Hi Freesurfers,
When conducting ROI analyses in Stable 5, is there a way to generate
a mean functional baseline offset value within the ROI which can be
used to help calculate percent signal change? This would correspond
to the value from row 4 in the output file generated by
roisummary-sess in Stable 4.
Thanks,
Adam
PS: Here are examples of the commands I've used in Stable 5 to generate
ROI Data:
funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi
MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs -thresh 1.3
funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -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
> You need to 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 Nitenson wrote:
>> Hi Freesurfers,
>>
>> I'm trying to analyze functional data in Stable 5, but have noticed
>> that the func2roi command is no longer used. My analysis involves 9
>> conditions (not including Fixation) and 1 timepoint for each. The
>> steps I used in Stable 4 to generate this data are as follows:
>>
>> func2roi-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals
>> -anatlabel LH_16MTH_7v1_DLPFC -sf
>> /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped
>> -d
>> /cluster/roffman/users/MTH_Study
>>
>> roisummary-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals
>> -sf
>> /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped
>> -d
>> /cluster/roffman/users/MTH_Study -sumfile
>> /cluster/roffman/users/MTH_Study/ROI_Analysis/LH_16MTH_7v1Label_DLPFC
>>
>> In Stable 5, I see that there are several commands, funcroi-config,
>> funcroi-sess, and funcroi-table-sess. Looking at other threads, it seems
>> like I need to make a roicfg file for each contrast. So far I have
>> tried:
>>
>> funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi
>> MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs
>>
>> and then
>>
>> funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf
>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH
>>
>> ...but for the latter, I get the following error:
>> PVF (null)
>> Thesholding hit volume.
>> done
>> mri_binarize --i
>> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/Cond7vFix/sig.nii
>> --frame 0 --mask
>> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii
>> --o
>> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii
>> --abs --min
>> ERROR: --min flag needs 1 argument
>>
>> I don't see the --min argument described for either funcroi-config or
>> funcroi-sess, so I was 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@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
>
>
>
Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
niten...@nmr.mgh.harvard.edu
Phone: 617-643-3215
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