Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Freesurfer Regions
by Ananth Narayanan 02 Dec '15

02 Dec '15

Hello freesurfer users, I am a new user of freesurfer. We are using FS to define ROIs for out PET analysis. I looked at the FS color lookup table, and saw the following ROIs. 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-posterior 120 21 133 0 8005 Thalamus-Ventral-lateral 195 61 246 0 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 8008 Thalamus-intralaminar 232 146 33 0 8009 Thalamus-centromedian 4 114 14 0 8010 Thalamus-mediodorsal 121 184 220 0 8011 Thalamus-medial 235 11 175 0 8012 Thalamus-pulvinar 12 46 250 0 8013 Thalamus-lateral-geniculate 203 182 143 0 8014 Thalamus-medial-geniculate 42 204 167 0 Where can I find these regions? 9000 ctx-lh-prefrontal 30 5 30 0 9001 ctx-lh-primary-motor 30 100 45 0 9002 ctx-lh-premotor 130 100 165 0 9003 ctx-lh-temporal 105 25 5 0 9004 ctx-lh-posterior-parietal 125 70 55 0 9005 ctx-lh-prim-sec-somatosensory 225 20 105 0 9006 ctx-lh-occipital 225 20 15 0 9500 ctx-rh-prefrontal 30 55 30 0 9501 ctx-rh-primary-motor 30 150 45 0 9502 ctx-rh-premotor 130 150 165 0 9503 ctx-rh-temporal 105 75 5 0 9504 ctx-rh-posterior-parietal 125 120 55 0 9505 ctx-rh-prim-sec-somatosensory 225 70 105 0 9506 ctx-rh-occipital 225 70 15 0 Also, where can I find functionally defined regions of interest? I noticed the above in the FS lookup table as well. Like the dlPFC (bilateral) and the SM1 regions of interest? But again, I can't find it. Thank you. 'Sincerely, - Ananth

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problems on matrix design
by nellie 02 Dec '15

02 Dec '15

Hi Freesurfer Experts,I have tried to alter wiki example FSGD table into my analyses these days, according to your advice, but there are still some problems. Supposed there are 6 groups (maleclass1, maleclass2, maleclass3, femaleclass1, femaleclass2, femaleclass3) and 2 Variables (age, education) in my study, I have already known that:male.class1-vs-class2.mtx 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0female. class1-vs-class3.mtx 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0but I am not sure whether it is right for:male-female.mtx [1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0]/3 (Null Hypothesis: is there a difference between Males and Females regressing out the effects of class, age, and education?)class1-class2.mtx [1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 ]/2 (Null Hypothesis: is there a difference between class1 and class2 regressing out the effects of gender, age, and education?)class.diff.mtx +0.5 -0.5 0 +0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.5 0 -0.5 +0.5 0 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 (Null Hypothesis: is there a difference between class1, class2 and class3 regressing out the effects of gender, age, and educatio?)gender-x-class.mtx |+1 -1 0 -1 +1 0 0 0 0 0 0 0 0 0 0 0 0 0 | |+1 0 -1 -1 0 +1 0 0 0 0 0 0 0 0 0 0 0 0 |/2 (Null Hypothesis: is there an interaction between gender and class regressing out the effects of age and education?)gender-x-class-x-age.mtx |0 0 0 0 0 0 +1 -1 0 -1 +1 0 0 0 0 0 0 0 | |0 0 0 0 0 0 +1 0 -1 -1 0 +1 0 0 0 0 0 0 |/2 (Null Hypothesis: is there an interaction between gender, class and age regressing out the effect of education?)gender-x-class-x-age-x-education.mtx |0 0 0 0 0 0 +1 -1 0 -1 +1 0 0 0 0 0 0 0 | |0 0 0 0 0 0 +1 0 -1 -1 0 +1 0 0 0 0 0 0 |/2 |0 0 0 0 0 0 0 0 0 0 0 0 +1 -1 0 -1 +1 0 | |0 0 0 0 0 0 0 0 0 0 0 0 +1 0 -1 -1 0 +1 |/2 (Null Hypothesis: is there an interaction between gender, class, age and education?)Truly need your advice. Thanks a lot !Best,Li

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Sign option of Monte Carlo simulation in QDEC
by Karl Liu 01 Dec '15

01 Dec '15

Dear experts: In examining QDEC results of a contrast of interest, I noticed the results are mainly in cold color (blue), with only two small clusters in warm color (red). When I proceeded with Monte Carlo simulation, if I chose the abs as the sign option in simulation, then no clusters survived. In contrast, some clusters would remain, if I chose the neg sign. Because the uncorrected results were mainly in cold color, it seems reasonable to me to use negative only in the simulation. But I am wondering how the option of abs/neg/pos leads to the disparities and will you please elaborate how the simulation works based on abs/neg/pos. Thank you in advance. Karl

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Still unsure how to create my 3g4v matrix
by nellie 01 Dec '15

01 Dec '15

Hi expert, Thank you for your reply. I had read the example tables, but I'm still not sure how to alter them into my analysis.Can you help me to check the matrix I designed and point out my mistakes? Thanks in advence. 3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca test score). group.diff.mtx 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 group-x-gender.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 group-x-education.mtx 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-moca.mtx 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group-x-gender-x-age-x-education.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 group-x-gender-x-age-x-education-x-moca.mtx 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 group.diff.mtx also can write as: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 group-x-age.mtx aslo can write as: 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 . Wishes, Li > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: How to create a 3g4v matrix (Lee Tirrell) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 23 Nov 2015 10:27:42 -0500 (EST) >From: Lee Tirrell <ltirrell(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] How to create a 3g4v matrix >To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: > <alpine.LRH.2.20.1511231020130.5623(a)vermis.nmr.mgh.harvard.edu> >Content-Type: text/plain; charset="iso-8859-7" > >Hi Li, > >You can find some example FSGD tables here, which you can alter to fit your >analyses. > >https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >Best, >Lee > >On Sun, 22 Nov 2015, nellie wrote: > >> >> Hi Freesurfer Experts, >> >> I?m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes ( >> A / B / C group) and 4 concomitant?variables (gender, age, education, and Moca test score). It?s supposed to be 15 regressors in this design, but I don?t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create a correct >> matrix. I wonder if you could provide a 3g4v matrix in detail for me. I?ll be grateful if you can help. I hope I?m not bothering you too much, and I?m looking for your reply. >> >> Best wishes, >> >> Li? >> >> >> >> ? >> >> >> > >------------------------------ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >End of Freesurfer Digest, Vol 141, Issue 40 >******************************************* > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. >

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Sign options of Monte Carlo simulation in QDEC
by Karl Liu 01 Dec '15

01 Dec '15

Dear Freesurfer experts: we would appreciate if anyone could advise on the sign choice of Monte Carlo simulation, a question we posted 2 days ago. In examining QDEC results of a contrast of interest, we noticed the results are mainly in cold color (blue), with only two small clusters in warm color (red). When I proceeded with Monte Carlo simulation, if I chose the abs as the sign option in simulation, then no clusters survived. In contrast, some clusters would remain, if I chose the neg sign. Because the uncorrected results were mainly in cold color, it seems reasonable to me to use negative only in the simulation. But I am wondering how the option of abs/neg/pos leads to the disparities and will you please elaborate how the simulation works based on abs/neg/pos. Can I state that my results survived the cluster-level correction if I chose the neg sign in simulation? Thank you very much. Karl

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'mkdir' error during the segmentation of hippocampal subfields using FreeSurfer 6 [2nd request for help]
by Fengji Geng 01 Dec '15

01 Dec '15

Dear FreeSurfer Users, I sent an email to this maillist a couple of weeks ago asking help for the error that I encountered after running 'recon-all -s ${Mysubject} -hippocampal-subfields-T1' with freesurfer 6. The content of this email is attached below. Since then, my colleague and I have been working on figuring out where the error is from, but we got two more questions here: First, is it possible that we can set the tmpdir to /tmp or something else globally? How can I do this? Second, is it possible to fix test for '-e/scratch' to test for '-dw/scratch', which is a directory writable by current user? Any comments and suggestions are appreciated. Thanks in advance! Fengji Previous email: I was trying to segment hippocampal subfields using FreeSurfer 6 with data that have already undergone the FreeSurfer 5 pipeline recon-all -all. According to the usage described on the webpage of HippocampalSubfields (http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) I ran the command: recon-all -s ${Mysubject} -hippocampal-subfields-T1 Then the following errors occurred. It seems that the program 'segmentSubjectT1_autoEstimateAlveusML (line 113)' was trying to make a directory in a Read-only place. But the error message did not indicate where this place was. I have tried to look codes in 'run_ segmentSubjectT1_autoEstimateAlveusML.sh" . But it does not have this information either. As segmentSubjectT1_autoEstimateAlveusML is a binary file, I could not dig out any more info. Does anyone know how to solve this error? Or know where the program was trying to mkdir? Here begins the error message: hippocampus:/<2>hippocampus/HMN/data/FG_Temp: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) -------------------------------------------------------------------------------------------------------- ----- Fengji

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OPPORTUNITY OF FULL-TIME POSTDOCTORAL FELLOWSHIP AT THE UNIVERSITY OF SÃO PAULO, BRAZIL
by Neuroimagem IPQHCFMUSP - LIM21 01 Dec '15

01 Dec '15

One postdoctoral position is available within the Laboratory of Psychiatric Neuroimaging (LIM21) (www.neuroimagem.org.br/) at the University of São Paulo Medical School, Brazil, directed by Geraldo F. Busatto, Ph.D. Candidates should send a message to neuroimagem.ipq(a)hc.fm.usp.br with his/her CV and a letter of support. Deadline: 13 Dec 2015 *JOB DESCRIPTION* We are looking for a full-time researcher with previous experience in the use of software for the analysis of neuroimaging data. This post-doctoral fellow will be requested to work mainly with data acquired using resting-state functional magnetic resonance imaging methods (rs-fMRI) to evaluate patterns of functional connectivity in the brain. In our project, funded by the *FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO, BRAZIL* (FAPESP), such brain imaging data is being acquired in groups of cognitively-intact elderly individuals, patients with Alzheimer´s disease (AD), and patients with mild cognitive impairment (MCI). Pre-processing steps will be carried out using the software Analysis of Functional NeuroImages (AFNI), while the actual processing of data will be conducted using Matlab-based programs. The work will also involve use of software to evaluate the diagnostic accuracy to distinguish between AD, MCI and healthy elderlies, generating multivariate classifiers based on machine-learning methods (support vector machine). With such strategy, we aim to identify which are the functional connectivity characteristics in the brain that are most critical for the progression from normal cognition to MCI and then to AD. The post-doctoral fellow should have knowledge about the acquisition and analysis of fMRI data and other neuroimaging modalities. We aim to bring an individual with abilities to carry out, independently, analyses and organization of computational brain imaging data, interaction with other researchers involved in the same project, and participating in the writing up of scientific papers. These characteristics are expected to boost the scientific productivity from the funded project, both quantitatively and qualitatively. The professional will also have the opportunity to interact with scientists who are at the forefront of technologies for amyloid imaging in the brain, and data will be combined with fMRI analyses in the same elderly subjects evaluated with those two imaging technologies. The post-doctoral fellow will have the opportunity to practice abilities in analysing data of a challenging scientifc project, and he/she will be expected to establish and use optimized processing pipelines for the analysis of rs-fMRI data and other neuroimaging modalities. *Requirements* - Completed PhD in areas related to computer sciences, neuroscience, neurology or psychiatry - Research interest and brain imaging applied to research studies of brain aging - Previous experience in the usage of processing and statistical analysis methods for research studies applied to magnetic resonance imaging studies of the brain. best regard *Laboratory of Psychiatric Neuroimaging - HCFMUSP*

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Freesurfer December 2015