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30099 discussions

asegstats2table for all subjects in the directory
by Luis Fernado Silva Castro de Araújo 22 Jan '16

22 Jan '16

Hi Freesurfer experts, I wonder if there is a way of extracting the stats for all patients in my last run at the same time. I have around 120 observations and the asegstats2table syntax works in such a way that all the patients names should be listed: asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table I hope I am wrong, but it seems that the —subjects argument does not accept substitution with wildcards, like * or *.* Is there a way to make the command run the extraction of the statistics in all subjects within the $SUBJECTS_DIR in order to avoid typing all the 120 folder names? A bash script would do too. Thanks, luis

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converting cache.th13.abs.sig.cluster.mgh into a binary mask
by Erik Lindberg 22 Jan '16

22 Jan '16

Dear Freesurfers, I like to convert a cache.th13.abs.sig.cluster.mgh into a binary mask - so that everything that is below 0.05 will be included in the mask - how can I do this? Eric

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mkanalysis-sess
by Thục Trinh 22 Jan '16

22 Jan '16

Hello, I am using mkanalysis-sess command to configure analysis and I have some questions. 1, After run preproc-sess on raw data, why would we want to repeat all the flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5). Is it gonna effect to our f.nii if I input different value from the previous preproc-sess command ? 2. -refeventdur: I read that if we have different duration of stimuli, we can set the -refeventdur equal the mean of all stimuli durations. But in my study, the duration of stimulus depends on the reaction time of subject, so it's gonna be different for each subject. how can I manage that? Thank you, Trinh

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surf mm coordinates do not match the individual anatomy
by Julia Berezutskaya 22 Jan '16

22 Jan '16

Hi all, I am loading a subject's surf (lh.pial) into MATLAB using read_surf(). At the same time I have a mesh based on the original subject's anatomy in .nii. The mm coordinates of these two do not match. Does anyone know why? The same anatomy was used for surface reconstruction. The very ranges of vertex coordinates differ by 10-20 mm, and simple translation of coordinates along each dimension does not solve it. Most difference is along Z axis. I understand, that along X axis it can be expected since there is only left hemisphere in surf and both in volume anatomy, but is there a way to coregister the other two dimensions? Thank you, Sincerely, Julia Berezutskaya

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transform statistical map in MNI to surface
by John Anderson 22 Jan '16

22 Jan '16

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Re: [Freesurfer] Sulcal depth units (Simon Vandekar)
by Simon Vandekar 22 Jan '16

22 Jan '16

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still unclear on what the units are. They are too small to be millimeters. Given other published measurements of sulcal depth I think they might be in centimeters, but can you confirm? Thanks again, Simon >Hi Simon > >I just took a look at the code and I believe that we make it 0 median >(not mean) and unit standard deviation. The curvatures can get quite large >in regions where the vertex spacing is small and the median is robust to >this. > >cheers >Bruce > > >On Sat, 24 Oct 2015, Simon Vandekar wrote: > >> Hi Bruce, >> >> I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. >> >> Thanks again, >> Simon >> >> >>> H I Simon >>> Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it >>> Bruce >>> >>>> On Oct 22, 2015, at 3:23 PM, Simon Vandekar <simonv(a)mail.med.upenn.edu> wrote: >>>> >>>> Hi Bruce, >>>> >>>> I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? >>>> >>>> >>>> sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) >>>>> mean(sulc$sulc) >>>> [1] -1.236923e-08 >>>> >>>>> var(sulc$sulc) >>>> [1] 0.3276958 >>>> >>>>> quantile(sulc$sulc) >>>> 0% 25% 50% 75% 100% >>>> -1.72503 -0.42128 -0.03963 0.40072 1.80980 >>>> >>>> >>>> Thanks again, >>>> Simon >>>> >>>> >>>> >>>> >>>> >>>> Hi Simon >>>> >>>> they are originally mm, but I believe we z-score normalize them so that >>>> the sulc file is 0 mean and unit variance. >>>> >>>> cheers >>>> Bruce >>>> On Wed, 21 Oct 2015, Simon >>>> Vandekar wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> >>>>> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. >>>>> Are the units for sulcal depth in mm or are they in arbitrary units? >>>>> >>>>> Thanks in advance, >>>>> Simon

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mkdir error when running FS 6.0 hippocampal segmentation
by Rosanna Olsen 21 Jan '16

21 Jan '16

Dear Dr. Eugenio Iglesias and FreeSurfer developers, Thank you for the development of this very useful segmentation tool! When I try to run FreeSurfer 6.0's hippocampal segmentation on our computing cluster, I get the following error: "error using mkdir; Permission denied". I am not sure which directory this part of the script is trying to write to (it might be the software directory where FreeSurfer is installed, in which I do not have write permission because it is on a shared resource) -- I will attach a screenshot of the error here. Your attention is appreciated! Thanks, Rosanna Olsen -- Rosanna Olsen, Ph.D. Scientist, Rotman Research Institute, Baycrest rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen

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12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. (fwd)
by Lilla Zollei 21 Jan '16

21 Jan '16

FYI: this is a great program for PhD students and postdocs. ---------- Forwarded message ---------- Date: Wed, 20 Jan 2016 17:09:55 +0100 From: Christian ROUX <christian.roux(a)mines-telecom.fr> To: ROUX Christian <c.roux(a)ieee.org> Subject: 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. Dear former Faculty member of the summer school, This school has become the world reference in the field since its launching in 1994. As previous lecturer, you are acknowledged to have contributed to this success and the biomedical imaging community worldwide is grateful to your commitment. The organization of the 12th edition of the summer school to be held next June is progressing as you can see from our website (http://conferences.telecom-bretagne.eu/ieeess/ <http://conferences.telecom-bretagne.eu/ieeess/>) and the programme is already in a good shape. As you may remember, the summer school was originally located in Berder but has been relocated since 2014 in Saint Jacut de la Mer in a wonderful facility close to Saint Malo and Mont Saint Michel. The basic of the summer school remain the same: The students are about 45 (they are selected by an international committee) and usually come from more than 20 countries. They are PhDs, post-doctoral students, engineers from industry, and already involved in some area of biomedical imaging. The school is aimed at offering to the best international junior researchers a place for learning, exchanging and future networking. And we have the chance to gather the best experts in the world in this very active field who are keen to share their experience and interact with the students in many ways. We would be very honored and very pleased if you could help us in disseminating and publicizing the call for participation that is attached. As you know, we are currently in this critical phase of dissemination where it is of utmost importance to reach the students who might be interested in joining this fantastic adventure. Jean-Louis, Jean-Christophe and myself are looking forward to receiving your assistance in this matter. We take this opportunity to extend you our best wishes for a healthy and successful year 2016. Best regards. JLC & JCOM & ChR <http://www.mines-telecom.fr/> Prof. Christian ROUX Directeur de la recherche et de l’innovation / Executive Vice President for Research and Innovation +33 (0)1 45 81 71 7037-39 rue Dareau 75014 Paris, France <http://www.mines-telecom.fr/> <https://twitter.com/Mines_Telecom> <https://www.facebook.com/mines.telecom> <https://plus.google.com/+mines-telecomFr/> <https://www.linkedin.com/company/institut-mines-t-l-com> <http://blogrecherche.wp.mines-telecom.fr/>

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tutorial assistance
by Jasmin Alves 21 Jan '16

21 Jan '16

Hello again freesurfer team, While running through the group analysis tutorial, on step "previously cached (qcached) Data I ran into the following issue with the command below. Any recommendations? Jasmins-MacBook-Pro:glm jasminalves$ mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh & [2] 5633 Jasmins-MacBook-Pro:glm jasminalves$ ERROR: cannot find /buckner_data/tutorial_subjs/group_analysis_tutorial Thanks! Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Regressing out various categorical variables
by Erik Lindberg 21 Jan '16

21 Jan '16

Dear Freesurfers, I am running a design in which I want to correct for a number of categorical variables: diagnosis, gender and apoe status and one continuous variable (age) in a correlation analysis Did I get this right? (below) Thanks, Eric GroupDescriptorFile 1 Title MyTitle Class AMCI_F_APOE- Class AMCI_F_APOE+ Class AMCI_MALE_APOE- Class AMCI_MALE_APOE+ Class CTL_FEMALE_APOE- Class CTL_FEMALE_APOE+ Class CTL_MALE_APOE- Class CTL_MALE_APOE+ Class NON_A_MCI_FEMALE_APOE- Class NON_A_MCI_FEMALE_APOE+ Class NON_A_MCI_MALE_APOE- Class NON_A_MCI_MALE_APOE+ Class SCI_FEMALE_APOE- Class SCI_FEMALE_APOE+ Class SCI_MALE_APOE- Class SCI_MALE_APOE+ Variables AGE_DEMEAN CSF_Ab40_ADx With the contrast matrix: corr.mtx: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

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