[Freesurfer] Two questions about csd (cluster simulation data)
Hi, These might be old questions, but I couldn't find any entries related to them in the archives. 1) In the surface and volume csd files, what are the units of the "maxclustsize" columns? Are they mm^2 and mm^3 for surface and volume, respectively? Or are the voxel / vertex counts? 2) When mri_surfcluster uses a csd file to compute the cluster-wise correct p-values, how does it do that? Does it only use the maxclustsize? Or does it take other columns, such as maxsig, into account as well? Thanks! Best, Shanqing Cai ___ 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] "Holes" in the mri_label2vol results
Hi, I am using mri_label2vol to generate some volume ROIs from surface labels. I noticed that the results contain "holes", by which I mean voxels that aren't label and are surrounded by labeled voxels. This seems to happen regardless of the step size I specify after the "--proj" option of mri_label2vol and this happens in both the gray- and white-matter projections. I am using FS 5.1.0. I wonder whether other people have experienced similar problems and how these holes can be gotten rid of. Thanks! Best regards, Shanqing Cai ___ 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] Tracula references
Hi, I am using Tracula in my diffusion data analysis and am interested in finding out what would be the best citations or references for this tool. A quick Internet search brings me to two conference papers, one in ISMRM and one in an IEEE conference. Are there any journal articles that have been published on Tracula? I need the information for better understanding of the tool and possible citations in future publications. Thank you. Best regards, Shanqing Cai ___ 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_glmfit weighted random effects
Hi,
I have a question about the "weighted random effects" option in the "mri_glmfit"
command. Are there any specific references (papers or books etc.) for that
approach, i.e., using contrast variance images to weigh the contrast images in
a second-level analysis. Also, would it be possible for me to access the source
code of that particular module ("mri_glmfit") to see how the algorithm is
implemented? The FreeSurfer source that used to be accessible from the ftp
server (surfer.nmr.mgh.harvard.edu) is not only there for some reason.
Thank you very much!
Best regards,
Shanqing Cai
___
Freesurfer mailing list
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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] Tracula bedp error
Hi, I am running Tracula on the MIT BCS cluster. The first step "-prep" finished without error. However, during the second step "-bedp" I received the following error messages. ba3:~/STUT/tracula> trac-all -bedp -c ~/STUT/tracula/tracula.cfg INFO: SUBJECTS_DIR is /users/cais/STUT/FSDATA INFO: Diffusion root is /users/cais/STUT/tracula Actual FREESURFER_HOME /software/Freesurfer/5.1.0 ln -sf /users/cais/STUT/tracula/S01/dlabel/diff/anat_brain_mask.bbr.nii.gz /users/cais/STUT/tracula/S01/dmri/nodif_brain_mask.nii.gz ln -sf /users/cais/STUT/tracula/S01/dmri/dwi.nii.gz /users/cais/STUT/tracula/S01/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /users/cais/STUT/tracula/S01/dmri subjectdir is /users/cais/STUT/tracula/S01/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: SGE: unexpected operator [: 314: SGE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator Queuing parallel processing stage [: 223: SGE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x67: unexpected operator Queuing post processing stage [: 223: SGE: unexpected operator [: 314: SGE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator It seems that there are errors related to SGE configurations. Anyone has any suggestions w.r.t. how to solve this problem? Thanks! Best regards, Shanqing ___ 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] A question about the Freesurfer version compatibility of Tracula
Hi, I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer. However, my data set are processed with the recon-all of an earlier version of FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the subjects in the data set with 5.1.0. Would running Tracula on 5.0.0 reconstructions cause any problems that render the results unusable/not trustable? Thank you! Best, Shanqing Cai ___ 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.
