[Freesurfer] func2roi-sess command issue

time points (e.g conditon 1, 2 sec after stimulus onset). How can this be if I included the masktail pos flag? I thought that only captured positive activation. If there is a way to solve this issue and capture only positive activation, please post when you can. Thank you, Dave Br

[Freesurfer] Top Quartile of Active Voxels

We would like to create a functional constraint including only the 25% most active voxels (top quartile). Is there a command that can achieve this? Thanks, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Problem with post-spm registered data

vious subjects) and there is no functional activity in the top inch or so of the cortex whatsoever. Please let me know if you have an answer to how this could have happened. Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Top Quartile of Active Voxels

I would like to create a functional constraint including only the 25% most active voxels (top quartile). Is there a command that can achieve this? Thanks, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] mri_volcluster question

Hello, Does the frame flag refer to offsets? If so, would frame 5 be the same as offset 5 (6 seconds)? Thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Discrepancy between talairach coordinates entered in tool bar and time course display

time course plot caption. Is this image legitimate? Which image accurately represents the original coordinates I want to use? Please write back when you can, and thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] SPM Register Issues

/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects Thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] SPM Issues

/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects Thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec for fMRI using categorical covariate?

Hello, I want to generate screenshots of group activation in an anatomical ROI on the left and right hemisphere for two different groups of subjects at a particular contrast and time point of our analysis. We want to use race as a covariate (categorical, with whites and blacks being the two racia

[Freesurfer] qdec for fMRI analysis with categorical covariate? (continued)

as a categorical covariate? Thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Y axis values in time course in relation to percent signal change

;s (1 2 3). We are looking for percent signal change values. Can you tell me what these y-axis values are, and if there is a way to calculate percent signal change from them if I write these time course values to file? Thank you very much, Dave Br

[Freesurfer] Monte Carlos for volume data?

run a mri_volcluster (as opposed to surfcluster) to assess volume clusters and see if they pass monte carlos with what I already have, then? Thanks for taking the time to read this through. I know this email is on the long side. Dave Brohawn ___ Freesurfer mailing

[Freesurfer] Monte Carlos for Volume? (Part 2)

need to do a volume-based monte carlo analysis. Thank you very much, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Non-FDR Multiple Corrections for Volume?

mmand could create a similar concatenated file using volume data that could produce an input file for the monte carlos? Thanks, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Non-FDR Multiple Corrections for Volume?

mmand could create a similar concatenated file using volume data that could produce an input file for the monte carlos? Thanks, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Using a Label with Volume-based Monte Carlos

e includes the left and right segmentations of the following regions: Amygdala, hippocampus, DC, Putamen, Accumbens, Pallidum, Thalamus Proper, and Caudate. The brain stem label is also included. Please let me know if running a monte carlo for volume with a label is possible. Thank you, Da

[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area

Hello, Here is my bugr info if you need it: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090428 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine:

[Freesurfer] fMRI FOV issue (Bay 8)

6 with recon-all! **** Thank you, Dave Brohawn FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090503 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exi

[Freesurfer] N-Back Test for E-prime?

from scratch, that would be nice. Please let me know, and thanks, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Recon-All Talairach error

old=0.0050) Linux seymour 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:20:55 EDT 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Mar 17 12:52:07 EDT 2010 Should I run without a talairach check if I manually look and it looks ok? Let me know, and thanks, Dave Brohawn FREESURFER_H

[Freesurfer] Recon All Failure during Fix topology lh step

) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Can someone help? Thanks, Dave Brohawn ___ Freesurfer ma

[Freesurfer] Question

Hello, While doing a autorecon-all, I experienced an error during the template deformation step. writing output transformation to transforms/talairach_with_skull.lta... registration took 187 minutes and 39 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/stable4/average/RB_all_wi

[Freesurfer] Snowy background for T1 images

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

[Freesurfer] Dummy Scans and Paradigm Files

Hello, My name is David Brohawn, and I am one of Dr. Roffman's research assistants. We run the SIRP and N-Back memory tests with our subjects. We have specified for 3 dummy scans to take place at the beginning of each of these protocols, which takes 6 seconds of scanning time, respectively. Whe