[Freesurfer] lme_mass_F error
External Email - Use Caution Dear All I am running the longitudinal post processing statistical analysis and this error comes up each time I run the lme_mass_F. Does anyone have an idea of why this is happening and how to resolve it. Any help will be appreciated *** F_lstats = lme_mass_F(tlstats,CM); Computing F statistics, degrees of freedom and P-values ... Error using lme_mass_F (line 92) The source code (/matlab filepath/lme_mass_F.m) for the parfor-loop that is trying to execute on the worker could not be found. Caused by: Undefined function 'fcdf' for input arguments of type 'double'. Error using remoteParallelFunction (line 84) Worker unable to find file. Undefined function 'fcdf' for input arguments of type 'double' Kind regards Emmanuel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_label2label: Empty label file
External Email - Use Caution Dear FreeSurfer users, I want to extract the thickness value of a significant cluster from all the subjects used for a comparison for further statistical analyses. I ran the mri_surfcluster first to create the ROI label with fsaverage and then used mri_label2label to map this label to all the subjects but the label generated for some of the subjects are empty (i.e the label file size is 0kb). Does anyone know the reason for this? and how it can be resolved? I need the label for all the subjects before running the mris_anatomical_stats and aparcstats2table. Any help on this will be appreciated. Kind regards Emmanuel ___ 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] Longitudinal LME cluster value extraction
External Email - Use Caution Dear FreeSurfer experts, Am analysing longitudinal structural data with the LME model algorithm. I will like to map the significant cluster after analysing the data to all subjects at all time points, extract the values for all and perform further statistical analyses. Please how do I go about extracting the cluster value from all subjects at all time points? Any help will be appreciated. Kind regards Emmanuel ___ 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] extracting morphometric values from co-ordinates
Many Thanks Bruce. Will try that out On Wed, Apr 4, 2018 at 2:57 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Emmanuel, > > you could create a label in MNI coords, then map it to a group of > subjects using mri_label2label. "Value at a point" only makes sense for > point measures like thickness though. > > cheers > Bruce > > > On Wed, 4 Apr 2018, Emmanuel > Nwosu wrote: > > > Dear FreeSurfer Experts, > > > > Am wondering if there is a way to extract morphometry (cortical > thickness, area, etc) values from a > > specific co-ordinate (talaraich, MNI, etc) of interest. > > > > Any help with this will be appreciated. > > > > Kind regards > > Emmanuel > > > > > ___ > 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] extracting morphometric values from co-ordinates
Dear FreeSurfer Experts, Am wondering if there is a way to extract morphometry (cortical thickness, area, etc) values from a specific co-ordinate (talaraich, MNI, etc) of interest. Any help with this will be appreciated. Kind regards Emmanuel ___ 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 Qcache
Hi All, I will want to know if this error on this link https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.html was resolved. I am having a similar problem while sampling to the fsaverage. Thanks Kind regards Emmanuel ___ 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] correlation in mri glmfit controlling for 2 categorical variables and 1 continuous variable
Hi All Am not sure if I can do this in mri glmfit I want to investigate the relationship between cortical thickness and a continuous variable (A) while accounting for two categorical variables with two levels each and one continuous variable. That is I want to account for : 1. categorical variable X - (levels - O and P) 2. categorical variable Y - (levels - K and L) 3. Continuous variable Z. What will the contrast file in mri glmfit look like? Have anyone got an idea? Thanks in advance Emmanuel ___ 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] grayscale display turns red in freeview
Ok. Will try to run it locally. thanks On Mon, Nov 21, 2016 at 5:00 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > This is likely due to remote display. Would it be possible for you to run > it locally? You can also adjust overlay settings from the command-line, > although it is not as convenient as the GUI. Run “freeview -h” and look for > surface overlay related options. > > On Nov 21, 2016, at 9:48 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> > wrote: > > Yes am running it on a remote server. Here is the screen shot > > On Mon, Nov 21, 2016 at 4:40 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> > wrote: > >> Can you post a screenshot? Are you running freeview remotely? >> >> On Nov 21, 2016, at 9:32 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> >> wrote: >> >> it opens a blank "configure overlay" dialog, then the screen goes dark >> >> On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu >> > wrote: >> >>> What happens when you click on the button? >>> >>> On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> >>> wrote: >>> >>> Thanks Ruopeng. I can't open the configure overlay button. Is there any >>> other means of changing it? >>> >>> On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang < >>> rpw...@nmr.mgh.harvard.edu> wrote: >>> >>>> You need to adjust the color scale. Click on “Configure Overlay” button >>>> to adjust it. >>>> >>>> Best, >>>> Ruopeng >>>> >>>> On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> >>>> wrote: >>>> >>>> Hi >>>> >>>> Am having a bit of a problem that may be easy to resolve. >>>> >>>> I want to view an LGI two-group comparison I did in mri glm-fit with >>>> freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). >>>> The grayscale inflated surface turns red like what is in picture-1 >>>> >>>> Please have anyone an idea why this is happening and what I can do to >>>> change it back to grayscale like picture 2 >>>> Thanks for your help >>>> >>>> Emmanuel >>>> >>>> __ >>>> _ >>>> 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 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 mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nm
Re: [Freesurfer] grayscale display turns red in freeview
it opens a blank "configure overlay" dialog, then the screen goes dark On Mon, Nov 21, 2016 at 4:29 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > What happens when you click on the button? > > On Nov 21, 2016, at 9:02 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> > wrote: > > Thanks Ruopeng. I can't open the configure overlay button. Is there any > other means of changing it? > > On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> > wrote: > >> You need to adjust the color scale. Click on “Configure Overlay” button >> to adjust it. >> >> Best, >> Ruopeng >> >> On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> >> wrote: >> >> Hi >> >> Am having a bit of a problem that may be easy to resolve. >> >> I want to view an LGI two-group comparison I did in mri glm-fit with >> freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). >> The grayscale inflated surface turns red like what is in picture-1 >> >> Please have anyone an idea why this is happening and what I can do to >> change it back to grayscale like picture 2 >> Thanks for your help >> >> Emmanuel >> >> __ >> _ >> 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 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 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] grayscale display turns red in freeview
Thanks Ruopeng. I can't open the configure overlay button. Is there any other means of changing it? On Mon, Nov 21, 2016 at 3:58 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > You need to adjust the color scale. Click on “Configure Overlay” button to > adjust it. > > Best, > Ruopeng > > On Nov 21, 2016, at 3:52 AM, Emmanuel Nwosu <emmanuel.c.nw...@gmail.com> > wrote: > > Hi > > Am having a bit of a problem that may be easy to resolve. > > I want to view an LGI two-group comparison I did in mri glm-fit with > freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). > The grayscale inflated surface turns red like what is in picture-1 > > Please have anyone an idea why this is happening and what I can do to > change it back to grayscale like picture 2 > Thanks for your help > > Emmanuel > > __ > _ > 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 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] Fwd:
Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea why this is happening and what I can do to change it back to grayscale like picture 2 Thanks for your help Emmanuel ___ 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] grayscale display turns red in freeview
Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea why this is happening and what I can do to change it back to grayscale like picture 2 Thanks for your help Emmanuel ___ 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] Longitudinal single time point cross sectional comparison
Dear Freesurfer users, I have longitudinal data with three time points but want to run a cross sectional comparison on the first instance between group on just one time point (using QDEC). Any Idea on how I could do that on longitudinal data. Thanks for your help. Emmanuel Nwosu ___ 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 from Generating mean value for clusters that survived multiple comparison correction in QDEC
Dear FreeSurfer experts, Am working on this machine: *FREESURFER_HOME: /usr/local/freesurferBuild stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0Debian version: jessie/sidKernel info: Linux 3.19.0-28-generic x86_64* Am trying to extract the mean LGI value for a cluster from QDEC using mri_glmfit-sim. This is for a correlation analysis, the directory of the cluster is *cor-46-lh *with this code: *mri_glmfit-sim --glmdir Drobo_Server/UserFolders/emmanuel/freesurfer/subjects/QDEC/cor-46-lh --cache 1.3 abs --cwpvalthresh 0.05 --overwrite* Each time I run this code it comes up with this error message: *Reporting on 4 segmentationsComputing spatial average of each frame 0 1 2 3*** Error in `mri_segstats': malloc(): memory corruption: 0x2eda2638 ***Writing to Drobo_Server/UserFolders/emmanuel/freesurfer/subjects/QDEC/Before-after-lgi/lh-Diff-after-before-Intercept-pial_lgi/cache.th13.abs.y.ocn.datAbort (core dumped)* And I can't see the file *cache.th13.abs.y.ocn.dat *in the directory specified. Please any idea on what is wrong and what can I do to resolve this. Any help will be appreciated. Thanks in advance Emmanuel University of Cape Town ___ 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.
