Hi Doug, many thanks for your help!
This is the command i used:
mri_label2vol --label lh.parstriangularis.label --temp $DIR/mri/orig.mgz
--subject sub${isub} --hemi lh --o
$OUTDIR/labels/sub${isub}_parstriangularis.nii.gz --proj frac 0 1 .1
--fillthresh .3 --reg $OUTDIR/labels/sub${isub}_register.dat
Here are the terminal outputs:
******************************************************************************************************************
PVF (null)
Thesholding hit volume.
mri_label2vol done
Number of labels: 1
/Users/EXPTS/sub01/labels/rh.rostralmiddlefrontal.label
Annot File: (null)
Template Volume: /Applications/freesurfer/subjects/sub01/mri/orig.mgz
Outut Volume: /Users/EXPTS/sub01/labels/sub01_rh_DLPFC.nii.gz
Registration File: /Users/EXPTS/sub01/labels/sub01_register.dat
Fill Threshold: 0.3
Label Vox Vol: 1
ProjType: frac
ProjTypeId: 2
ProjStart: 0
ProjStop: 1
ProjDelta: 0.1
Subject: sub01
Hemi: lh
UseNewASeg2Vol: 1
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: --------
-1.000 0.000 0.000 128.000;
-0.000 -0.000 -1.000 128.000;
-0.000 1.000 -0.000 128.000;
0.000 0.000 0.000 1.000;
Template Voxel Volume: 1
nHits Thresh: 0.3
Loading registration from /Users/EXPTSsub01/labels/sub01_register.dat
RegMat: --------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Label RAS-to-Vox: --------
-1.000 0.000 0.000 128.000;
0.000 0.000 -1.000 128.000;
0.000 1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading surface /Applications/freesurfer/subjects/sub01/surf/lh.white
nvertices = 145372
Reading thickness /Applications/freesurfer/subjects/sub01/surf/lh.thickness
nlabels = 1
Allocating Hit Volume (16777216) voxels
Loading /Users/EXPTS/sub01/labels/rh.rostralmiddlefrontal.label
************************************************************************************************************************
On Jan 9, 2014, at 9:24 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Frank, can you send the commands you used and the terminal output?
> doug
>
> On 01/09/2014 04:35 AM, Frank Hsieh wrote:
>> Hi Gari, Thanks so much for the tips!
>> @ Doug: I basically followed the instructions on this site
>> <http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/>
>> to obtain my ROIs. Any thoughts?
>>
>> Many thanks!
>> Frank
>>
>>
>> On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga
>> <gariko...@gmail.com <mailto:gariko...@gmail.com>> wrote:
>>
>> Hi,
>> sorry to jump in, but maybe this solves your problem. What I've
>> been doing is:
>>
>> 1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL:
>> mri_convert --in_type mgz --out_type nii --out_orientation RAS
>> roi.mgz roi.nii
>>
>> 2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii.
>> Select it in the menu and just save it as *_mricron.nii again. (I
>> converted nu.mgz with the same procedure as above to check that
>> the roi was in place). This was the only way to make it visible in
>> fslview and work with the roi in fsl afterwards.
>>
>>
>> Hope this workaround works for you!
>> Gari
>>
>>
>> On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> what was your mri_label2vol command and terminal output?
>> doug
>>
>> On 01/06/2014 02:35 AM, Frank Hsieh wrote:
>> > Dear FreeSurfer Users,
>> >
>> > I ran recon -all on my structural image and created ROI
>> masks (using
>> > mri_label2vol) based on FreeSurfer's cortical parcellation.
>> I'd like
>> > to use these masks for further analysis with FSL. However,
>> it seems
>> > that the ROI masks generated with mri_label2vol have
>> different header
>> > information than that of the original structural image. As a
>> result, I
>> > was unable to carry out further analysis with FSL (e.g.,
>> converting
>> > these ROI masks into functional space with
>> hires2example_func.mat). I
>> > was wondering if there is a way to solve this issue.
>> >
>> > Many thanks in advance.
>> > Frank
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
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>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> Phone Number: 617-724-2358 <tel:617-724-2358>
>> Fax: 617-726-7422 <tel:617-726-7422>
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://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
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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
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>> dispose of the e-mail.
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>>
>>
>>
>> --
>> Frank
>
> --
> 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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