[Freesurfer] Surface area intepretation problem
Dear FS experts We divided the superior temporal sulcus derived from the aparc.a2009s.annot into parcellations of 300mm2 (using mris_divide_parcellation) and computed the mean cortical thickness within each parcellation. So far so good. But we noticed that each parcellation has a unique surface area that deviates largely from 300mm2 (96-480mm2). We defined the parcells on the fsaverage template and transformed them back into the native space of each individual. Therefore, we expected some variation in the surface area, but not such large differences. How to explain it? Thanks in advance Regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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 problems
Dear Bruce and all, I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question: 1. Regarding mri_gcut: should I use the default intensity of 110 for white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36? 2. Regarding manual removing of some voxels: the 'Edit Voxels' tool doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong? Thank you, Tetiana. On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tetiana, do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut. cheers Bruce On Mon, 31 Jan 2011, Tetiana Dadakova wrote: Dear FreeSurfer users, I run a recon-all -all for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana. 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
Re: [Freesurfer] Segmentation problems
try disabling use of gcut by adding -no-gcut to the end of recon-all. sometimes it can cut too much (something thats fixed in the upcoming release). n. On Wed, 2011-02-02 at 11:28 +0100, Tetiana Dadakova wrote: Dear Bruce and all, I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question: 1. Regarding mri_gcut: should I use the default intensity of 110 for white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36? 2. Regarding manual removing of some voxels: the 'Edit Voxels' tool doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong? Thank you, Tetiana. On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tetiana, do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut. cheers Bruce On Mon, 31 Jan 2011, Tetiana Dadakova wrote: Dear FreeSurfer users, I run a recon-all -all for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana. 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
[Freesurfer] Am I losing T2* info in MEMPRAGE data by differential scaling?
Dear Freesurfer, I am concerned that I may not be processing the MEMPRAGE images to full take advantage of the T2* info in the multi-echos. I have been separating each echo as 001.mgz, 002.mgz, 003.mgz 004.mgz when using recon-all. This works well if motion exists in any of the individual echos. However of late, I have noticed a that a reference was made to the problem of losing T2* info by differential scaling in the archive if a particular file format memprage_echo0.mgz was not used. Here is the link to the archive note: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15303.html It has been hard to identify a difference between our standard MPRAGE images and the MEMPRAGE images (we currently collect both on our Siemens 3T 32 channel system). Am I processing the MEMPRAGE correctly? Thanks! -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• ___ 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] Problem running recon-all with option -qcache
Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was: number of vertices in ../subjectID/surf/lh.thickness does not match surface (141969,131763). It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness. I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected. What can I do to use the -qcache option? Ed ___ 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] testing FreeSurfer
Hi FreeSurfer's user, I'm new using this software, I try to install on Ubuntu and to set up following the recommendation of the webpage. Then I tried to test but any commmand seems to be recognized, also when I started a new terminal a warning is shown: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 Thanks in advance for the support, Best regards, cvalencia ___ 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 problems
This is probably ok. Run it all the way through and see if it affects the surfaces. If not, you are all set On Feb 2, 2011, at 10:30 AM, Tetiana Dadakova tetian...@gmail.com wrote: I attach a picture of what I get if I run recon-all -autorecon1 -subjid name_of_subj -no-gcut. I feel that I need to change the -T threshold of WM intensity, does it make sense? If I put this -T value to 0.5, the out-of-brain structures are cut, but I wonder how it affects the white matter. Thank you, Tanja On Wed, Feb 2, 2011 at 2:36 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: try disabling use of gcut by adding -no-gcut to the end of recon-all. sometimes it can cut too much (something thats fixed in the upcoming release). n. On Wed, 2011-02-02 at 11:28 +0100, Tetiana Dadakova wrote: Dear Bruce and all, I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question: 1. Regarding mri_gcut: should I use the default intensity of 110 for white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36? 2. Regarding manual removing of some voxels: the 'Edit Voxels' tool doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong? Thank you, Tetiana. On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tetiana, do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut. cheers Bruce On Mon, 31 Jan 2011, Tetiana Dadakova wrote: Dear FreeSurfer users, I run a recon-all -all for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana. 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 skull_strip.tiff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Am I losing T2* info in MEMPRAGE data by differential scaling?
Hi Carl, you're probably better off taking the RMS (root-mean-square) of the echoes rather than averaging them together. Our scanner outputs these in addition to the echoes, but they are easy to compute with calls to mri_concat. doug btw, you can't really have motion between the echoes. All four echoes for each line of k-space are acquired within 20ms of each other. Carl Anderson wrote: Dear Freesurfer, I am concerned that I may not be processing the MEMPRAGE images to full take advantage of the T2* info in the multi-echos. I have been separating each echo as 001.mgz, 002.mgz, 003.mgz 004.mgz when using recon-all. This works well if motion exists in any of the individual echos. However of late, I have noticed a that a reference was made to the problem of losing T2* info by differential scaling in the archive if a particular file format memprage_echo0.mgz was not used. Here is the link to the archive note: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15303.html It has been hard to identify a difference between our standard MPRAGE images and the MEMPRAGE images (we currently collect both on our Siemens 3T 32 channel system). Am I processing the MEMPRAGE correctly? Thanks! -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com mailto:remfr...@gmail.com; carl_ander...@hms.harvard.edu mailto:carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Problem running recon-all with option -qcache
Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted. doug Ed Gronenschild wrote: Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was: number of vertices in ../subjectID/surf/lh.thickness does not match surface (141969,131763). It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness. I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected. What can I do to use the -qcache option? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] One Way Anova and multiple comparisons
Hi to everybody, I am a very inexperienced users of FreeSurfer. I have 3 groups of subjects and I have run recon-all and checked the results for all the subjects (very good results). Now what I need to do, is to calculate the differences in the regional cortical thickness between these 3 groups (using age and gender as covariates) and to perform multiple comparisons, in order to detect possible local differences in cortical thickness. Is it possible to perform this kind of analysis also for comparing surfaces between different groups? Could you give me a short pipeline about the steps I need to do, or redirect me to some focused documentation? Thank's. Marco ___ 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] One Way Anova and multiple comparisons
Yes, you can do these types of things. You'll need to create an FSGD file. Search for FSGD on the wiki and go to the examples page, there's not an example of 3 groups and 2 covariates, but there are enough examples there that you can piece it together. After you have your FSGD file, run mris_preproc, mri_surf2surf to smooth, mri_glmfit, then mri_glmfit-sim to correct for multiple comparisons. There's a group analysis tutorial on the website too. doug marco battaglini wrote: Hi to everybody, I am a very inexperienced users of FreeSurfer. I have 3 groups of subjects and I have run recon-all and checked the results for all the subjects (very good results). Now what I need to do, is to calculate the differences in the regional cortical thickness between these 3 groups (using age and gender as covariates) and to perform multiple comparisons, in order to detect possible local differences in cortical thickness. Is it possible to perform this kind of analysis also for comparing surfaces between different groups? Could you give me a short pipeline about the steps I need to do, or redirect me to some focused documentation? Thank's. Marco ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 during autorecon2-wm routine
Dear experts, after correcting WM, I got the following error running recon-all - autorecon-wm -subjid XXX ERROR: _FindFacePath: could not find path! It happens in the middle of the correcting topology routine. I'd appreciate any input on as to why it happens and how to fix it. Cheers Larissa ___ 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] transform to original mri
you'll have to first create a registration file, you can do that with cd subject/mri tkregister2 --mov orig/001.mgz --targ T1.mgz --regheader --s subject --reg register.dat --noedit then apply this to the surface with mri_surf2surf --s $subject --sval-xyz white --hemi lh --reg register.dat orig/001.mgz \ --tval-xyz --tval ./lh.white.001 This creates lh.white.001, and the coordinate will/should be in the tkregister coorindates of the 001.mgz space (usually they are in the tkregister coords of the T1.mgz space). See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.ppt for how to get from this space to other spaces. doug Seok Lew wrote: Dear all, I am trying to transform the reconstructed surface like rh.pial into the original mri's (like 001.mgz) coordinate. I found some matrices in the ./transform directory, but not sure of which one (or a set of matrices) would do the transform? Seok s...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] using mri_glmfit-sim
These are two distinct methods of correcting. One, is to synthesize, smooth, analyze, and cluster. The second is to permute, analyze, and cluster. These are realized by two different arguments to the --sim flag in mri_glmfit-sim (either --sim mc-z ... or --sim perm ...) doug Chris Hyatt wrote: I've read both Hagler et al 2006 Neuroimage (Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data) and B. Douglas Ward's description of AlphaSim that both describe clusterwise correction for multiple comparisons. I recently found, however, an MGH Freesurfer presentation that mentioned that after synthesizing Gaussian noise and smoothing (Monte Carlo), the rows of the design matrix were permuted. Does the mri_glmfit-sim clusterwise correction method permute rows of the design matrix? I'm still a bit confused about the exact method the clusterwise correction for multiple comparisons work in Freesurfer. Thanks for your help. Christopher Hyatt, PhD IOL/Olin Neuropsychiatry Research Center Hartford, CT ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Am I losing T2* info in MEMPRAGE data by differential scaling?
Well our primary reason for using this sequence is to better delineate the amygdala. On Wed, Feb 2, 2011 at 5:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: what do you want to do with the echoes? On Wed, 2 Feb 2011, Douglas N Greve wrote: Hi Carl, you're probably better off taking the RMS (root-mean-square) of the echoes rather than averaging them together. Our scanner outputs these in addition to the echoes, but they are easy to compute with calls to mri_concat. doug btw, you can't really have motion between the echoes. All four echoes for each line of k-space are acquired within 20ms of each other. Carl Anderson wrote: Dear Freesurfer, I am concerned that I may not be processing the MEMPRAGE images to full take advantage of the T2* info in the multi-echos. I have been separating each echo as 001.mgz, 002.mgz, 003.mgz 004.mgz when using recon-all. This works well if motion exists in any of the individual echos. However of late, I have noticed a that a reference was made to the problem of losing T2* info by differential scaling in the archive if a particular file format memprage_echo0.mgz was not used. Here is the link to the archive note: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15303.html It has been hard to identify a difference between our standard MPRAGE images and the MEMPRAGE images (we currently collect both on our Siemens 3T 32 channel system). Am I processing the MEMPRAGE correctly? Thanks! -- ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com mailto:remfr...@gmail.com; carl_ander...@hms.harvard.edu mailto:carl_ander...@hms.harvard.edu ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ~~ÿÿ ___ 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. -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• ___ 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] Surface area interpretation confusion
Dear FS experts Sorry, for reposting this question, but I'am not sure whether something went wrong. We divided the superior temporal sulcus derived from the aparc.a2009s.annot into parcellations of 300mm2 in size (using mris_divide_parcellation) and computed the mean cortical thickness within each parcellation. But after running mris_anatomical-stats, we noticed that each parcellation has a unique surface area that deviates largely from 300mm2 (ranging between 96mm2 to 480mm2). Does anybody have any ideas? Is this a bug or is this what one should expect? We defined the parcells on the fsaverage template and transformed them back into the native space of each individual. Therefore, we expected some variation in the surface area, but not such large differences. Thanks in advance Regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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.
