For some subject, analysis run fine.For others subjects (processes are the same
for all) I have this error
fcseed-sess -s Sess001 -cfg MRS_MASK.configmri_label2vol --seg
/Applications/freesurfer/subjects/subject_prova/Control01/mri/MRS_MASK.mgz
--reg /Applications/freesurfer/subjects/subj/Sess001/rest/001/register.dof6.dat
--temp /Applications/freesurfer/subjects/subj/Sess001/rest/001/template.nii.gz
--fillthresh .5 --o
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/seg.nii.gz
--pvf
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/pvf.nii.gzPVF
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/pvf.nii.gzNumber
of labels: 0Annot File: (null)Template Volume:
/Applications/freesurfer/subjects/subj/Sess001/rest/001/template.nii.gzOutut
Volume:
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/seg.nii.gzRegistration
File:
/Applications/freesurfer/subjects/subj/Sess001/rest/001/register.dof6.datFill
Threshold: 0.5Label Vox Vol: 1ProjType: (null)ProjTypeId:
0ProjStart: 0ProjStop: 0ProjDelta: 0.1Subject: (null)Hemi:
(null)UseNewASeg2Vol: 1DoLabelStatVol 0LabelCodeOffset 0setenv SUBJECTS_DIR
/Applications/freesurfer/subjects/subj$Id: mri_label2vol.c,v 1.34.2.5
2012/06/08 17:31:03 greve Exp $Template RAS-to-Vox: ---------0.278 0.000
0.000 32.000;-0.000 -0.000 -0.278 32.000;-0.000 0.200 0.000 10.500;
0.000 0.000 0.000 1.000;Template Voxel Volume: 64.5752nHits Thresh:
32.2876Loading registration from
/Applications/freesurfer/subjects/subj/Sess001/rest/001/register.dof6.datRegMat:
---------0.992 0.119 0.048 -0.573;-0.002 -0.387 0.922 -31.108;-0.128
-0.914 -0.384 -21.190; 0.000 0.000 0.000 1.000;Label RAS-to-Vox:
-------- 0.276 -0.033 -0.013 32.159; 0.036 0.254 0.107 37.896;-0.000
-0.077 0.184 4.278; 0.000 0.000 0.000 1.000;ASeg2Vol: Building
LUTASeg2Vol: Sorting ASeg2Vol: MappingASeg2Vol: Reverse Mapnmisses = 4031 (0
filled)ASeg2Vol: donePVF
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/pvf.nii.gzComputing
PVF 64.5752mri_binarize --i
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/seg.nii.gz
--o
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/mask.nii.gz
--match 1
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $cwd
/Applications/freesurfer/subjects/PDEcmdline mri_binarize --i
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/seg.nii.gz
--o
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/mask.nii.gz
--match 1 sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user
Stefano
input
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/seg.nii.gzframe
0nErode3d 0nErode2d 0output
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/mask.nii.gzBinarizing
based on matching valuesnMatch 1 0 1binval 1binvalnot 0Found 0
values in rangeCounting number of voxelsFound 0 voxels in final
maskmri_binarize donemri_segstats --i
/Applications/freesurfer/subjects/subj/Sess001/rest/001/fmcpr.nii.gz --seg
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/mask.nii.gz
--id 1 --sum
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/junk.sum
--avgwfvol
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/avgwf.mgh
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $cwd cmdline
mri_segstats --i
/Applications/freesurfer/subjects/subj/Sess001/rest/001/fmcpr.nii.gz --seg
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/mask.nii.gz
--id 1 --sum
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/junk.sum
--avgwfvol
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/avgwf.mgh
sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user
StefanoUseRobust 0Loading
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/mask.nii.gzLoading
/Applications/freesurfer/subjects/subj/Sess001/rest/001/fmcpr.nii.gzVoxel
Volume is 64.5752 mm^3Generating list of segmentation idsFound 1
segmentationsComputing statistics for each segmentation 0 1
0 0.000MRIalloc(0, 1, 1): bad parm
Reporting on 0 segmentationsComputing spatial average of each frame
Writing to
/Applications/freesurfer/subjects/subj/Sess001/rest/001/tmp.fcseed-sess.78940/avgwf.mghSegmentation
fault
I have checked the MRS mask and the FS-FAST on subcortical structures as target
(e.i. amygdala) run fine.
Thanks,
Stefano
----Messaggio originale----
Da: std...@virgilio.it
Data: 22-set-2015 21.02
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Import mask from FSL to FS for
performing seed-based FS-FAST functional connectivity
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/
_______________________________________________
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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
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