[Freesurfer] mri_glmfit
One of our volume analyses does not look as it should after we perform the mri_glmfit. Our block design paradigm has 2 separate sessions for each subject with alternating periods of task and rest. We did individual analyses for task-rest for each session. We then concatenated the data into 2 files: one for each session. Then we ran fscalc to add the 2 concatenated files. Up until this point, the data looked like it should. subjects dir: /cluster/manoach/milton/subjects freesurfer 5 However, when we then ran the group analysis using mri_glmfit, we got results that looked abnormal. Our command: mri_glmfit --y mstmct_v_base.nii --glmdir group_analysis/volume/mstmct_v_base/ --osgm We were unsure if we should put in the fsgd file, because we weren't sure which subjects should be included because we added the two sessions using fscalc. (Each subject has two sessions and 2 subject IDS). We realize it could be a problem that arose before the mri_glmfit , but we aren't sure if there was anything else we should consider when running the mri_glmfit itself. Thank you! ___ 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] mri_surfcluster -ocn
Hi all, We ran mri_surfcluster on our group data (we didn't do montecarlo simulations), so we used our .mgh file. We used the -ocn flag to make an output file so we could look at the specific clusters. When we looked at the data of the ocn file using tksurfer, the most significant cluster wasn't visible at the .05 level (which is the min threshold we specified in the mri_surfcluster). We tried playing with the threshold, but it was the opposite of what we expected. The most significant clusters disappeared at the lowest threshold but the less significant ones appeared even when we raised the threshold. This happened when we ran the other hemisphere as well. Do you have any idea how to fix this? we are using freesurfer v5 subjects_dir: cluster/manoach/milton/subjects Our commands: mri_surfcluster --in ./group_analysis/mct_lh/osgm/sig.mgh --hemi lh --thmin 1.3 --thmax infinity --subject fsaverage --sum ./group_analysis/mct_lh/osgm/mst_v_mct.txt --ocn /cluster/manoach/milton/subjects/group_analysis/mct_lh/osgm/sig.cluster.p05.ocn.mgh tksurfer fsaverage lh inflated -overlay sig.cluster.p05.ocn.mgh Thanks in advance! Best, Mandy Nagy ___ 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] Gammafit parameters
Hi all, We are trying to use -gammafit when running the mkanalysis-sess command. In the FsFast Tutorial, the flag -gammafit 2.25 1.25 is used. Are those numbers the default? If not, what is the default? Thanks in advance. Best, Mandy Nagy ___ 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] Between Task Analysis
Thank you for your response! We decided to run an isxconcat-sess on both analyses (day1 and day2), and we used fscalc to do day1 - day2. Now we're trying to run mri_glmfit. However, the FSGD files we used before either specified day1 or day2 sessions. How do we create an FSGD file now that each data point is actually 'day1 - day2' for one subject and not one of the pre-existing subject folders? Thanks! --Mandy Nagy On Tue, Feb 15, 2011 at 5:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: In principle you can do it either way and get the same result. From a practical standpoint, it is probably easier to do the day2-day1 subtraction, then do the group analysis. doug Mandy Nagy wrote: Hi all, We are attempting to do an analysis for subjects that came in on two different days to perform two similar but different tasks (one learning condition, one control). Each of the tasks is structured such that there are 30sec rest epochs alternating with 30sec active (typing) epochs for a total of 12.5 minutes (the task begins and ends with rest). We are trying to compare the typing period for the control task to the typing period for the learning task. We currently have first-level analyses of each of the tasks (active condition vs. null rest condition). Can we do within-subject comparisons and then do a group analysis on those? Or did we need to concatenate the learning and control conditions in the first-level analysis? If that is the case, how would you suggest that we do this? Paradigm file: 0 0 30 1 Rest 30 1 30 1 Typing 60 0 30 1 Rest 90 1 30 1 Typing 120 0 30 1 Rest 150 1 30 1 Typing 180 0 30 1 Rest 210 1 30 1 Typing 240 0 30 1 Rest 270 1 30 1 Typing 300 0 30 1 Rest 330 1 30 1 Typing 360 0 30 1 Rest 390 1 30 1 Typing 420 0 30 1 Rest 450 1 30 1 Typing 480 0 30 1 Rest 510 1 30 1 Typing 540 0 30 1 Rest 570 1 30 1 Typing 600 0 30 1 Rest 630 1 30 1 Typing 660 0 30 1 Rest 690 1 30 1 Typing 720 0 30 1 Rest Thanks in advance! --Mandy Nagy ___ 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 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] Between Task Analysis
Hi all, We are attempting to do an analysis for subjects that came in on two different days to perform two similar but different tasks (one learning condition, one control). Each of the tasks is structured such that there are 30sec rest epochs alternating with 30sec active (typing) epochs for a total of 12.5 minutes (the task begins and ends with rest). We are trying to compare the typing period for the control task to the typing period for the learning task. We currently have first-level analyses of each of the tasks (active condition vs. null rest condition). Can we do within-subject comparisons and then do a group analysis on those? Or did we need to concatenate the learning and control conditions in the first-level analysis? If that is the case, how would you suggest that we do this? Paradigm file: 0 0 30 1 Rest 30 1 30 1 Typing 60 0 30 1 Rest 90 1 30 1 Typing 120 0 30 1 Rest 150 1 30 1 Typing 180 0 30 1 Rest 210 1 30 1 Typing 240 0 30 1 Rest 270 1 30 1 Typing 300 0 30 1 Rest 330 1 30 1 Typing 360 0 30 1 Rest 390 1 30 1 Typing 420 0 30 1 Rest 450 1 30 1 Typing 480 0 30 1 Rest 510 1 30 1 Typing 540 0 30 1 Rest 570 1 30 1 Typing 600 0 30 1 Rest 630 1 30 1 Typing 660 0 30 1 Rest 690 1 30 1 Typing 720 0 30 1 Rest Thanks in advance! --Mandy Nagy ___ 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] Blocked Design
Our mkanalysis-sess command: mkanalysis-sess -analysis mandylh2 -surface fsaverage lh -fwhm 8 -event-related -paradigm paradigm.par -TR 3 -nconditions 2 -runlistfile task -gammafit 2.25 1.25 -refeventdur 30 Our paradigm file: 0 0301Rest 30 1301Typing 60 0301Rest 90 1301Typing 1200301Rest 1501301Typing 1800301Rest 2101301Typing 2400301Rest 2701301Typing 3000301Rest 3301301Typing 3600301Rest 3901301Typing 4200301Rest 4501301Typing 4800301Rest 5101301Typing 5400301Rest 5701301Typing 6000301Rest 6301301Typing 6600301Rest 6901301Typing 7200301Rest Thanks! --Mandy On Mon, Feb 14, 2011 at 10:20 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Usually this means that there is something wrong with your design or paradigm files. CAn you send the paradigm files and the mkanalysis-sess command? doug Mandy Nagy wrote: Hello, We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using: freesurfer v5 Our subjects directory: /cluster/manoach/milton/subjects Command that was run: selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06 Output that was given: Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using == svd Input to SVD must not contain NaN or Inf. Error in == cond at 40 s = svd(A); Error in == fast_selxavg3 at 256 XCond = cond(XtX); -- ERROR: fast_selxavg3() failed\n Do you know what might cause this? Thanks! --Mandy ___ 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 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] Blocked Design
Hello, We are attempting to run an analysis using selxavg3-sess but keep getting an error. We are using: freesurfer v5 Our subjects directory: /cluster/manoach/milton/subjects Command that was run: selxavg3-sess -analysis mandylh2 -fwhm -s PAMST06 Output that was given: Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 250, nX = 5, DOF = 245 Saving X matrix to /autofs/cluster/manoach/milton/subjects/PAMST06/bold/mandylh2/Xtmp.mat ??? Error using == svd Input to SVD must not contain NaN or Inf. Error in == cond at 40 s = svd(A); Error in == fast_selxavg3 at 256 XCond = cond(XtX); -- ERROR: fast_selxavg3() failed\n Do you know what might cause this? Thanks! --Mandy ___ 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.
