Hi Doug,
Thank you very much for your support. It seems to me that the typos in the
command lines are related to the auto correction property in Outlook So I am
attaching a text file including all the command lines that I used in the
analysis:
I ran the analysis successfuly for the spaces lh and rh my problem is when I
started running the analysis for mni305:
Actually I don't know what I am doing wrong because I am thinking that the
difference in the pipeline for the spaces lh,rh and mni305 is in step 6 in the
attached file ( by replacing --surface lh or rh with the flag -mni305 1 in the
command mkanalysis-sess ). I did that and I continued the analysis tell step 9
in the attached file ( I tried to run mri_glmfit without the flag -surface lh )
but I got an error message that I need to use the flag -surface lh (It supposed
to be volume based analysis so why I need to enter the surface flag)
Any advises are highly appreciated
Mohamad
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, May 06, 2015 1:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FSFAST_Volume based analysis
wow, I don't know what is going on here. When I run
mkanalysis-sess -mni305 1
It responds as it should:
ERROR: must specify either -per-run or -per-session
you probably want to use -per-run unless you used
-per-session when you ran preproc-sess
However, when I cut and paste the "-mni305" part from your command line
below, I get
ERROR: Flag –mni305 unrecognized.
But if I go onto the command line and delete the dash ("-") and retype
it, it runs properly. It is pretty bizarre but that seems to do the
trick. Did you cut and paste that command from a document? Maybe the web
page?
doug
On 05/05/2015 07:58 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
>
> I want to do volume based analysis using FSFAST using the FC seed as a task
> regressor. I ran the following command lines:
>
> 1. preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd
> bold -per-run
>
> 2. fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd bold
> -mean -cfg mean.L_Precentralgyrus.config
> fcseed-config -segid 2024 -fcname R_Precentralgyrus.dat -fsd bold
> -mean -cfg mean.R_Precentralgyrus.config
>
>
> 3. fcseed-sess -s ${i} -cfg mean.L_Precentralgyrus.config
> 4. fcseed-sess -s ${i} -cfg mean.R_Precentralgyrus.config
>
>
> 5. fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config
> fcseed-sess -s ${i} -cfg wm.config
>
> fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config
> fcseed-sess -s ${i} -cfg vcsf.config
>
>
>
> I configured analysis for lh , rh , and mni305 using the following command
> lines:
>
> For lh I used the command:
>
> mkanalysis-sess -analysis precentralgyrus.lh -surface fsaverage lh -fwhm 5
> -notask -taskreg L_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg wm.dat
> 13 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run -force
>
> For rh I used the command:
>
> mkanalysis-sess -analysis precentralgyrus.rh -surface fsaverage rh -fwhm 5
> -notask -taskreg R_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg wm.dat
> 13 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run –force
>
>
>
> My Question is :
>
> how can I configure an analysis for mni305 without the paradigm file, just by
> using the FC seed as a task regressor:
>
> I tried to configure the analysis twice for the right and left hemispheres?
>
> mkanalysis-sess -analysis precentralgyrus.305.lh –mni305 1 -fwhm 5 -notask
> -taskreg L_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg wm.dat 13
> -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run -force
> mkanalysis-sess -analysis precentralgyrus.305.rh –mni305 1 -fwhm 5 -notask
> -taskreg R_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg wm.dat 13
> -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run -force
>
>
> But when I ran the command mri_glmfit. It called me that the flag --surface
> hemi is missing
>
>
> I highly appreciate any advice
> Thank you
>
> Mohamad
>
> _______________________________________________
> 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
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferIn order to do Volume based analysis (task regressor is the seed L precentral
gyrus)I did the following
1.Pre-process your bold data using preproc-sess:
preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd bold
-per-run &
register-sess -s ${i} -fsd bold -per-run &
2.Use fcseed-config to configure the parameters you wish to pass to your
connectivity analysis.
fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd bold -mean -cfg
mean.L_Precentralgyrus.config &
3.Create the FC seed for an individual:
fcseed-sess -s ${i} -cfg mean.L_Precentralgyrus.config &
4.Create nuisance variables for white matter:
fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config &
fcseed-sess -s ${i} -cfg wm.config &
5.Create nuisance variables for ventricles and csf:
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config &
fcseed-sess -s ${i} -cfg vcsf.config &
6.Use mkanalysis-sess to configure an analysis for your FC data. Like the
fcseed-config above, this is done once regardless of how many sessionds you
have:
mkanalysis-sess -analysis precentralgyrus.rh -mni305 1 -fwhm 5 -notask -taskreg
L_Precentralgyrus.dat 1 -nuisreg vcsf.dat 13 -nuisreg wm.dat 13 -mcextreg
-polyfit 5 -nskip 4 -fsd bold -TR 2.01 -per-run -force &
7.Use selxavg3-sess to run the subject-level analysis outlined by the above
mkanalysis-sess cmd just as you would with a task-based analysis
selxavg3-sess -s ${i} -a 305.lh &
#===============================================
8. Concatenating the Data
isxconcat-sess -sf sessid.txt -analysis 305.lh -contrast L_Precentralgyrus -o
Group_lh &
9.Run the Group GLM for the Left Hemisphere
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir my-glm.wls
--nii.gz
Here I got an error message that I need to use the flag--surface hemi!?
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