[Freesurfer] prefrontal cortex values
Hello, I require values (total volume) for the prefrontal cortex. I see labels for "G_frontal_middle" and "G_frontal_superior" in the lh.aparc.annot files - are these correct to use? If so, could I add up the values for these to get one total volume for the PFC? Thank you, Fatima ___ 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] Question about getting fusiform stats
look in the subject/stats/?h.aparc.stats file doug On Tue, 8 Jun 2010, Weisinger, Brian (NIH/OD) [E] wrote: > Hello I am trying to retrieve the fusiform volumes of a sample. I looked in > the subject output files but didn't see any mention of the fusiform and when > I searched the website so far all I could find involved fsl and functional > data which mine is not. If it is possible to do could you please point me in > the right direction to figure this out. > > Thank you for your help > > ___ > 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] Freesurfer to DTI space
I'm not sure if you can use that or not. The best thing is to use bbregister to align the low-b to the anatomical, then use the resulting matrix as input to mri_label2vol. doug On Tue, 8 Jun 2010, Tina Jeon wrote: > Hello all, > > I am using surface tracking in FSL to align my freesurfer surfaces to my > diffusion data. I am wondering if it were possible to use the > freesurfer2fa.mat registration file as the registration input for > mri_label2vol. The freesurfer2fa.mat was generated using FLIRT in FSL by > registering the freesurfer conformed structural space to diffusion space. > > Ultimately I want to align the gyri and sulci volumes to the diffusion images > I have. Is this a viable solution? > Thanks in advance, > > Tina Jeon > > > > ___ > 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] fsaverage aseg
It was created by mapping all the individual asegs of the input subjects to mni305, then detertermining the most frequently occuring label. It should only be used for display purposes. doug On Tue, 8 Jun 2010, Michael Waskom wrote: > Hi all, > > How was the fsaverage aseg.mgz (in the 4.5 distribution, if it differs) > created? I can't seem to find this information anywhere on the Freesurfer > website. > > Thanks! > Mike > -- 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] sorry for repeating, PFC question
Sorry for repeating myself, but I'm unsure if my first post got through successfully. My post is detailed below: I require values (total volume) for the prefrontal cortex. I see labels for "G_frontal_middle" and "G_frontal_superior" in the lh.aparc.annot files - are these correct to use? If so, could I add up the values for these to get one total volume for the PFC? Thank you, Fatima ___ 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] Snowy background for T1 images
Hello, I keep seeing a snowy background for my T1 structural images. Here is my info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects/ PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects/ cd /space/seymour/1/users/folate_subjects The command I entered and one of the subjects we are seeing this with - tkmedit-sess -s FB0011089A -a fmcsm5_functionals -c Cond1vFix Is this a problem? What can I do to fix this? Dave Brohawn ___ 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] Registration of talairach and original space?
Hi all, We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this registration. However, we are stuck because as far as we know bbregister only works in one direction, fmri to anatomical. We have a region of interest defined as a sphere around a coordinate in Talairach space. What we need to do is to translate that region of interest into the space of an individual subject's fmri data. How can Freesurfer do this? Any suggestions would be greatly appreciated!! Best, Elise and Kathleen * Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 * Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickins...@mail.nih.gov ___ 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] Snowy background for T1 images
Hi Dave, 001.mgz in /mri/orig/ looks okay but 002.mgz looks strange, which I think is the reason for what you are seeing in T1.mgz. Did you collect 2 runs for structurals. Can you point me to the dicom files for this dataset or the scan log. Sita. On Wed, 9 Jun 2010, Dave Brohawn wrote: > Hello, > > I keep seeing a snowy background for my T1 structural images. > > Here is my info: > > FREESURFER_HOME: /usr/local/freesurfer/stable4 > > Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 > > RedHat release: CentOS release 5.3 (Final) > > Kernel info: Linux 2.6.18-128.7.1.el5 i686 > > NMR Center info (/space/freesurfer exists): > > machine: seymour > > SUBJECTS_DIR: /space/seymour/1/users/folate_subjects/ > > PWD: /space/seymour/1/users/folate_subjects > > ssh seymour > setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects/ > cd /space/seymour/1/users/folate_subjects > > > > The command I entered and one of the subjects we are seeing this with - > > tkmedit-sess -s FB0011089A -a fmcsm5_functionals -c Cond1vFix > > > Is this a problem? What can I do to fix this? > > Dave Brohawn > > ___ > 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] Registration of talairach and original space?
We have another question that is very related, so I will ask that at the same time: We have a region of interest defined on an individual subject's surface. How can Freesurfer translate that ROI into the coordinates of the original fmri data? It's clear to us how to get from fmri to the surface, but not the other way around. Thanks, Kathleen and Elise On 6/9/10 12:49 PM, "Dickinson, Annelise (NIH/NIMH) [F]" wrote: Hi all, We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this registration. However, we are stuck because as far as we know bbregister only works in one direction, fmri to anatomical. We have a region of interest defined as a sphere around a coordinate in Talairach space. What we need to do is to translate that region of interest into the space of an individual subject's fmri data. How can Freesurfer do this? Any suggestions would be greatly appreciated!! Best, Elise and Kathleen * Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 * Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickins...@mail.nih.gov ___ 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] retinotopy: MGH vs UCSD
Hi all, I would ask you about freesurfer and retinotopy. I'm going to begin the analysis of some retinotopic data. I would ask if you know if the retinotopic analysis made by MGH freesurfer is qualitatively comparable to, or it's good as, that made by USCD freesurfer (old freesurfer). Thank you kindly in advance. Francesca ___ 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] retinotopy: MGH vs UCSD
what do you mean by "Old FreeSurfer"? -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Wed, Jun 9, 2010 at 17:44, francesca strappini < francescastrapp...@gmail.com> wrote: > Hi all, > I would ask you about freesurfer and retinotopy. I'm going to begin the > analysis of some retinotopic data. I would ask if you know if the > retinotopic analysis made by MGH freesurfer is qualitatively comparable to, > or it's good as, that made by USCD freesurfer (old freesurfer). > Thank you kindly in advance. > > Francesca > > ___ > 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] advise on generating individual standard deviation map
Dear FS experts, could someone advise on how to create from an individual thickness file (?h.thickness) a standard deviation or z-score map of the thickness with respect to a control group. Thanks, Michael ___ 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] retinotopy: MGH vs UCSD
old freesurfer, or csurf, is this: http://kamares.ucsd.edu/~sereno/csurf/tarballs/ made by Marty Sereno ___ 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] Calc stats on ROI in qdec
Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff ___ 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.
