Yes, selxavg3-sess runs fine.
Stefano ----Messaggio originale---- Da: gr...@nmr.mgh.harvard.edu Data: 22-set-2015 20.50 A: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity So it is working now? On 09/22/2015 02:49 PM, std...@virgilio.it wrote: > Thanks, > > the error occurred in the command line because I have used > > fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg > mean.MRS_MASK.config > fcseed-sess -sf sessid -cfg mean.MRS_MASK.config > > and the correct form is MRS_MASK without mean. > > fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg > MRS_MASK.config > fcseed-sess -sf sessid -cfg MRS_MASK.config > > > Stefano > > ----Messaggio originale---- > Da: gr...@nmr.mgh.harvard.edu > Data: 21-set-2015 23.44 > A: <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for > performing seed-based FS-FAST functional connectivity > > Is there a file in that folder named something like "MRS_MASK" > > On 09/19/2015 06:03 AM, std...@virgilio.it wrote: > > Hi listi, > > > > the following error now occur: > > > > ------- matlab output -------------------- > > > > > > < M A T L A B (R) > > > > > Copyright 1984-2014 The MathWorks, Inc. > > > > R2014a (8.3.0.532) 64-bit (maci64) > > > > February 11, 2014 > > > > > > To get started, type one of these: helpwin, helpdesk, or demo. > > > > For product information, visit www.mathworks.com. > > > > Warning: Control Character '\%' is not valid. See 'doc sprintf' for > > control > > > > characters valid in the format string. > > > > > In startup at 3 > > > > In matlabrc at 189 > > > > >> >> >> >> >> >> >> > > > > sxa3pwd = > > > > > > /Applications/freesurfer/subjects/fMRI > > > > > > >> > > > > sxa3cmd = > > > > > > /Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess130 -a > > fc.MRS_MASK.surf.lh > > > > > > >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m > > > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > > > > #@# Sess130 ############################### > > > > /Applications/freesurfer/subjects/fMRI/Sess130 > > > > ------------------------- > > > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > > > > /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m > > > > /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > > > /Applications/freesurfer/matlab/MRIread.m > > > > ------------------------- > > > > outtop = /Applications/freesurfer/subjects/fMRI > > > > Extension format = nii.gz > > > > ERROR: cannot find volume matching > > /Applications/freesurfer/subjects/fMRI/Sess130/rest/001/MRS_MASK > > > > ERROR: loading nonpar reg > > /Applications/freesurfer/subjectsfMRI/Sess130/rest/001/MRS_MASK > > > > ------------------------------------------ > > > > ERROR: fast_selxavg3() failed\n > > > > > > > > Thanks > > > > > > > > Stefano > > > > > > > > > > > > My concern is whether this command line is correctfcseed-config > -segid 1 -seg > > ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s > SessXXX -cfg > > mean.ROI_MASK.configThank youStefano > > ----Messaggio originale---- > > Da: gr...@nmr.mgh.harvard.edu > > Data: 20-lug-2015 19.17 > > A: <freesurfer@nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: R: Re: Import mask from FSL to FS for > performing > > seed-based FS-FAST functional connectivity > > > > > > > > On 07/20/2015 02:10 AM, std...@virgilio.it wrote: > > > Hi list, > > > > > > in the previous mail you have suggested to run fcseed-config and > > > specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in > > > $SUBJECTS_DIR/subject/mri). > > > I have two question please. > > > A- my mask is on vmPFC, thus it include the both hemispheres. Should I > > > divide it in right and left? If yes, how can I do? > > You do not need to, just specify the appropriate index value. If they > > were divided between lh and rh and you wanted to merge them, you would > > just list the lh and rh indices. > > > B- I have difficulties to run the fcseed-conf command: > > what do you mean by "difficulties"? > > > > > fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg > > > mean.ROI_MASK.config > > > fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config > > > Is these command lines corrected? > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > ----Messaggio originale---- > > > Da: std...@virgilio.it > > > Data: 13-lug-2015 10.16 > > > A: <freesurfer@nmr.mgh.harvard.edu> > > > Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing > > > seed-based FS-FAST functional connectivity > > > > > > Hi list, > > > > > > When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem > > > to correspond. However, when I added the ROI_MASK.nii.gz, the orig is > > > vanished, and is remained the ROI_MASK in correct position (and in > > > white) and around all black. My concern is the correct binarization of > > > ROI_MASK which it seem correct when I use fslview. > > > > > > fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs. > > > > > > > > > > > > After > > > mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg > > > $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp > > > $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o > > > func.vmPFC_MASK.nii > > > > > > The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with > > > tkmedit and too big (a red bar which cover the whole) when I use > fslview. > > > With MRIcron, is screen is irregularly divided in half in black > and white. > > > > > > Which should be the advised folder for func.vmPFC_MASK.nii? > > > > > > > > > Thank you very much > > > > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: gr...@nmr.mgh.harvard.edu > > > Data: 30-giu-2015 0.36 > > > A: <freesurfer@nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing > > > seed-based FS-FAST functional connectivity > > > > > > Hi Stefano, sorry for the delay, I was traveling. It sounds like you > > > just need to run fcseed-config and specify -seg ROI_MASK.mgz and > -segid > > > 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the > mask > > > is in the orig.mgz space, then everything should work ok, but you can > > > look at it with > > > > > > tkmedit -f orig.mgz -aux ROI_MASK.mgz > > > > > > You can also run > > > > > > mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg > > > register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o > > > func.ROI_MASK.nii > > > > > > where template.nii.gz and register.dof6.dat are in the functional run > > > folder > > > doug > > > > > > > > > On 06/12/2015 04:39 PM, std...@virgilio.it wrote: > > > > Hi list, > > > > I working on the combination of MRS and FS-FAST analysis. > > > > I have extracted the grey matter within voxel (I will call it > > > > "ROI_MASK") by using FSL tools and now it is in the same space of > > > > orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I > > > > use fslview). > > > > > > > > I'd like to import it to FS for performing seed-based FS-FAST > > > > functional connectivity. > > > > The seed should the ROI MASK (GM within voxel). > > > > > > > > I know that the FSL and FS operate in different space and > orientation. > > > > I think to have resolved the problem of different space by using > > > > orig.nii.gz to create ROI mask by FSL. > > > > However, I'm strongly worried for orientation issues. > > > > I have read the guidelines in FSL and FS sites, but I'm quite > confused. > > > > In detail, I'd like to ask whether I should use "mri_cor2label" to > > > > transform ROI mask created by FSL to label. > > > > > > > > Furthmore, I'd like to be sure of the position of the ROI. How can I > > > > visualize it to be sure that the seed of my FS-FAST analysis is > > > > effectively the my ROI_MASK? > > > > > > > > I hope in your help. > > > > > > > > Thanks in advanced. > > > > > > > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > _______________________________________________ > > 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. > > > > > > > > _______________________________________________ > > 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 > > > > > _______________________________________________ > 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
_______________________________________________ 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.
