can be found in a GitHub pull request (https://github.com/bids-standard/bids-specification/pull/265) This pull request has identified a few conversations left to reach a consensus before the final review! If you are interested in particular modalities in BIDS, we have established teams on GitHub (https://github.com/bids-standard/bids-specification/issues/285) to more easily follow the conversations that are most relevant to you! We also have a starter kit (https://github.com/bids-standard/bids-starter-kit) to help you get started using BIDS or finding ways to contribute to the effort! If you have any questions regarding this process or BIDS please feel free to email Franklin (ffein(a)stanford.edu) Thank you in advance for taking the time to vote! Franklin

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Research Assistant Position at Brown University
by Hwamee Oh 01 Oct '19

01 Oct '19

External Email - Use Caution Dear colleagues: We are looking for a Research Assistant who will join a group of researchers studying Aging and Alzheimer's disease at Brown University. 50% of time of the position will be devoted to behavioral and fMRI experiment preparation, data collection, and MRI/PET neuroimaging data analysis and the other 50% of time will be devoted to other types of data analysis and data management including online survey, biospecimen, and cognitive assessment. The successful candidate should have BS or BA in Psychology, Biology, Neuroscience, Computer Science, or closely related field, computer programming skills (e.g., Python, Unix), and prior experience or willingness to work with human participants and data in research or clinical settings. Knowledge on statistics and a career interest in pursuing age- and Alzheimer's disease-related fields are a plus. Interested applicants can submit applications through this website ( https://brown.wd5.myworkdayjobs.com/en-US/staff-careers-brown/job/Butler-Ho…) For any inquiries on the research and the position, please contact Dr. Hwamee Oh at hwamee_oh(a)brown.edu.

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Freesurfer