[Freesurfer] mean and stdev group-wise
Dear list, I would like to calculate mean and stdev of thickness group-wise. Could you please give me a hint how to do it? Thank you, Tanja. ___ 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] flipped orientation in tksurfer and tkmedit
Hi there, We recently had a problem that tksurfer and tkmedit were flipped relative to each other. Basically, when saving a point in the left hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. Any ideas how this could have happened? Thanks ilana -- ** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property ___ 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] .img extension read as analyze even though hdr says nifti1
hi all, when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type be detected from the header? also it would be good to know if this behavior is consistent across all of freesurfer or restricted to certain binaries. see below for mri_info output cheers, satra $ mri_info con_0001.img Volume information for con_0001.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2., 2., 2. type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -1. : x_a = 0., y_a = 1., z_a = 0., c_a = -17. : x_s = 0., y_s = 0., z_s = 1., c_s = 18. Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2. 0. 0.78. 0. 2. 0. -112. 0. 0. 2. -50. 0. 0. 0. 1. voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0. 0.39. -0. 0.5000 -0.56. -0. -0. 0.500025. 0. 0. 0. 1. $ mri_info con_0001.hdr Volume information for con_0001.hdr type: nifti1 dimensions: 79 x 95 x 68 voxel sizes: 2., 2., 2. type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -1. : x_a = 0., y_a = 1., z_a = 0., c_a = -17. : x_s = 0., y_s = 0., z_s = 1., c_s = 18. Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2. 0. 0.78. 0. 2. 0. -112. 0. 0. 2. -50. 0. 0. 0. 1. voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0. 0.39. -0. 0.5000 -0.56. -0. -0. 0.500025. 0. 0. 0. 1. ___ 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] statical question recon-all -qcache -s (subject) ?
Hi Can I use a different version of Freesurfer to run recon-all -qcache -s (subject) than the version used for recon-all -all -s (subject)? Knut J ___ 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] statical question recon-all -qcache -s (subject) ?
I think that's ok, right Nick? As long as you do all your subjects the same way Bruce On Sep 11, 2011, at 4:01 PM, Knut J Bjuland knut...@hotmail.com wrote: Hi Can I use a different version of Freesurfer to run recon-all -qcache -s (subject) than the version used for recon-all -all -s (subject)? Knut J ___ 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.
Re: [Freesurfer] statical question recon-all -qcache -s (subject) ?
correct. qdec uses mri_glmfit, which operates on data already processed (and so versioning is not an issue). the exception is that the 'volume' and 'area' measures shouldnt be selected as the independent variable (there is a problem that will fix that in the next release). n. I think that's ok, right Nick? As long as you do all your subjects the same way Bruce On Sep 11, 2011, at 4:01 PM, Knut J Bjuland knut...@hotmail.com wrote: Hi Can I use a different version of Freesurfer to run recon-all -qcache -s (subject) than the version used for recon-all -all -s (subject)? Knut J ___ 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 ___ 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.
