[Freesurfer] Error finding glmdir with mri_glmfit-sim
Hi FS team, I ran a mri_glmfit for a 3 groups comparison and now I'm trying to run the cwp correction with mri_glmfit-sim command. When I type in my command, it says: ERROR: cannot find /Applications/freesurfer/subjects/fsgd/lh.thickness.10fhwm/ Which is exactly the emplacement of my group analysis file. The weird thing is, I ran the very same analysis a few months ago with fewer subjects and it ran well. Can you help me with this? Nick Corriveau-Lecavalier Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Président de l'Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7818 ___ 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] GLM error - cannot read fsgd file for reading
Hi Freesurfer team, First, sorry making a new post, I'm having trouble with my email and I'm not able to reply directly on my yesterday's post. Here's my issue: I'm trying to make a group analysis with 3 groups using the mri_glmfit command. This it what the terminal says: Loading y from /Applications/freesurfer/subjects/fsgd/y.mgh mghRead(/Applications/freesurfer/subjects/fsgd/y.mgh, -1): could not open file ERROR: loading y /Applications/freesurfer/subjects/fsgd/y.mgh The terminal says that it cannot load the y.mgh file, which seems logic to me, since there is no such file in my folder. What is that file supposed to be? It isn't mentionned in the tutorial I've been following (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V). I also attached the log file. Thank you! FYI, here is my previous discussion with Douglas about this issue: Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N+Greve%22> Wed, 09 Aug 2017 14:17:05 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20170809> make sure you pass the full path to the fsgd, otherwise it looks in the current folder. Also make sure it is readable by you > Hi Freesurfer team, > > > I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) > with 0 covariables at the moment, but I would like to add two > eventually. I've been following the tutorial on this link: > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write > the command it says ''cannot open g3v0.fsgd for reading''. > > > In my /subjects/fsgd file, there is my fsgd file, and my contrast > file. Am I missing an additionnal file or something? Is the format of > my files correct? > > > If it can help, here's what my fsgd file looks likes: > > > GroupDescriptorFile 1 > Title OSGM > Class Control > Class SCD > Class MCI > Variables > Input 3431566 CTL > Input 3514091 CTL > Input 4051959 CTL > Input 4344061 CTL > Input 4557550 CTL > Input 7060373 CTL > Input 7274924 CTL ETC Nick Corriveau-Lecavalier, B.Sc. (Hons) Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819 mri_glmfit.log Description: mri_glmfit.log ___ 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] GLM error - cannot read fsgd file for reading
Hi Freesurfer team, I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) with 0 covariables at the moment, but I would like to add two eventually. I've been following the tutorial on this link: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write the command it says ''cannot open g3v0.fsgd for reading''. In my /subjects/fsgd file, there is my fsgd file, and my contrast file. Am I missing an additionnal file or something? Is the format of my files correct? If it can help, here's what my fsgd file looks likes: GroupDescriptorFile 1 Title OSGM Class Control Class SCD Class MCI Variables Input 3431566 CTL Input 3514091 CTL Input 4051959 CTL Input 4344061 CTL Input 4557550 CTL Input 7060373 CTL Input 7274924 CTL Input 7308293 CTL Input 7424803 CTL Input 7459501 CTL Input 7543023 CTL Input 7661810 CTL Input 8069157 CTL Input 8330218 CTL Input 8656527 CTL Input 8875385 CTL Input 9296157 CTL Input 3025432 SCD Input 3494204 SCD Input 3702154 SCD Input 3708747 SCD Input 3865361 SCD Input 4316663 SCD Input 4509950 SCD Input 4548020 SCD Input 4893763 SCD Input 5381177 SCD Input 5477234 SCD Input 5522727 SCD Input 6121388 SCD Input 6168985 SCD Input 6258913 SCD Input 6274286 SCD Input 6334263 SCD Input 6417837 SCD Input 6427603 SCD Input 7435733 SCD Input 7485585 SCD Input 7712552 SCD Input 8827943 SCD Input 8980899 SCD Regards, Nick Corriveau-Lecavalier, B.Sc. (Hons) Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819 ___ 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] From structural ROIs to functional data
Hi Freesurfer team, I used Qdec to do my group analysis (MCI vs Control). I also analyzed fMRI data with SPM. My plan is to investigate functional activity where there are group differences in thickness. Is there a way to make a ROI using Qdec and to transfer it into SPM/MarsBar format (.mat) so I can get the functional beta values in this ROI? I tried to make functional ROIs with MarsBar by taking the coordinates of the thickness clusters, but the size and shape of those ROIs are kind of arbitrary. Do you have anything to suggest? Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819 ___ 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] mris_calc cluster infos
Hi Freesurfer team, I have a 2 Group (MCI, CTL) x 2 (Time1, Time2) protocol. As suggested in an earlier discussion, I measured the rate atrophy for each group between my two time points. Then I applied the clusterwise correction for multiple comparison, which give a lot of information about each group (for example, number of clusters, # of voxels, regions where there's a significant difference). Then I used mris_calc to compute the difference between my groups. My question is: Is there a way to obtain the same informations on the group difference? Since mris_calc doesn't have a .log as output, I can't compute mris_glmfit-sim on it and I cannot get any infos on the cluster summary. Regards, Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819 ___ 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] Paired analysis - mismatch between matrix and contrast
Hi Freesurfer team, I'm trying to run a longitudinal group analysis (2 groups, 2 time points) using the paired analysis procedure: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. I have followed all the instructions but when it comes to the mri_glmfit, it says that my contrast files has 2 columns, while the matrix has 44. What did I go wrong? I join with this message the log, fsgd and contrasts files. Thank you! Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819 mri_glmfit.log Description: mri_glmfit.log group Description: group paired.diff.fsgd Description: paired.diff.fsgd paired.fsgd Description: paired.fsgd ___ 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] qcache for qdec longitudinal analysis
Thank you very much. I will be looking forward to this. Nick Corriveau-Lecavalier ?tudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur ? la recherche, Association ?tudiante des cycles sup?rieurs en psychologie de l'Universit? de Montr?al (A?CSPUM) Universit? de Montr?al Centre de recherche de l'Institut universitaire de g?riatrie de Montr?al, Bureau M7819 On Aug 23, 2016, at 4:57 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>> wrote: Hi Nick, when using the 2 stage model (mris_long slopes ) you do not need the qcache. In qdec you will not look at thickness, but at the percent change or the rate of thickness changes as computed by long_slopes. For that to work, you need to create/modify the .qdecrc file so that qdec finds the files in the base. Furthermore, you need to pass a "cross sectional" qdec table, with one row per subject where the fsid contains the id of the the base. This is all described on the wiki page. Best, Martin On Aug 22, 2016, at 10:24 PM, Nick Corriveau Lecavalier <nick...@hotmail.com<mailto:nick...@hotmail.com>> wrote: Hi Freesurfer team, I am planning on following this page for my longitudinal group analysis using QDEC: http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. However, it tells me to run -qcache for all of my subjects. Since I already ran the -long stream for all my subjects, do I need to rerun them all adding the -qcache command? Also, I have also run the long_mris_slopes on all of my subjects, which produced smoothed thickness files for all of my subjects (which are all in the ''base'' files). Does these files are okay for my QDEC analysis, or I really need to run all of my subjects all over again adding -qcache? Thank you very much, Nick Corriveau-Lecavalier, B.Sc. (Hons.) ?tudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur ? la recherche, Association ?tudiante des cycles sup?rieurs en psychologie de l'Universit? de Montr?al (A?CSPUM) Universit? de Montr?al Centre de recherche de l'Institut universitaire de g?riatrie de Montr?al, bureau M7819 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] qcache for qdec longitudinal analysis
Hi Freesurfer team, I am planning on following this page for my longitudinal group analysis using QDEC: http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. However, it tells me to run -qcache for all of my subjects. Since I already ran the -long stream for all my subjects, do I need to rerun them all adding the -qcache command? Also, I have also run the long_mris_slopes on all of my subjects, which produced smoothed thickness files for all of my subjects (which are all in the ''base'' files). Does these files are okay for my QDEC analysis, or I really need to run all of my subjects all over again adding -qcache? Thank you very much, Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819 ___ 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.
