There should be a .log file created by mris_preproc. Is that good enough? Also, when you run mri_sestats you can add "--id 1" and it will only report the results for things inside your mask.
doug

Marco Loggia, PhD wrote:

Thank you so much Michael for clarifying this.

Final, related question: is there a way to retrieve the name/paths of the files concatenated with mris_preproc to create the .mgh file mentioned below? I usually have everything logged, but was wondering if there was something like a flag for mri_info to directly find this information.

Marco

On Mar 1, 2012, at 1:18 AM, Michael Waskom wrote:

Hi Marco,

The columns correspond to the integer IDs in the --seg image, so assuming you passed in a binary mask the first column is mean over everything that isn't your ROI and the second column is the mean in your ROI.

Cheers,

Michael

On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia <marco@nmr.mgh.harvard.edu <mailto:marco@nmr.mgh.harvard.edu>> wrote:

   Dear all,

   Given a series of fsaverage-registered rCBF maps, I am trying to

   extract

   the average rCBF value from one specific region. This region,

   which was a

   significant cluster from a volumetric (fsl) analysis, was

   binarized and

   then converted to surface.

   When I run mri_segstats with the --avgwf I obtain two columns.

   Can you

   please remind me which one is the average extracted from that

   ROI, and

   what is the other column?

   Thanks!

   Marco

   mri_vol2surf --mov

   DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz

   --mni152reg --hemi rh --o

   /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz

   cd

   /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF

   for f in `ls *.mgz` ; do

   mri_segstats --seg $f --in

   /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh

   --avgwf "$f"_RH_nopaired_diff.txt

   done

   nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt &

   38.2811 47.6476

   40.3997 36.0856

   42.6304 46.2465

   44.4789 36.7066

   69.2376 51.4098

   66.0043 47.2098

   34.5957 40.3854

   36.8976 42.2028

   38.2475 35.875

   39.9503 37.0186

   35.1582 36.6949

   35.1924 38.874

   43.4415 36.2505

   43.3516 34.5041

   58.3073 50.3295

   61.8703 60.8415

   61.1754 51.3476

   47.9508 51.594

   51.5809 48.2985

   49.6545 50.974

   62.9431 72.1211

   54.0272 55.7234

   35.0701 34.5995

   37.9241 35.3844

   37.2277 42.3105

   38.2136 46.7896

   45.0951 51.9831

   45.4391 51.6242

   46.2971 47.5424

   44.3713 41.1725

   37.4132 36.1166

   36.7285 39.2947

   44.0285 46.501

   45.4698 50.5906

   51.0392 48.2324

   55.0885 50.9392

   66.7224 67.7807

   64.8932 68.5847

   45.5101 45.6065

   46.7002 45.232

   40.6324 48.9768

   44.3654 45.9017

   39.4908 32.8936

   39.5983 36.4909

   55.9295 59.1527

   55.6738 55.7016

   44.7433 50.9412

   42.6953 50.0857

   42.4522 48.7366

   43.5595 42.3424

   43.9283 36.5026

   41.9838 36.8662

   39.9873 44.505

   43.442 49.2243

   57.6304 55.5628

   53.3496 49.4215

   43.2505 42.5797

   43.5452 42.0694

   50.4555 47.993

   49.8977 49.6568

   41.5077 42.8473

   40.2357 42.3246

   40.3846 39.1473

   38.7073 41.502

   ______________________

   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 <mailto:marco@nmr.mgh.harvard.edu>

   _______________________________________________

   Freesurfer mailing list

   Freesurfer@nmr.mgh.harvard.edu

   <mailto:Freesurfer@nmr.mgh.harvard.edu>

   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

   The information in this e-mail is intended only for the person to

   whom it is

   addressed. If you believe this e-mail was sent to you in error

   and the e-mail

   contains patient information, please contact the Partners

   Compliance HelpLine at

   http://www.partners.org/complianceline . If the e-mail was sent

   to you in error

   but does not contain patient information, please contact the

   sender and properly

   dispose of the e-mail.

______________________________

Marco L. Loggia, PhD

Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital

Harvard Medical School

Massachusetts General Hospital

120 Second Avenue, Charlestown, MA 02129

Phone: (617) 643-7267

Fax: (617) 643-7340

marco@nmr.mgh.harvard.edu <mailto:marco@nmr.mgh.harvard.edu>

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