The problem was in the way I documented the flag for mris_preproc. It should be mris_preproc "--projfrac-max Min Max Delta" instead of "Min Delta Max". I've updated the documentation, and that will be live on the next stable and/or dev update. But you can use the version that is there, just change the order of the Min, Max, and Delta.
doug
Marco Loggia, PhD wrote:
Sorry again, even in that email I hadn't mentioned the where the surfaces are:
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 18, 2010 11:06 AM To: marco@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bug in --projfrac-max?
0.5.mgh and max.mgh do not exist in that directory.
doug
Marco Loggia wrote:
Dear all,
Is it possible that the --projfrac-max has a bug (at least when used with mris_preproc)?
I sampled the same volume using --projfrac 0.5 and --projfrac-max (see below) and, when I overimposed the two surfaces, I noticed that in some vertices the first surface (i.e., 0.5) appear to have a higher value than the second (i.e., max).
Thanks! Marco
dir_lbp=/autofs/cluster/randy/2/lbp/patients
mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac 0.5 --out 0.5.mgh
mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac-max 0 .1 1 --out max.mgh
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the correction, Doug.
So, if I understand correctly, with the current settings I should be sampling very close to the white surface (i.e., between the white and 10% along the normal between white and pial). But how would a delta of '1' be interpreted in this case, as it is larger than the 'max'?
Marco
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 18, 2010 11:30 AM To: Marco Loggia, PhD; freesurfer Subject: Re: [Freesurfer] bug in --projfrac-max?
The problem was in the way I documented the flag for mris_preproc. It should be mris_preproc "--projfrac-max Min Max Delta" instead of "Min Delta Max". I've updated the documentation, and that will be live on the next stable and/or dev update. But you can use the version that is there, just change the order of the Min, Max, and Delta.
doug
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 18, 2010 11:06 AM To: marco@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bug in --projfrac-max?
0.5.mgh and max.mgh do not exist in that directory.
doug
Marco Loggia wrote:
Dear all,
Is it possible that the --projfrac-max has a bug (at least when used with mris_preproc)?
I sampled the same volume using --projfrac 0.5 and --projfrac-max (see below) and, when I overimposed the two surfaces, I noticed that in some vertices the first surface (i.e., 0.5) appear to have a higher value than the second (i.e., max).
Thanks! Marco
dir_lbp=/autofs/cluster/randy/2/lbp/patients
mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac 0.5 --out 0.5.mgh
mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac-max 0 .1 1
--out
max.mgh
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is only going to sample it at the gray/white
Marco Loggia, PhD wrote:
Thanks for the correction, Doug.
So, if I understand correctly, with the current settings I should be sampling very close to the white surface (i.e., between the white and 10% along the normal between white and pial). But how would a delta of '1' be interpreted in this case, as it is larger than the 'max'?
Marco
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 18, 2010 11:30 AM To: Marco Loggia, PhD; freesurfer Subject: Re: [Freesurfer] bug in --projfrac-max?
The problem was in the way I documented the flag for mris_preproc. It should be mris_preproc "--projfrac-max Min Max Delta" instead of "Min Delta Max". I've updated the documentation, and that will be live on the next stable and/or dev update. But you can use the version that is there, just change the order of the Min, Max, and Delta.
doug
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 18, 2010 11:06 AM To: marco@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bug in --projfrac-max?
0.5.mgh and max.mgh do not exist in that directory.
doug
Marco Loggia wrote:
Dear all,
Is it possible that the --projfrac-max has a bug (at least when used with mris_preproc)?
I sampled the same volume using --projfrac 0.5 and --projfrac-max (see below) and, when I overimposed the two surfaces, I noticed that in some vertices the first surface (i.e., 0.5) appear to have a higher value than the second (i.e., max).
Thanks! Marco
dir_lbp=/autofs/cluster/randy/2/lbp/patients
mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac 0.5 --out 0.5.mgh
mris_preproc --target fsaverage --hemi lh --iv $dir_lbp/PH5/session1/data/pasl_RS2/cbf_24sept10.nii.gz $dir_lbp/PH5/session1/data/pasl_RS2/aslcal.reg --projfrac-max 0 .1 1
--out
max.mgh
Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School
Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Marco Loggia, PhD