,
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
niten...@nmr.mgh.harvard.edu
Phone: 617-643-3215
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The information
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
-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
-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
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Freesurfe
/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
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
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
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
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F
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
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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
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
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
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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
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
aexp 2.00
-timewindow 24.00
-prestim 4.00
-autostimdur
Thank you,
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
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,
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
mkanalysis-sess level?
Thanks,
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
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The information in this e
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
>
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
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
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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
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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
>
> 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
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
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,
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
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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
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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
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
difference.
Thanks,
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
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The information in this e-mail is intended on
changes, but it only saved the default config.
Thanks,
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
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The
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:
>>
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
/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
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
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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
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is func2roi the standby command
for such tasks?
Thanks!
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
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The
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 -
t; Fax: 617-726-1351
> Email: swoodm...@partners.org
>
>
>
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>
>
>
Adam Nitenson, B.S.
Brain
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
; >> >> 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
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
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