[Freesurfer] hippocampal subfields analysis took 10 min
Dear Eugenio, I had to run the hippocampal subfield segmentation analysis in Freesurfer v6 manually by running segmentSF_T1.sh program. When I call it through recon-all, it only processed the left hemisphere but not the right. The issue is that running segmentSF only took 10 min per hemisphere. I didn't use multicores. Although the analysis resulted in all the files correctly, I am just concerned if running this manually completed the analysis prematurely. Sincerely, Jiook ᐧ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg
Hi Kari I think that's not a real error. They are both surface overlays, just with the nvertices dimension in different slots. You could load one of them into matlab and use reshape to make it the same dimensions as the other, then write it out cheers Bruce On Fri, 20 May 2016, Kari Parsons wrote: > Hi, > > I'm trying to get some cortical thickness volumes for an ROI that I have > (I'm pretty much following the instructions at > https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness > verbatim), but for some of my subjects I'm getting errors that look like this > when I run mdi_segstats: > > ERROR: dimension mismatch between input volume and seg > input 1 1 145283 > seg 145283 1 1 > > Does anyone have any thoughts on how to trouble-shoot this one? > > Thanks! > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Lab coordinator position at the University of Michigan
Please see the ad below concerning a research position available in the new M(SD) lab at the University of Michigan directed by Dr. Adriene Beltz in the department of Psychology. Interested candidates should apply at http://umjobs.org/job_detail/125962/lab_coordinator and can reach Dr. Beltz at abe...@umich.edu. Lab CoordinatorHow to Apply A cover letter is required for consideration for this position and should be attached as the first page of your resume. The cover letter should describe your interest in the position, relevant experience, and future goals. In addition, please provide contact information for three references. Job Summary The Methods, Sex differences, and Development Lab, or M(SD), directed by Dr. Adriene Beltz in the Department of Psychology seeks to hire a full-time Lab Coordinator. The goal of the research in the lab is to develop and apply novel quantitative approaches in order to reveal the ways in which the brain mediates biological and environmental influences on behavioral sex differences across development. To achieve this goal, data are collected from children, adolescents, and young adults using multiple methods, such as functional magnetic resonance imaging (fMRI), salivary hormones, observations of social interactions, daily diaries, cognitive tests, and online self reports. This would be an excellent position for a recent graduate seeking to gain additional research experience prior to graduate school. There will be training in multiple methods and opportunities for co-authorship on presentations and publications. The successful candidate will be highly-motivated, reliable, conscientious, and organized. Responsibilities* The Lab Coordinator will play an integral role in the establishment and functioning of the lab by fulfilling research, management, and supervisory responsibilities. - Lab management tasks (*20% time*) - Ordering supplies - Running and maintaining equipment - Organizing materials and resources - Overseeing the website - Research tasks (*60% time*) - Writing and maintaining Institutional Review Board protocols - Establishing data collection procedures - Developing study stimuli and data collection instruments - Creating project manuals and code books - Collecting, entering, processing, managing, and analyzing data - Supervisory tasks (*20% time*) - Training Assistants in Research (temporary positions) - Overseeing and supporting Assistants in Research assignments (e.g., data collection, coding, and entry) Required Qualifications* - High school diploma or Associate's degree - At least 1 year of experience - Excellent organizational, communication, problem-solving, writing, and computing skills - Familiarity with SPSS or similar software - Ability to work well independently and as part of a team - Attentive to details and able to manage simultaneous projects Desired Qualifications* - Bachelor’s degree in Psychology, neuroscience, or a related field - Experience with or an eagerness to learn fMRI methods, advanced statistics, programming (e.g., in Matlab or R), and online data collection - Research interests in the development of brain and behavioral sex differences Additional Information - One year term-limited position with excellent possibility of extension - Start date is negotiable, but August 1, 2016 is preferred Background Screening The University of Michigan conducts background checks on all job candidates upon acceptance of a contingent offer and may use a third party administrator to conduct background checks. Background checks will be performed in compliance with the Fair Credit Reporting Act. U-M EEO/AA Statement The University of Michigan is an equal opportunity/affirmative action employer. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] LME MATLAB, X matrix error
Dear FreeSurfer Team, I processed in MATLAB for Linear Mixed Effects Models Analysis with this X matrix: X matrix is 'Subjects N X 11', 11 columns are as follow, 1. Intercept (all '1') 2. time (from baseline time point) 3. time2 4. Patients group = 1, Control = 0 5. 4.X time 6. 4.X time2 7. Patients group = 0, Control = 1 8. 7. X time 9. 8. X time2 10. age 11. extra values for covariate 1. When I process this command, [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4) The MATLAB windows print the warning alarm repeatedly. " Warning: Matrix is close to singular or badly scaled. Results may be inaccurate." Is this X matrix something wrong? 2. After complete 'lme_mass_fit_EMinit' process with the warning, I tried the next command, [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95); This command took a long time to process, and it caused the whole stop MATLAB works. Is it also because of the X matrix...? Could you let me know the solution for the X matrix problems ? Best Wishes, Han ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Group Analysis: Two Groups and Two Covariates.
Dear FreeSurfer Team, I processed the Group analysis by FreeSurfer 5.3.0 Our data has two groups (Patient, Control) and two covariate values (age, extra value) mtx, contrast is 1 -1 0 0 0 0 The mris_preproc, and mri_surf2surf command were completed without error. mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas thickness --out lh.**G2V2.dods.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh --fwhm 15 --cortex --tval lh.**G2V2.dods_sm15.mgh mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C **G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir After mri_glmfit command, I saw the error message. = ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C **G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir 2. The FSGD file (if using one) 3. And the design matrix above = I think our fsgd and mtx compositions are equal to the g2v2.fsgd which FreeSurfer wiki example. (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V) In this situation, how can I correct my fsgd or mtx files? Is there any other command option? Best Regards, Han ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] LME MATLAB, X matrix error
Hi Han, Try to find a local statistician to help you with your analysis. About your matrix: rows need to be number of all time points from all subject. Time 2 should probably not be there. Also columns 7-9 need to be dropped (they are just the negative of the rows before). Best Martin On May 21, 2016 3:32 PM, Hanbyul Cho wrote:Dear FreeSurfer Team,I processed in MATLAB for Linear Mixed Effects Models Analysis with this X matrix:X matrix is 'Subjects N X 11', 11 columns are as follow,1. Intercept (all '1')2. time (from baseline time point)3. time24. Patients group = 1, Control = 05. 4.X time6. 4.X time27. Patients group = 0, Control = 18. 7. X time9. 8. X time210. age11. extra values for covariate1. When I process this command, [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4)The MATLAB windows print the warning alarm repeatedly." Warning: Matrix is close to singular or badly scaled. Results may be inaccurate."Is this X matrix something wrong?2.After complete 'lme_mass_fit_EMinit' process with the warning, I tried the next command,[lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95);This command took a long time to process, and it caused the whole stop MATLAB works.Is it also because of the X matrix...?Could you let me know the solution for the X matrix problems ?Best Wishes,Han ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] LME MATLAB, X matrix error
Dear Martin Reuter, Thank you for your reply. Our patients have several time points, but controls have only 1 time points, so when I coded the patients group =1, controls groups = 0 , the 2. time and 3. time2 column were same as 5. 4.X time 6. 4.X time2 column. and 8. 7. X time and 9. 8. X time2 were all zeros. And then, how about this X matrix (Subjects N X 5)? 1. Intercept (all '1') 2. 4.X time (from baseline time point) 3. 4.X time2 4. age 5. extra values for covariate is it a vallid matrix for test the effects of group X time2 ? Thank you, Han. On Sat, May 21, 2016 at 3:13 PM, Martin Reuter wrote: > Hi Han, > Try to find a local statistician to help you with your analysis. > About your matrix: rows need to be number of all time points from all > subject. Time 2 should probably not be there. Also columns 7-9 need to be > dropped (they are just the negative of the rows before). > > Best Martin > On May 21, 2016 3:32 PM, Hanbyul Cho wrote: > > Dear FreeSurfer Team, > > I processed in MATLAB for Linear Mixed Effects Models Analysis with this X > matrix: > > X matrix is 'Subjects N X 11', 11 columns are as follow, > > 1. Intercept (all '1') > 2. time (from baseline time point) > 3. time2 > 4. Patients group = 1, Control = 0 > 5. 4.X time > 6. 4.X time2 > 7. Patients group = 0, Control = 1 > 8. 7. X time > 9. 8. X time2 > 10. age > 11. extra values for covariate > > > 1. > When I process this command, > [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4) > The MATLAB windows print the warning alarm repeatedly. > " Warning: Matrix is close to singular or badly scaled. Results may be > inaccurate." > Is this X matrix something wrong? > > > 2. > After complete 'lme_mass_fit_EMinit' process with the warning, I tried > the next command, > [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, > lhTh01,lhcortex,2,95); > This command took a long time to process, and it caused the whole stop > MATLAB works. > Is it also because of the X matrix...? > > > Could you let me know the solution for the X matrix problems ? > > Best Wishes, > > Han > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] DTI error
Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
