By default, you are using aparc+aseg.mgz as the ROI atlas, so use 1021 or 2021 for V1.
1021 ctx-lh-pericalcarine 120 100 60 0 On 07/26/2017 12:37 PM, Jessica Huang wrote: > > Hi freesurfer experts, > > > I’m using the fcseed-config and fcseed-sess commands to create a seed > at V1 in accordance with the FsFastFunctionalConnectivity Walkthrough > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough>Steps: > > > *STEP 4: Use fcseed-config to configure the parameters you wish to > pass to your connectivity analysis.Sample command: fcseed-config > -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg > mean.L_Posteriorcingulate.config*STEP 5: Create the FC seed for an > individualfcseed-sess -s sessionid -cfg L_Posteriorcingulate.config > > V1 corresponds to the number 400 in > $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m > running is B101. The data is rest data but I named the file bold. > Overall, with this information specific to my data, I ran the > following commands: > > > INPUT > > $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg > mean.V1.config > > OUTPUT > > fcname is V1.dat > > fcseed-config done > > > INPUT > > $ fcseed-sess -s B101 -cfg mean.V1.config > > OUTPUT > > Logfile is > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/log/fcseed-sess.V1.dat.log.B101 > > Wed Jul 26 12:27:17 EDT 2017 > > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version > 16.6.0: Fri Apr 14 16:21:16 PDT 2017; > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 > > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects > > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir > > /Applications/freesurfer/fsfast/bin/fcseed-sess > > -s B101 -cfg mean.V1.config > > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > Wed Jul 26 12:27:17 EDT 2017 > > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version > 16.6.0: Fri Apr 14 16:21:16 PDT 2017; > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 > > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects > > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir > > /Applications/freesurfer/fsfast/bin/fcseed-sess > > -s B101 -cfg mean.V1.config > > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > > mri_label2vol --seg > /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/aparc+aseg.mgz > --reg > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta > > --temp > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz > > --fillthresh .5 --o > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz > > --pvf > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz > > PVF > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz > > Number of labels: 0 > > Annot File: (null) > > Template Volume: > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz > > Outut Volume: > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz > > Registration File: > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta > > Fill Threshold: 0.5 > > Label Vox Vol: 1 > > ProjType: (null) > > ProjTypeId: 0 > > ProjStart: 0 > > ProjStop: 0 > > ProjDelta: 0.1 > > Subject: (null) > > Hemi: (null) > > UseNewASeg2Vol: 0 > > DoLabelStatVol 0 > > LabelCodeOffset 0 > > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects > > $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ > > Template RAS-to-Vox: -------- > > -0.50000 -0.00000 -0.00000 56.00000; > > -0.00000 -0.00000 -0.50000 56.00000; > > -0.00000 0.45455 -0.00000 32.00000; > > -0.00000 -0.00000 -0.00000 1.00000; > > Template Voxel Volume: 8.8 > > nHits Thresh: 4.4 > > Loading registration from > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta > > regio_read_register: loading lta > > RegMat: -------- > > 0.99785 0.02664 0.05987 0.19449; > > -0.06077 0.03415 0.99757 -39.76084; > > -0.02453 0.99906 -0.03570 2.27075; > > 0.00000 0.00000 0.00000 1.00000; > > Label RAS-to-Vox: -------- > > -0.49893 -0.01332 -0.02994 55.90276; > > 0.01227 -0.49953 0.01785 54.86462; > > -0.02762 0.01552 0.45344 13.92689; > > 0.00000 0.00000 0.00000 1.00000; > > PVF > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz > > Computing PVF 8.8 > > mri_label2vol done > > mri_binarize --i > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz > > --o > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz > > --match 400 > > > $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ > > cwd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir > > cmdline mri_binarize.bin --i > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz > > --o > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz > > --match 400 > > sysname Darwin > > hostname Caramazza-Labs-Mac-Pro.local > > machine x86_64 > > user caramazzalab > > > input > > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz > > frame 0 > > nErode3d 0 > > nErode2d 0 > > output > > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz > > Binarizing based on matching values > > nMatch 1 > > 0 400 > > binval 1 > > binvalnot 0 > > fstart = 0, fend = 0, nframes = 1 > > Found 0 values in range > > Counting number of voxels in first frame > > Found 0 voxels in final mask > > Count: 0 0.000000 802816 0.000000 > > mri_binarize done > > mri_segstats --i > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz > > --seg > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz > > --id 1 --sum > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum > > --avgwfvol > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh > > > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ > > cwd > > cmdline mri_segstats --i > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz > > --seg > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz > > --id 1 --sum > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum > > --avgwfvol > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh > > > > sysname Darwin > > hostname Caramazza-Labs-Mac-Pro.local > > machine x86_64 > > user caramazzalab > > UseRobust 0 > > Loading > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz > > Loading > /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz > > Voxel Volume is 8.8 mm^3 > > Generating list of segmentation ids > > Found 1 segmentations > > Computing statistics for each segmentation > > > Reporting on 0 segmentations > > Using PrintSegStat > > Computing spatial average of each frame > > > ERROR: no voxels found in segmentation > > > > > I attached the error log below - any idea what happened? Is there > something I can change in these commands to yield the timecourse of > V1? These are all subjects 18+ years of age. > > > What do you think? > > > Thank you in advance, any and all feedback would be greatly appreciated. > > > Thanks, > > Jess > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list 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.
