Hi Dr. Greeve, Oh I see, thank you for the fix for V1. To probe further, I'm curious why the visual areas weren't implemented? Is there an additional step I could take to access other regions in the visual hierarchy such as V2, V3, and V5?
Thanks for your insight Dr. Greeve, Jess On Jul 26, 2017 5:37 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > 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/FsFastFunctionalConnectivityWa > lkthrough>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. >
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