Please see the file attached.Thanks Stefanofile
----Messaggio originale----
Da: greve@nmr.mgh.harvard.edu
Data: 5-nov-2015 15.43
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST
sorry, should have been
fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log
On 11/4/15 6:05 PM, stdp82@virgilio.it wrote:
Hi Dough, in summary: I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the MRS_MASK.mgz and run: fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean - cfg MRS_MASK.config fcseed-sess -s Control22_FS -cfg MRS_MASK.config
...Writing to /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.fcseed- sess.12305/avgwf.mgh Segmentation fault
Therefore, according with your suggestion, I have now run: fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log ERROR: cound not find session -cfg
The doug.log is attached.
Thanks,
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 4-nov-2015 16.58 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST
First, when running fcseed-config, don't give it the full path, just
the
path relative to subject/mri (in this case only MRS_MASK.mgz)
However, I don't think that is the problem. Please run
fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log
and send me doug.log
On 11/04/2015 04:14 AM, stdp82@virgilio.it wrote:
Hi list, this error is still occurring:
mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -
fsd
rest -mean -cfg MRS_MASK.config fcseed-sess -s -cfg MRS_MASK.config
During
fcseed-sess -s subj -cfg MRS_MASK.config
Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame
Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. fcseed-sess.97908/avgwf.mgh Segmentation fault
I have read your previous message and you can check the MRS voxel features. MRS voxel mask is in subj directory where I have run recon all -
all.
data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
The features are same of other subject that runs fine. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
Thank you very much.
Stefano
----Messaggio originale---- Da: stdp82@virgilio.it Data: 16-ott-2015 23.15 A: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL
I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in --
template?
It should be in Tailairach space? Where can I find the template
that
I
should added? Thanks,
Stefano
subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz data_type FLOAT32 dim1 27307 dim2 1 dim3 6 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1100.000000 cal_max 49.1815 cal_min -12.3855 file_type NIFTI-1+
Thanks,
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 29-set-2015 22.09 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL
Do you mean surface-based analysis? You'd have to put them back
into
the
volume using mri_surf2vol, write them out as nifti and then run
fslview
on them
On 09/29/2015 11:17 AM, stdp82@virgilio.it wrote:
Hi list,
I would like to import FS-FAST results (conjunction maps)
in
FSL,
opening them by fslview. Could you provide me any suggestion?
Thank you very much Best regards,
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 greve@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
_______________________________________________ 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 greve@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
How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, 1mm3 ?
On 11/05/2015 04:47 PM, stdp82@virgilio.it wrote:
Please see the file attached. Thanks
Stefanofile
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 5-nov-2015 15.43 A: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST sorry, should have been fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log On 11/4/15 6:05 PM, stdp82@virgilio.it wrote:Hi Dough, in summary: I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the MRS_MASK.mgz and run: fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean - cfg MRS_MASK.config fcseed-sess -s Control22_FS -cfg MRS_MASK.config ...Writing to /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.fcseed- sess.12305/avgwf.mgh Segmentation fault Therefore, according with your suggestion, I have now run: fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log ERROR: cound not find session -cfg The doug.log is attached. Thanks, Stefano----Messaggio originale---- Da:greve@nmr.mgh.harvard.edu Data: 4-nov-2015 16.58 A:<freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST First, when running fcseed-config, don't give it the full path, justthepath relative to subject/mri (in this case only MRS_MASK.mgz) However, I don't think that is the problem. Please run fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log and send me doug.log On 11/04/2015 04:14 AM,stdp82@virgilio.it wrote:Hi list, this error is still occurring: mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -fsdrest -mean -cfg MRS_MASK.config fcseed-sess -s -cfg MRS_MASK.config During fcseed-sess -s subj -cfg MRS_MASK.config Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. fcseed-sess.97908/avgwf.mgh Segmentation fault I have read your previous message and you can check the MRS voxel features. MRS voxel mask is in subj directory where I have run recon all -all.data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ The features are same of other subject that runs fine. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ Thank you very much. Stefano----Messaggio originale---- Da:stdp82@virgilio.it Data: 16-ott-2015 23.15 A:<freesurfer@nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in --template?It should be in Tailairach space? Where can I find the templatethatIshould added? Thanks, Stefano subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz data_type FLOAT32 dim1 27307 dim2 1 dim3 6 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1100.000000 cal_max 49.1815 cal_min -12.3855 file_type NIFTI-1+ Thanks, Stefano----Messaggio originale---- Da:greve@nmr.mgh.harvard.edu Data: 29-set-2015 22.09 A:<freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL Do you mean surface-based analysis? You'd have to put them backintothevolume using mri_surf2vol, write them out as nifti and then runfslviewon them On 09/29/2015 11:17 AM,stdp82@virgilio.it wrote:> Hi list, > > I would like to import FS-FAST results (conjunction maps)
inFSL,> opening them by fslview. > Could you provide me any suggestion? > > Thank you very much > Best regards, > > > 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 greve@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 towhom it isaddressed. If you believe this e-mail was sent to you in errorandthe e-mailcontains patient information, please contact the PartnersComplianceHelpLine athttp://www.partners.org/complianceline . If the e-mail was senttoyou in errorbut does not contain patient information, please contact thesenderand properlydispose of the e-mail._______________________________________________ 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 greve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
stdp82＠virgilio.it