[Freesurfer] Inter-rater and intra-rater reliability
Dear FreeSurfer experts, I have a question regarding manual interventions during the recon-all script of FreeSurfer 5.3.0 (i.e. setting control points, performing white matter edits). How can we check for inter- and intra-rater reliability? In an earlier post you mentioned an intra- and inter-rater reliability study you did. Could you tell me the name of this publication? Thank you in advance for your help! Best regards, Anne ___ 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] qdec analysis with two covariates
Dear Freesurfer experts, I would like to study the cortical thickness difference between two groups (two different genotypes) and include age and years of education as covariates. I processed my data with Freesurfer 5.3.0 und I am now running analysis in Qdec. I don't know how to set the design of my analysis in Qdec. I have chosen ´genotype´ as a fixed factor. Since it is only possible to use one continuous factor as a covariate in the analysis, should I declare ´age´ and ´years of education´ as nuisance factors? Thank you very much for your help! Best regards, Anna ___ 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] Error in Analyze: command failed: mri_concat /
*Dear Freesurfer experts,* I am conducting cortical thickness analysis using freesurfer-5.3.0 and have received the error message *Error in Analyze: command failed: mri_concat / *when clicking the 'Analyze' button in order to run a qdec group analsysis (please see the output below). Prior to this I have run recon-all –s subject –qcache for all my subjects and I have add a copy of fsaverage into my SUBJECTS_DIR (using the command [ -L fsaverage ] || ln –nfs $FREESURFER_HOME/subjects/fsaverage ). Uploading of the data table has been successful, too. I would be very grateful for your comments. Yours sincerely, Annemarie $ bugr FREESURFER_HOME: /apps/prod/x86_64/freesurfer-5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.8 Kernel info: Linux 3.12.38-ql-generic-50 x86_64 SUBJECTS_DIR: '/data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec' Error message: aparcstats2table --hemi rh --parc aparc.a2009s --meas meancurv --tablefile /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/qdec/stats_tables//rh.aparc.a2009s.meancurv.stats.dat --subjects AB39_mdeft. AB48_mdeft. BS39_mdeft. CB46_mdeft. CR55_mdeft. EB48_mdeft. EG47_mdeft. EH44_mdeft. GU46_mdeft. HT36_mdeft. IB34_mdeft. IS47_mdeft. JW39_mdeft. KM42_mdeft. KU44_mdeft. KW35_mdeft. LD50_mdeft. MB53_mdeft. MG43_mdeft. MR49_mdeft. AS36_mdeft. CM41_mdeft. EB35_mdeft. EF42_mdeft. EF53_mdeft. EL52_mdeft. EN34_mdeft. ER52_mdeft. ES54_mdeft. GE54_mdeft. HA49_mdeft. JM36_mdeft. LR48_mdeft. MP41_mdeft. MS36_mdeft. MS38_mdeft. MS54_mdeft. RK48_mdeft. WK39_mdeft. EH40_mdeft. SUBJECTS_DIR : /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec Parsing the .stats files Building the table.. Writing the table to /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/qdec/stats_tables//rh.aparc.a2009s.meancurv.stats.dat Completed creation of aseg and aparc stats data tables. lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000; lh-Diff-0-1-Intercept-thickness --- Does the average thickness differ between 0 and 1? 1.000 -1.000; ninputs = 42 Checking inputs ERROR: could not find volume healthy. Does it exist? ERROR: reading healthy *Error in Analyze: command failed: mri_concat /*data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/AB39_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/AB48_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/BS39_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/CB46_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/CR55_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/EB48_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/EG47_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/EH44_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/GU46_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/HT36_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/IB34_mdeft./surf/lh.thickness.fwhm10.fsaverage.mgh /data/projects/oertelmatura/Neurodegeneration_Alte/Annemarie_Qdec/IS47_mdeft./etc. ___ 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] improvement of segmentation qualitiy by setting control points
Dear freesurfer community, we are conducting cortical-thickness analysis and we have encountered some problems with setting control points to improve segmentation quality. Mainly, white matter was classified as grey matter after completion of the first run that incorporated control points. Now we have several questions, we would be very thankful for your comments: 1. According to your expereince, how many control points for the overall brain are usually necessary to obtain good segmentation results? 2. Are control points necessary at all? Is there a way to control the segmentation quality? 3. Is there any visual example on how to best set control points? Thank you for your help, Annemarie ___ 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] improvement of segmentation qualitiy by setting control points
Dear freesurfer community, we have encountered some problems with setting control points to improve segmentation quality. Mainly, white matter was classified as grey matter after completion of the first run that incorporated control points. Now we have several questions, we would be very thankful for your comments: 1. According to your expereince, how many control points for the overall brain are usually necessary to obtain good segmentation results? 2. Are control points necessary at all? Is there a way to control the segmentation quality? 3. Is there any visual example on how to best set control points? Thank you for your help, Annemarie ___ 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.
