Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Longitudinal prediction
by Alexandru Hanganu 31 Oct '14

31 Oct '14

Dear FreeSurfer Experts, How could the longitudinal analysis be performed in order to show whether a parameter at time 1 is predictive of changes in cortical thickness over time ? and can thecorresponding regions be shown in FreeSurfer ? In a statistical analysis, as we see it, we must perform the correlation between the parameter at time 1 and the cortical thickness difference (or ROI)time 2-time1, yet in this case we cannot see it on the cortex. Thank you, Alex

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Re: [Freesurfer] adding insula voxels
by Adam Mezher 30 Oct '14

30 Oct '14

I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam

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Converting lesion volume to surface area
by Timothy Meier 30 Oct '14

30 Oct '14

Hello, Previously we have used a lesion of 128 microliters and have filtered out anything smaller in volume than that for analyses (single subject "pothole" analysis). Now we want to do something similar on the surface. So we need to approximate the surface area of that 128 microliters when translated to group analysis surface (fsaverage). 128 microliters is 128 data points in 1x1x1 resolution. Let's say those data points only exist in the cortical ribbon volume. Question 1: How many of the 128 data points from cortical ribbon volume get translated into surface space? What is the volume to surface translation ratio? Question 2: Because we want to filter clusters with mri_surfcluster, we are interested in the resulting area of our original 128 lesion. Therefore, how much area is represented by each data point when translated onto the surface? Is this simply "AvgVtxArea" of the inflated surface multiplied by the number of data points that get translated from volume to surface? And what is the best way to answer these two questions from standard Freesurfer output: e.g. Should we calculate from the ("NumVert" "SurfArea" "GrayVol") columns of the lh.aparc.stats file, get the mean of all SurfArea/GrayVol from aparc.stats, and then multiple by our 128? Any thoughts or suggestions would be appreciated. Thanks, Tim

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Senior Researcher position in Madrid, Spain
by José Ángel Pineda 30 Oct '14

30 Oct '14

Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the area of scientific-technological initiatives in Biotech indicated below, in accordance with the procedure established in the Regulatory Bases of 30 April 2009 for the ISAAC PERAL Program for Senior UPM Researchers (in the attached document). The candidate degree may be from any specialization in Engineering, Physics, Mathematics, Statistics, Biology, Biochemistry, etc. Location: The activities will be carried out in the Campus of International Excellence: Campus of Montegancedo at the CTB: Centre for Biomedical Technology (www.ctb.upm.es) in Madrid, Spain. Beneficiaries: 1. Have held a PhD for more than 10 years, effectively pursuing uninterrupted research activity during that time. 2. Have extensive research experience in the sphere of the profile of the contract announced, i.e. biomedical imaging. 3. Have pursued their research activity following the award of their PhD in relevant foreign Research Centers for at least six years or have studied the whole of the PhD and graduated in a foreign University or Research Centre and have pursued subsequent research activity in a relevant foreign research center for at least three years. 4. Have certified experience in the management of research groups in university institutions or relevant research centers. All the requirements demanded and the merits argued by candidates must have been fulfilled prior to the date of termination of the period for the submission of applications. Conditions of the position: 1. Gross remuneration shall not be less than 80000 € nor more than 90000 € per year. 2. Three year contracts for two young PhDs 3. Three positions for PhD studies (four years) 4. A 30000 € support for the Senior researcher during the first year of contract to facilitate the start of the research activities 5. A minimum of 100m2 space available in the Centre for Biomedical Technology N.B.: All the the details of the call can be consulted at the following link: *http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf <http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servici…>* Interested candidates should send CV to the following email address francisco.delpozo(a)ctb.upm.es. [image: http://www.upm.es/sfs/Montegancedo/Noticias/imagenes/ctb.gif] Prof. Francisco del Pozo Director Center for Biomedical Technology (CTB) Universidad Politécnica de Madrid Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES Tfo: +34 913364632 (Tfo: +34 913364631) www.ctb.upm.es

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Fwd:
by José Ángel Pineda 30 Oct '14

30 Oct '14

1 0

Error with asegstats2table function
by Claire Morley 30 Oct '14

30 Oct '14

Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' [dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt Password: ERROR: SUBJECTS_DIR environment variable not defined! Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt ERROR: output table name should be specified (use --tablefile FILE) Please help! I have tried everything I can think of. Thank you for everything, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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Unknown problem with fsgd file
by Bronwyn Overs 30 Oct '14

30 Oct '14

Dear Freesurfer Mailing list, I have been attempting to run mri_glmfit using a complicated fsgd file (1 categorical varible with 5 levels, 3 categorical variables with 2 levels, age as covariate). When I run the command, I receive the following error: gdfReadHeader: reading site-gender-group-riskhaplotype.fsgd Input line 5, subjid = 100121, class siteMelbourne-anyRiskAnyRisk-genderFemale-groupControl not defined FSGDF Format Error: file = site-gender-group-riskhaplotype.fsgd, tag=Input I have double checked the fsgd file and confirmed that the class for participant 100121 was specific correctly at the beginning of the file (correct spelling and case was used). So I cannot identify the source of the error. Can you advise me as to what may be going wrong? My full fsgd file begins like this (I have 389 subjects but have provided only the first 20 for brevity): GroupDescriptorFile 1 Title GLM_SiteGender Class siteBrisbane-anyProtNoProt-genderMale-groupCase Class siteBrisbane-anyProtNoProt-genderFemale-groupCase Class siteBrisbane-anyProtNoProt-genderMale-groupControl Class siteBrisbane-anyProtNoProt-genderFemale-groupControl Class siteBrisbane-anyProtAnyProt-genderMale-groupCase Class siteBrisbane-anyProtAnyProt-genderFemale-groupCase Class siteBrisbane-anyProtAnyProt-genderMale-groupControl Class siteBrisbane-anyProtAnyProt-genderFemale-groupControl Class siteMelbourne-anyProtNoProt-genderMale-groupCase Class siteMelbourne-anyProtNoProt-genderFemale-groupCase Class siteMelbourne-anyProtNoProt-genderMale-groupControl Class siteMelbourne-anyProtNoProt-genderFemale-groupControl Class siteMelbourne-anyProtAnyProt-genderMale-groupCase Class siteMelbourne-anyProtAnyProt-genderFemale-groupCase Class siteMelbourne-anyProtAnyProt-genderMale-groupControl Class siteMelbourne-anyProtAnyProt-genderFemale-groupControl Class siteNewcastle-anyProtNoProt-genderMale-groupCase Class siteNewcastle-anyProtNoProt-genderFemale-groupCase Class siteNewcastle-anyProtNoProt-genderMale-groupControl Class siteNewcastle-anyProtNoProt-genderFemale-groupControl Class siteNewcastle-anyProtAnyProt-genderMale-groupCase Class siteNewcastle-anyProtAnyProt-genderFemale-groupCase Class siteNewcastle-anyProtAnyProt-genderMale-groupControl Class siteNewcastle-anyProtAnyProt-genderFemale-groupControl Class sitePerth-anyProtNoProt-genderMale-groupCase Class sitePerth-anyProtNoProt-genderFemale-groupCase Class sitePerth-anyProtNoProt-genderMale-groupControl Class sitePerth-anyProtNoProt-genderFemale-groupControl Class sitePerth-anyProtAnyProt-genderMale-groupCase Class sitePerth-anyProtAnyProt-genderFemale-groupCase Class sitePerth-anyProtAnyProt-genderMale-groupControl Class sitePerth-anyProtAnyProt-genderFemale-groupControl Class siteSydney-anyProtNoProt-genderMale-groupCase Class siteSydney-anyProtNoProt-genderFemale-groupCase Class siteSydney-anyProtNoProt-genderMale-groupControl Class siteSydney-anyProtNoProt-genderFemale-groupControl Class siteSydney-anyProtAnyProt-genderMale-groupCase Class siteSydney-anyProtAnyProt-genderFemale-groupCase Class siteSydney-anyProtAnyProt-genderMale-groupControl Class siteSydney-anyProtAnyProt-genderFemale-groupControl Variables age Input 100105SA sitePerth-anyProtNoProt-genderMale-groupCase 23 Input 100112SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 22 Input 100117SA siteBrisbane-anyProtNoProt-genderMale-groupCase 39 Input 100118 siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100121 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 21 Input 100122 siteMelbourne-anyProtAnyProt-genderMale-groupControl 53 Input 100151 siteMelbourne-anyProtNoProt-genderFemale-groupControl 58 Input 100185SA siteBrisbane-anyProtNoProt-genderFemale-groupControl 24 Input 100187 siteBrisbane-anyProtNoProt-genderMale-groupCase 24 Input 100189 siteBrisbane-anyProtNoProt-genderFemale-groupCase 21 Input 100190 siteSydney-anyProtNoProt-genderMale-groupControl 41 Input 100191 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 19 Input 100193SA siteSydney-anyProtNoProt-genderMale-groupControl 26 Input 100196 siteBrisbane-anyProtNoProt-genderMale-groupControl 55 Input 100197SA siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100200SA siteBrisbane-anyProtNoProt-genderMale-groupControl 39 Input 100204 siteSydney-anyProtAnyProt-genderFemale-groupControl 50 Input 100208 siteBrisbane-anyProtNoProt-genderMale-groupControl 25 Input 100209SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 35 Input 100214 siteSydney-anyProtAnyProt-genderMale-groupCase 44 The mri_glmfit command I am using is as follows: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C gender.mtx --C group.mtx --C haplotype.mtx --C groupXgender.mtx --C haplotypeXgender.mtx --C groupXhaplotype.mtx --C genderXgroupXhaplotype.mtx --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

2 1

Name external disk not recognized
by Righart, Ruthger 30 Oct '14

30 Oct '14

Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger

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Venous system on 3D models
by rwlodar2＠uic.edu 30 Oct '14

30 Oct '14

Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. Thanks!!

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Re: [Freesurfer] adding insula voxels
by Adam Mezher 30 Oct '14

30 Oct '14

Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go about editing them manually by adding the correct label to the empty voxels with the Edit Segmentation tool in tkmedit. Thank you, Adam

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