sorry, should have been
fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log
On 11/4/15 6:05 PM, std...@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: gr...@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, std...@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: std...@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: gr...@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, std...@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to
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_______________________________________________
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
_______________________________________________
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
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