Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Increase VBOX disksize
by shi yao wang 30 Mar '16

30 Mar '16

Dear Sir/Madam I am using freesurfer to proceeding brain MRI data. I have 30 cases. However, the space for home is no enough. I am wondering how can I increase disk space to computing my data. I use Vbox unbentu system. thanks Lawrence

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Re: [Freesurfer] Surface area of an fsaverage label
by Jaiashre Sridhar 29 Mar '16

29 Mar '16

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Re: [Freesurfer] Surface area of an fsaverage label
by Jaiashre Sridhar 29 Mar '16

29 Mar '16

Douglas, This is my command line: label_area lh fsaverage lh.temporalpole Output: bash-3.2$ label_area lh fsaverage lh.temporalpole reading /Volumes/project/fsaverage/surf/lh.smoothwm... adjusting for group surface area 1.31 (82220 / 62822) fsaverage: lh.temporalpole - 512.352 square mm Thanks, Jaiashre. Re: [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46383.html> 2016-03-29<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> what is your command line? Re: [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46368.html> 2016-03-28<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Bruce Fischl<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hi Jaiashre, yes, it should do the correction for average surface area, and should print out a message indicating it is doing so. Something like: adjusting for group surface area ... cheers Bruce [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46366.html> 2016-03-28<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Jaiashre Sridhar<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hello, I have used label_area to compute the surface area of a desikan label on fsaverage. Is the correction factor taken into account during computation with this function? Thanks, Jaiashre.

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Surface area of an fsaverage label
by Jaiashre Sridhar 29 Mar '16

29 Mar '16

Hello, I have used label_area to compute the surface area of a desikan label on fsaverage. Is the correction factor taken into account during computation with this function? Thanks, Jaiashre.

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Visualising regional values on the surface
by Kirstie Whitaker 29 Mar '16

29 Mar '16

Hi, I'd like to show correlation coefficients by region on the brain surface. So for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color each atlas region according to the module it has been assigned to. It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what. Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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Cognitive & Brain Sciences PhD opening call, University of Trento, Italy
by Jovicich, Jorge 29 Mar '16

29 Mar '16

Dear All, We are pleased to announce the opening of a call for 14 fellowships for our international PhD Program in Cognitive and Brain Sciences (CIMeC), commencing in November 2016 at the University of Trento, Italy. As you will see from the links below, the PhD call is open to several fields of cognitive neuroscience research. Interested candidates should feel free to contact the PIs that might have topics of interest to them. PhD areas outline: http://web.unitn.it/en/drcimec/37990/32nd-cycle-research-topics-2016-call PhD Application summary: http://web.unitn.it/en/drcimec/10141/application-summary-and-process PhD Application link: https://webapps.unitn.it/Apply/en/Web/Home/dott *PhD Application deadline: Tuesday May 10, 2016, at 4pm ECT* CIMeC: http://web.unitn.it/en/cimec Supplementary information about CIMEC's doctoral program: -CIMeC ranked 1^st in Italy for Quality of Research 2013 <http://www.unitn.it/en/ateneo/1684/anvur-report-2013-trento-is-ranked-first…> -2014-2015 UNITrento ranks 1st in Italy in the rankings of THE - Times Higher Education <http://www.unitn.it/en/ateneo/1636/rankings> -3-yr program: Nov. 1, 2016- Oct. 31, 2019 -Courses are given in English -14 positions, 100% funded -Salary: starting at €1.100/mo., tax-free -Winners receive a €2800 tax-free research/mobility budget -Winners are eligible for a €150/month residential contribution -Why choose UniTrento <http://www.unitn.it/en/ateneo/1629/why-choose-unitrento> - FAQ: http://www.unitn.it/en/drcimec/10142/frequently-asked-questions - More information: phd.cimec(a)unitn.it <mailto:phd.cimec@unitn.it> -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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registering data to template
by Clara Kühn 29 Mar '16

29 Mar '16

Dear FreeSurfer experts, I would like to analyze my longitudinal data also cross-sectionally at single time points. I am a little confused as to how to register my data to the template and smooth it accordingly. Do I have to do it once with a cross-sectional command and once with a longitudinal command? This is what I thought I understood: for LME this registers the data to the template: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template --hemi lh --meas thickness --out lh.thickness.mg and this smoothes it: recon-all -s name -qcache -target name_of_template In that order? for QDEC (single tp) I use this to register and smooth: long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache kids_template --sd $SUBJECTS_DIR So then, when would I use this?: long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out qdec/cross.qdec.table.dat I am a little confused by the longitudinal option for QDEC when it can't really deal with such data. Should I register and smooth (eg) time point 1 of all my participants to look at it in QDEC as if it were cross-sectional data with this?: mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh And when do I need to use this?: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target kids_template --hemi lh --meas thickness --out lh.thickness.mgh? The possibilities and the ever so slightly changing commands are somewhat overwhelming, sorry... Thanks in advance, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Cross sectional analysis of a longitudinal data
by Kasper Jessen 29 Mar '16

29 Mar '16

Dear FreeSurfer experts, We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following: 1. The [CROSS], edited [BASE] and [LONG] is processed. 2. We will create a qdec table called qdec.table.dat. However, because we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?). SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ... 2. We transfer the default fsaverage to the subject directory. 3. To presmooth the data onto the target we run the following command: *recon-all -long <tpid> <baseid> -qcache* When the above steps are done we plan to load it into QDEC. Is the above steps correct for doing a cross-sectional group analysis in QDEC? Best regards, Kasper Jessen MD, PhD student

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Error of invalid license file
by Yuan Lin 28 Mar '16

28 Mar '16

Hello, I installed the Freesurfer tool several months ago. Today when I run the "recon-all" command, it showed the error "ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment." I have created a .license file and copied the following information from the email. Y***(a)hotmail.com 26162 *C0m0U2INd.0M FS1DlaVbYasqE But the error still exits. I don't how to solve it. Can anyone help me? Thank you so much. Best Lin Yuan

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Pial segmentation error
by Deniz Ozgen 28 Mar '16

28 Mar '16

Hi everyone, We have been having consistent errors, where the extreme left and extreme right of the brain are mis-segmented. Basically, it looks like the intensity normalization is not working well. I'm sending a screenshot to illustrate the problem. We added control points to fix the errors before, but this one seems like a lot of work. Is there a solution you can offer? Such as changing parameters for segmentation etc. FYI: image is acquired on a Skyra scanner with FA 9 degrees, TI 930, TR 2300, TE 2.39. We may be able to change the parameters in the future, but we still need to get these scans processed. Thank you. [image: Inline image 1]

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