Re: [Freesurfer] Difficult results from our PD data
Hi Bruce, I checked the surface of every subject with tksurfer, inaccuracy's were founded in 13 of 140 subjects. These subjects were manually edited with control points and pial edits. Then i start recon-all on the subjects with edits again. After these procedure tksurfer showed a correct segmentation. Is that the correct procedure for checking inaccuracy's? Or do i need to check more? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Many thanks, Stan From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 05 February 2013 15:54 To: Berg, S.F. van den Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Difficult results from our PD data Hi Stan we have found positive correlations between performance (in this case CVLT) and thickness, so it is certainly possible. And negative correlations aren't necssarily false - you could certainly imagine that successful pruning for example could help performance. Have you visually inspected the surfaces for accuracy? cheers Bruce On Tue, 5 Feb 2013, Berg, S.F. van den wrote: Dear Freesurfer experts, We investigated the relation between cortical thickness and performance on several cognitive tasks within a large group of Parkinson?s disease patients, but are slightly puzzled by the results. We obtained several, both in the vertex-wise analysis in qdec and in the SPSS analysis in the a-priori parcelated areas, negative correlations (i.e. better performance relates to a thinner cortical area) for all our neuropsychological tasks. These negative correlations were unexpected and we are having a hard time interpreting them. After correcting for multiple comparisons, all effects failed to reach the statistical threshold, rendering no results at all. When we compared our patient group on a structural level with healthy controls, we did find expected results that made sense. We also ran the exact same analyses (same group, same data) in VBM and there found several positive task-related correlations in expected areas. We noticed that in previous literature almost no studies investigated the relation between cortical thickness and cognitive task-performance. This made us wonder whether Freesurfer is suited for these correlation-based analyses, or is it better to be used in between group analyses? And do you have any idea on how to explain our negative correlations? Is it possible we might have done something wrong? Many thanks, Stan 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
Re: [Freesurfer] mean cluster thickness in qdec
Hi Doug, Thanks for the fast respons. I did the correction for multiple comparisons with the following configurations: abs, z=1.3 (p0.05). Is the output from mri_glmfit-sim in the command line the same as the correction for multiple comparisons in qdec? is the file xxx.y.ocn.dat created after multiple comparisons simulations in qdec? The problem is where can i find the xxx.y.ocn.dat file? in which directory? I did not find the file in the (group comparison) output directory called Pd_vs_HC_1 or in the subdirectories of the directory Pd_vs_HC_1 lh-Diff-1.00-2.00-Intercept-thickness or the other subdirectory lh-Avg-Intercept-thickness Many thanks, Stan From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 14 January 2013 16:40 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean cluster thickness in qdec Stan, QDEC will create an output directory (the glmdir). This is actually created by mri_glmfit which is run by QDEC. If you did not run mri_glmfit-sim from QDEC, you can run it from the command line. To get help, run mri_glmfit-sim --help. The file you want is xxx.y.ocn.dat (help section for this is below) doug csdbase.y.ocn.dat - this is a summary of the input (y) over each cluster. It has a column for each cluster. Each row is a subject. The value is the average of the input (y) in each cluster. This is a simple text file. On 01/14/2013 09:08 AM, Berg, S.F. van den wrote: Dear Freesurfer Experts, I would like the mean thickness measures of each cluster i found in qdec. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 5 different significant clusters. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. If this is not possible the mean cortical thickness of the peak/max vertex is also enough information. Where can i found the file with this information? the problem is what do i have to do? run mri_glmfit-sim? but qdec do not create a .glmdir file? so do i have to run the mri_glmfit first? or is mri_glmfit-sim enough but where is the .glmdir file? I use mri_glmfit-sim --glmdir ?.glmdir --sim mc-z 1 1.3 mc-z.negative --sim-sign abs --cwpvalthresh 0.5 --overwrite I want to create the csdbase.y.ocn.dat (explaind in mri_glmfit-sim --help) for the mean cluster thickness. This is the file where i can find the mean thickness of each cluster, right? A jpeg file is attached to this email. Many thanks, Stan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
[Freesurfer] correcting for discrete variables in Qdec
Hi Freesurfer Experts, In my design i want to use a general linear model tot relate cognitive performance and cortical thickness. I want to control for age, total gray matter, gender and education. I have two discrete variables, including gender (0,1) and Education (1-7). The problem is that the discrete variables do not appear in the nuisance screen in qdec. How can i control for this discrete variables? Can i put these variables in the nuisance screen? Or should i remove the gender.levels and education.levels file? Just highlighting the two variables gender and age result in an error in analyze: command failed: mri_glmfit --y In the qdec screen. When i just highlight gender and education in the discrete screen, highlight cogitive_performance in the continous screen, and Age and Total_gray in the nuisance screen. Analysing gives a error. But when i highlight only cognitive_performance in the continuous screen and nuisance factors age and total_gray in the nuisance screet. It work very well. And a vertex-wise cluster analyses can be done. Thanks, Stan ___ 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
Hello Freesurfer experts, I have got some problems with qdec. For testing my data i make an design with age, sexe and right and left hippocampus. The same design as the tutorial on the freesurfer wiki. When starting anlalyze i get an Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh. surf is the map with the smoothings. The correct smoothings file. In this design is 10 is correctly presented in the map surf. Thanks, Stan lh-Avg-Intercept-volume --- Does the average volume differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-volume-Left-Hippocampus-Cor --- Does the correlation between volume and Left-Hippocampus, accounting for gender, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-male-female-Intercept-volume --- Does the average volume differ between male and female? 1.000 -1.000 0.000 0.000; lh-Diff-male-female-Cor-volume-Left-Hippocampus --- Does the volume--Left-Hippocampus correlation differ between male and female? 0.000 0.000 1.000 -1.000; ninputs = 9 Checking inputs reading MRI_FRAME structure from file... Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh lh-Avg-Intercept-volume --- Does the average volume differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-volume-Left-Hippocampus-Cor --- Does the correlation between volume and Left-Hippocampus, accounting for gender, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-male-female-Intercept-volume --- Does the average volume differ between male and female? 1.000 -1.000 0.000 0.000; lh-Diff-male-female-Cor-volume-Left-Hippocampus --- Does the volume--Left-Hippocampus correlation differ between male and female? 0.000 0.000 1.000 -1.000; ninputs = 9 Checking inputs reading MRI_FRAME structure from file... Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh Type: Error Time: Tue Nov 13 11:57:43 2012 Description: Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh Type: Error Time: Tue Nov 13 11:45:07 2012 Description: Error in Analyze:
