[Freesurfer] Incorporating T2 and T1 images in recon-all

around the sagittal sinus. I thought adding the T2-weighted scan into the mix might improve things a bit. Can this be done, and if so, how? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail

[Freesurfer] Command works in optseq, not optseq2

or did I make a mistake with my optseq2 command? Also, I'm assuming there is a reason why I should use optseq2 rather than optseq, but I don't know what it is. Can someone clue me in? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology,

RE: [Freesurfer] Possible to constrain FDR to a label in the volume?

Hi Doug. Yup, the FDR button is working for me in tkmedit. I see the mask to brain, but as you can probably guess I'm interested in masking to the basal ganglia. DD From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tuesday, December 02, 2008 12:04 PM To: Dan Dillon Cc: frees

[Freesurfer] Possible to constrain FDR to a label in the volume?

g similar in tkmedit. Any help greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]

[Freesurfer] Possible to regress whole-brain functional data against continuous variables in the volume?

istered to each participant. I understand the basic fsgd/mri_glmfit approach from the FS tutorial, but I want to stay in the volume in order to examine sub-cortical structures (e.g., nucleus accumbens). Is this possible? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience

[Freesurfer] Citation for FSFAST

Hi Doug. What's the preferred citation/reference for FSFAST? Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] Question re: extracting functional data from cortical ROIs

tical ROIs? Is there a set of flags that generally works well that I should use to make sure I'm getting data from all the gray matter? Thanks! Dan -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 17, 2008 4:56 PM To: Dan Dillon Cc: 'Fre

[Freesurfer] Question re: extracting functional data from cortical ROIs

I have a question about extracting functional data from structurally defined cortical labels. Here's what I'm doing: 1) Run a gammafit analysis; 2) Define cortical ROIs by using mri_annotation2label to make labels from aparc.annot; 3) Define sub-cortical ROIs by using mri_co

RE: [Freesurfer] Odd tkmedit behavior

Thanks Bruce! DD -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Tuesday, March 04, 2008 10:54 AM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior Hi Dan, I managed to track thi

RE: [Freesurfer] Odd tkmedit behavior

Okay, sounds good-thanks. DD -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 03, 2008 3:44 PM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior We're tracking it down, but it appears to b

RE: [Freesurfer] Odd tkmedit behavior

rby position and the Talairach coordinates change slightly from what I entered. -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 03, 2008 3:24 PM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior What do

[Freesurfer] Odd tkmedit behavior

! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Obtaining cortical parcellations

"-autorecon3-parcellation"? I am running version 4.0.1. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurf

[Freesurfer] mri_convert problem while unpacking functionals

functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz) ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] Question about brain masking

nd tweaking the "-threshold" argument? Thanks! Dan Dillon Affective Neuroscience Lab Harvard University <><>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Error encountered while running selxavg3

3 not recognize this option? Thanks in advance for any help you can provide. Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesur

RE: [Freesurfer] Another talairach question . . .

Wonderful, thanks. DD -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Thursday, November 29, 2007 5:19 PM To: Dan Dillon Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Another talairach question . . . Dan, Include the flag

[Freesurfer] Another talairach question . . .

usly wrong. How do I make use of my edited Talairach and get autorecon1 to continue? Thanks in advance, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL

[Freesurfer] Volume of sub-cortical structures

Dear FreeSurfers, Hopefully a very easy question . . . I want to compare the volume of subcortical structures in two groups of subjects. All I need to do that is the volume information contained in aseg.stats, right? Just want to double-check before I get started. Thanks! Dan Dillon

[Freesurfer] Problem concerning maximum values from mri_volcluster

te the output for the examples: mri_volcluster --in FPP_HiRisk_MC_375/bold/FPP_MCReg_8_23/tal-rfx/Rcue_v_RSF/sig --in_type bfloat --reg FPP_HiRisk_MC_375/bold/FPP_MCReg_8_23/tal-rfx/register.dat --thmin 3 --minsizevox 12 --out Test_FPPHiRisk_MC375_Rc_v_RSF --out_type bfloat Thanks in advance. Dan Dill

[Freesurfer] Possible to pass 2 identical analyses but with different names to intergroupavg-sess?

"). Is there a way to run intergroupavg-sess without having to either re-name or re-run one of these analyses? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:[E

[Freesurfer] How to extract beta weights, by condition, for whole-brain regression analysis

ROIs, but I don't know how to do this for the whole brain. Any help will be greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [

[Freesurfer] Masking at the individual level

I'm doing stats on (which is what I want it to do)? Thanks for your endless help! Dan Dillon PS. This is a a typical mkanalysis step . . . mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm mg_3_7.par -designtype event-related -funcstem fmcs tcsm6

[Freesurfer] Masking group data using mri_volcluster

uster? Without a mask, I'm currently getting stats on extra-brain voxels that I do not want, and I can't use the Talairach brainmask.mgz file b/c it doesn't match my input volume. Any help would be appreciated. Dan Dillon PS. The command I'm currently running,

[Freesurfer] Gammafit vs. SPMHRF

Dear FreeSurfers, What exactly is the difference between the HRF function in gammafit vs. SPMHRF? Are there reasons to prefer one to the other? Thanks, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E

[Freesurfer] Where to get mri_binarize?

I would like to use mri_binarize but don't seem to have it (running stable 3.0.3). Where can I get it? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: [EMAIL PROT

[Freesurfer] Temporal derivative in mkanalysis-sess

Dear FreeSurfers, I'd like to add a temporal derivative to my gammafit model and understand that this can be done using mkanalysis-sess. However, I can't seem to track down the relevant flag (using -help or the wiki). Can someone point me in the right direction? Thanks!

[Freesurfer] Output of mri_volcluster

the first cluster change? Also, where is cluster 4 from the second output in the first output? Is there some re-calculation going on here? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222

[Freesurfer] Question about trials w/subject errors

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[Freesurfer] Register.dat for mri_volcluster

UBJECTS_DIR when I run func2tal-sess, or is this a part of a library I should have somewhere? Or do I create this file? Any help would be appreciated. Thanks! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m

[Freesurfer] Problem with T1 intensities

! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Slice Time Correction Error

ucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/FPPREW01/bold/013/tmp.10997/in.img -o /net/tucson/Raid/shart slicetimer: /usr/lib/libstdc++.so.5: version `GLIBCPP_3.2.2' not found (required by slicetimer)  Is there a simple way to address this issue? Tha