[Freesurfer] error in mri_glmfit-sim using a per-vertex regressor
Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_MMSE.fsgd dods --C PDcorr.mtx --pvr rh.wgc_corr_MMSE.mgh --surf fsaverage rh --cortex --glmdir rh.cth_corr_MMSE.glmdir But when I try to run mri_glmfit-sim I think it doesn't consider the regressor (mri_glmfit-sim --glmdir lh.cth_corr_MMSE.glmdir/ --cache 1.3 abs) because I get this warning: *WARNING: unrecognized mri_glmfit cmd option --pvr* *WARNING: unrecognized mri_glmfit cmd option rh.wgc_corr_MMSE.mgh* How can I run the simulation with the regressor? Thank you very much for your help, Carme ___ 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] Merge both hemispheres in cortical parcellations
Dear FreeSurfer users, I've been looking for an appropiate way to merge both hemispheres in the Desikan parcellations but I can't find it in the list. Which formula do I need to use to consider, for example, the bilateral posterior cingulate as an only measure (not lh and rh separated)? I'm not sure if I can just add them in a mean... Thank you very much for your help! Carme ___ 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] Merge both hemispheres in cortical parcellations
​Thanks Bruce. It's the surface area 2015-12-17 17:25 GMT+01:00 Bruce Fischl : > Hi Carme > > what measure do you mean? If you wanted an average it would be: > > > average_thick = ((nvertices_lh) * (lh_average_thick) + (nvertices_rh) * > (rh_average_thick)) > -- > nvertices_lh + nvertices_rh > > cheers > Bruce > > > On Thu, 17 > Dec 2015, Carme Uribe Codesal wrote: > > > Dear FreeSurfer users, > > > > I've been looking for an appropiate way to merge both hemispheres in the > > Desikan parcellations but I can't find it in the list. > > > > Which formula do I need to use to consider, for example, the bilateral > > posterior cingulate as an only measure (not lh and rh separated)? > > > > I'm not sure if I can just add them in a mean... > > > > Thank you very much for your help! > > > > Carme > > > > > ___ > 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] Segmentation of hippocampal subfields and nuclei of the amygdala
Dear FreeSurfer users, I wanted to run the new script that segments the hippocampus and amygdala (segmentHA_T1.sh: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) but I can't find it in FreeSurfer 6.0. Is it already available? Where can I find it? Thanks in advance! Carme Uribe ___ 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] Segmentation of hippocampal subfields and nuclei of the amygdala
Great! Thanks! 2018-01-08 16:44 GMT+01:00 Hoopes, Andrew : > Hi Carme, > > segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh. > harvard.edu/pub/dist/freesurfer/dev > > best, > Andrew > > > On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal > wrote: > > Dear FreeSurfer users, > > I wanted to run the new script that segments the hippocampus and amygdala > (segmentHA_T1.sh: https://surfer.nmr.mgh.harvard.edu/fswiki/ > HippocampalSubfieldsAndNucleiOfAmygdala) but I can't find it in > FreeSurfer 6.0. Is it already available? > > Where can I find it? > > Thanks in advance! > > Carme Uribe > ___ > 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] motion parameter in preprocessing stream
Dear all FreeSurfer users, I was wondering if I can extract any parameter of movement from the recon-all processing using FreeSurfer 5.1. Thanks in advance! Kind regards, Carme ___ 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] matlab MEXFile error in thalamic nuclei segmentation script
External Email - Use Caution Dear FreeSurfer users, I am trying to run the Thalamic nuclei and the hippocampal/amygdala segmentation scripts but there is an error with the matlab license. The error message is: LD_LIBRARY_PATH is .:/nas01/users/carme/freesurfer/MCRv84//runtime/glnxa64:/nas01/users/carme/freesurfer/MCRv84//bin/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/os/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/libexec/NX3/lib64/Xinerama:/usr/lib/nx/X11 Invalid MEX-file '/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64': /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64) Error in kvlClear (line 11) Error in SegmentThalamicNuclei (line 203) MATLAB:invalidMEXFile Thanks! Carme Uribe ___ 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] Convert sig.cluster.mgh file to a binary mask in .nii format
External Email - Use Caution Dear FreeSurfer users, I am trying to extract a binary mask from the file cache.th13.abs.sig.cluster.mgh (I want a ROI from the clusters p<0.05) and convert this mask into a .nii file. I have found a previous message in the forum that reccomends using mri_binarize: mri_binarize --i cache.th13.abs.sig.cluster.mgh --min 1.3 --o lh_AP.mgh And from this output I have run: mri_convert --in_type mgh --out_type nii --out_orientation RAS lh_AP.mgh lh_AP.nii However, I can't visualize the lh_AP.mgh and of course the lh_AP.nii is not created properly when I try to visualize it with mricron. Another command that I have tried without success is: mri_surf2surf --sval lh_AP.mgh --tval test.nii --hemi lh How can I get the mask to operate with it in FSL for example? Thanks in advance! Carme Uribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
