[Freesurfer] (no subject)

-fold and the second timepoint 7-fold? If this is the case then this analysis may not best represent what we are looking for. Is there a way to modify the paradigm file so that the analysis can focus on slope of the best fit line — as opposed to the weighted average? Thanks, Josh Adam Nitenson, B.S

[Freesurfer] Linear Regression Analysis - Significant Slope?

on slope of the best fit line — as opposed to the weighted average? Thanks, Josh Forwarded from: Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 slopepar Description: Binary data analysis.info Description: Binary data

[Freesurfer] Glmfit subtraction between 2 individuals

, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Adding new contrasts to an analysis

exists. You must specify whether to -skip or -overwrite ...even though that specific contrast does not yet exist within that folder. Any ideas? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list

[Freesurfer] Timecourse plots based on fsgd, not analysis?

timecourse plot that can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct? Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.h

Re: [Freesurfer] Timecourse plots based on fsgd, not analysis?

Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously. -Adam > Do you mean something like you have two conditions (say A and B) and two > groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B? > > Adam Nitenson wrote: >> Hello Freesurfers,

Re: [Freesurfer] Timecourse plots based on fsgd, not analysis?

ts in each waveform. > > you can then run > > tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii > > or tkmedit if these are volumes. > > doug > > > Adam Nitenson wrote: >> Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously. >> >> -Adam

Re: [Freesurfer] Timecourse plots based on fsgd, not analysis?

> > tksurfer fsaverage lh inflated -t h.g1A.g1B.g2A.g2B.nii > > or tkmedit if these are volumes. > > doug > > > Adam Nitenson wrote: >> Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously. >> >> -Adam >> >> >>> Do you mea

[Freesurfer] Confused with Monte Carlo results

edControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.nii --ocn /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.ocn.nii Adam Nitenson, B.S. Brain Genomics Lab Massachuse

[Freesurfer] Problems with --bg njobs flag in mri_glmfit-sim

ame error. How can I use that flag to divide 1 simulations into, say, 10 jobs with 1000 each (assuming I am understanding the purpose of the flag correctly). Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Fre

[Freesurfer] Whole Surface SNR Calculation for Individual Functional Runs

e can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Whole Surface SNR Calculation for Individual Functional Runs

files. -Adam > There should be an fsnr.dat file in the fsfast analysis directory with > the value that you want. > > doug > > On 12/20/10 1:30 PM, Adam Nitenson wrote: >> Hello Freesurfers, >> >> We are beginning to perform QC on our subjects and want

Re: [Freesurfer] Whole Surface SNR Calculation for Individual Functional Runs

give me the relevant data? My main concern is that I used "selxavg3-sess" instead of "selxavg-sess" during processing; I'm not sure what the difference between the two is, and I am hesitant to use a different command that might change other aspects of our data. -Adam >

[Freesurfer] Regression: Activation as a function of condition

mkanalysis-sess level? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] Regression: Activation as a function of condition

, Adam > you can't do it in stable4, but you can in stable 5. > > doug > > > Adam Nitenson wrote: >> Hello Freesurfers, >> >> We are using the Sternberg Item Recognition Paradigm in our study, >> which involves the memorization and recogniti

[Freesurfer] mkanalysis-sess in Stable 5

aexp 2.00 -timewindow 24.00 -prestim 4.00 -autostimdur Thank you, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre

[Freesurfer] Volume output from Stable 5 isxconcat-sess

data. Is there a way to get a tal output? I noticed a -talres argument, but I wasn't sure if that was necessary. Running the above command with the -hemis argurment seems to produce lh.ces.nii, etc as in Stable 4. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hos

Re: [Freesurfer] Regression: Activation as a function of condition

ation as a function of > condition > From:"Douglas N Greve" > Date:Tue, January 11, 2011 11:52 am > To: "Adam Nitenson" > -- > > You don't need to re-unpack. you don't r

[Freesurfer] Func2ROI in Stable 4 --> FuncROI in Stable 5

wondering what I needed to add/change to generate data similar to what I did for Stable 4. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list

[Freesurfer] FuncROI in Stable 5

specify a threshold (-thresh) with a contrast. This is the > equivalent to the -min in funcroi-sess. There was a bug in > funcroi-config that prevented it from catching that you did not specify > a threshold (which has been fixed now). > thanks > doug > > Adam Nite

[Freesurfer] Baseline Offset in Stable 5 funcroi

g -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH funcroi-table-sess -roi MTH_7vFix_DLPFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH -c Cond7vFix -o /cluster/roffman/users/Stable5_PerRun/DLPFC_ROI_7vFix_MTH Adam Nitenson

[Freesurfer] Strange issue with isxconcat

dd that the commands for both would simultaneously terminate. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list Freesurfer@nmr.m

[Freesurfer] Minimum n for glmfit maps?

1/2_FB_DEP_TT_1T3T5T7T/SIRP_Stable5/osgm/LH1v7 --surf fsaverage lh --fwhm 4.6 Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list F

[Freesurfer] Modifying Regression Analysis

ing process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

Re: [Freesurfer] Modifying Regression Analysis

uld be pretty quick). > > doug > > Adam Nitenson wrote: >> Hi Doug and Freesurfers, >> >> I am currently analyzing data acquired from the Sternberg memory >> task, which involves memorizing sets of 1, 3, 5, and 7 letters. I >> have created an analysis (see

[Freesurfer] preproc-sess - cannot find AFNI command 3dvolreg

/users/Stable5_PerRun cd $SUBJECTS_DIR preproc-sess -s MTH20100AA -fwhm 5 -per-run I've run this set of commands many times without this problem, so did something change or am I missing something simple? Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

[Freesurfer] FSGD Contrast Setup Question

-0.5 0.5 0 0 0 0" is best. Is this the best way to go about analyzing these two questions? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfe

[Freesurfer] functional ROI analysis for DLPFC

o quote my PI, "look at the dorsolateral prefrontal cortex ROI data, which will generate a single value for the average activation within the right or left DLPFC for each subject, during each condition". Adam Nitenson, B.S. Brain Genomics Lab Massachuse

[Freesurfer] spmregister-sess error

; >> >> ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg" I have unpacked several other subjects before using these same commands without issues. Why might I be re

[Freesurfer] Interpreting roisummary-sess

conditions with only 1 estimate for each. How do I generate multiple estimates for each condition, and, even better, how can I incorporate multiple conditions (3vFix, 5vFix, etc) into the same roisummary? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

Re: [Freesurfer] spmregister error

t; Fax: 617-726-1351 > Email: swoodm...@partners.org > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > Adam Nitenson, B.S. Brain

[Freesurfer] Calculating % Signal Change from roisummary-sess readout

ultiplying by 100 to get % signal change. Is this a valid method? Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital PS Here are the commands I used if that helps: func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -

[Freesurfer] Automatic Plotting of Hemodynamic Response???

is func2roi the standby command for such tasks? Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] Automatic Plotting of Hemodynamic Response???

considered). Is there any way to create a more automatic, streamlined hemodynamic response curve, or are func2roi and roisummary the standard means of doing this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer

[Freesurfer] whoops

Sorry for the double post (and, I suppose, the triple post as well) Only consider the more recent email, and it's just a completed version of my first one. Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer ma

[Freesurfer] preproc-sess failing

/outvol.nii.gz... ERROR: Read 14, expected 64 ERROR: converting output Invalid null command. ERROR: mc-sess failed Any idea what might be going on? I've done these same steps many times for processing data and have not before received this error. Thanks! Adam Nitenson, B.S. Brain Genomic

Re: [Freesurfer] preproc-sess failing

o look at > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for other ways to improve > your bug reports. Also, please start to send these kinds of things to > martinos-tech or the freesurfer list. > > thanks > > doug > > > Adam Nitenson wrote: >> Hi Doug, >> &g

Re: [Freesurfer] preproc-sess failing

ything wrong with it and did not try to regenerate it. Try > deleting fmc.nii and re-running. > > doug > > Adam Nitenson wrote: >> Hi Doug, >> >> My original email was sent to the freesurfer list. >> >> Here is the more detailed terminal info: >>

[Freesurfer] Changing and Saving Overlay Config in Tksurfer

changes, but it only saved the default config. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] Creating Brainmaps for Significant Regression

difference. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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 on

[Freesurfer] selxavg3 problems - missing mcextreg files

cts/FB0011099AA/bold/015which seems to halt the command What is the best way to recover these files for this one BOLD folder? Thanks, Adam Nitenson PS Here is the additional computer info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0

Re: [Freesurfer] Creating Brainmaps for Significant Regression

arch for FSGD on the wiki for more info. > > doug > > Adam Nitenson wrote: >> Hi all, >> >> So far I have only been using Freesurfer analyses to look at the >> functional activation for individuals, single groups, and subtractions >> between 2 groups. W