Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

Thank you very much Michael. Now I'm running probtrackx, I will update you. Stefano ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 22.25 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>, "Harms, Michael"<mharms(a)wustl.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL Yes, the S/I/A/P labels are all correct. (Can never tell with R/L). So, FSLview is reading the orientation info correctly. Orientation, as coded in the NIFTI, is a completely separate issue from how a given viewing tool chooses to display the data. You may not like the manner in which FSLview displays the data, but it is respecting the orientation info. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Date: Tuesday, April 29, 2014 3:20 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>, "Harms, Michael" <mharms(a)wustl.edu> Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL Please, see the snapshot attached. A/P/S/I/L/R labels seem correct. What do you think about? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 21.13 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>, "Harms, Michael"<mharms(a)wustl.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL Yes, they need to be the same dimensions to overlay in FSLview. Run 'mri_convert' on orig.mgz, and you should be able to underlay the orig. -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Date: Tuesday, April 29, 2014 2:09 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>, "Harms, Michael" <mharms(a)wustl.edu> Subject: R: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no. fslinfo T1_STRUCT.nii.gz (T1 used for recon-all) data_type FLOAT32 dim1 212 dim2 320 dim3 320 dim4 1 datatype 16 pixdim1 0.800000 pixdim2 0.800000 pixdim3 0.800000 pixdim4 0.011000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ fslinfo Right_Thalamus.nii.gz data_type INT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 8 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.011000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ fslinfo dtifit_FA.nii.gz data_type FLOAT32 dim1 128 dim2 128 dim3 60 dim4 1 datatype 16 pixdim1 1.750000 pixdim2 1.750000 pixdim3 2.000001 pixdim4 1.000000 cal_max 1.0000 cal_min 0.0000 file_type NIFTI-1+ Specifically I have 1. Registered FreeSurfer conformed structural space to diffusion space net della T1 e rinominarla come struct_brain struct<->freesufer tkregister2 --mov $SUBJECTS_DIR/mri/orig.mgz --targ $SUBJECTS_DIR/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat fa<-->freesurfer flirt -in $SUBJECTS_DIR/dmri/dtifit_FA.nii.gz -ref struct_brain -omat fa2struct.mat convert_xfm -omat struct2fa.mat -inverse fa2struct.mat convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 2. Creating a label file from FreeSurfer mri_binarize --i aparc+aseg.mgz --match 49 --o Right_Thalamus.nii.gz mri_annotation2label --subject Control02 --hemi rh --outdir $SUBJECTS_DIR/label --lobesStrict --lobesStrict mri_annotation2label --subject Control02 --annotation lobesStrict --hemi rh --outdir $SUBJECTS_DIR/label produce rh.frontal.label rh.occipital.label rh.parietal.label rh.temporal.label cd $SUBJECTS_DIR/surf mris_convert rh.white rh.white.gii mris_convert lh.white lh.white.gii echo $SUBJECTS_DIR/label/rh.frontal.label $SUBJECTS_DIR/label/rh.occipital.label $SUBJECTS_DIR/label/rh.parietal.label $SUBJECTS_DIR/label/rh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt label2surf -s rh.white.gii -o rh.frontal.gii -l listOfAreas_right.txt label2surf -s rh.white.gii -o rh.occipital.gii -l listOfAreas_right.txt label2surf -s rh.white.gii -o rh.parietal.gii -l listOfAreas_right.txt label2surf -s rh.white.gii -o rh.temporal.gii -l listOfAreas_right.txt label2surf -s rh.white.gii -o rh.Right_Thalamus.gii -l listOfAreas_right.txt echo $SUBJECTS_DIR/label/lh.frontal.label $SUBJECTS_DIR/label/lh.occipital.label $SUBJECTS_DIR/label/lh.parietal.label $SUBJECTS_DIR/label/lh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txt label2surf -s lh.white.gii -o lh.frontal.gii -l listOfAreas_right.txt label2surf -s lh.white.gii -o lh.occipital.gii -l listOfAreas_right.txt label2surf -s lh.white.gii -o lh.parietal.gii -l listOfAreas_right.txt label2surf -s lh.white.gii -o lh.temporal.gii -l listOfAreas_right.txt label2surf -s lh.white.gii -o lh.Right_Thalamus.gii -l listOfAreas_right.txt ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 20.56 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Harms, Michael"<mharms(a)wustl.edu>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy. It is very unlikely that FSLview is ignoring the orientation information. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Date: Tuesday, April 29, 2014 1:52 PM To: "Harms, Michael" <mharms(a)wustl.edu>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: R: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Michael, please, see the file attached. They are reffered to FS and FSL visualization of the same file (R_thalamus overlapped on T1). Thanks, Stefano ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 20.32 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Is the brain merely shown "sideways" in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 29, 2014 1:19 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL How do you know the orientation is wrong? Is it right in tkmedit? On 04/29/2014 10:23 AM, stdp82(a)virgilio.it wrote: > My apologies, how can I visualize mri_binarize output? I tried in > fslview but orientation is wrong. Different orientation is a file's > feature or swapdim is request? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: fischl(a)nmr.mgh.harvard.edu > Data: 29-apr-2014 16.01 > A: <stdp82(a)virgilio.it>, "Freesurfer support > list"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL > > Hi Stefano > > you can use either mri_binarize --match or mri_extract_label with labels > 10 and 49 (which I got from FreeSurferColorLUT.txt) > > cheers > Bruce > On Tue, 29 Apr 2014, > stdp82(a)virgilio.it wrote: > > > Hi list, > > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it > as seed > > mask in probtrackx. > > > > Thanks, > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL
by Harms, Michael 29 Apr '14

29 Apr '14

1 0

R: Re: R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

I'm trying to do it. But I have an error. It shoud be due to difference in size? In freeviewer the files are shown in fslview no. fslinfo T1_STRUCT.nii.gz (T1 used for recon-all)data_type FLOAT32dim1 212dim2 320dim3 320dim4 1datatype 16pixdim1 0.800000pixdim2 0.800000pixdim3 0.800000pixdim4 0.011000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ fslinfo Right_Thalamus.nii.gz data_type INT32dim1 256dim2 256dim3 256dim4 1datatype 8pixdim1 1.000000pixdim2 1.000000pixdim3 1.000000pixdim4 0.011000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ fslinfo dtifit_FA.nii.gz data_type FLOAT32dim1 128dim2 128dim3 60dim4 1datatype 16pixdim1 1.750000pixdim2 1.750000pixdim3 2.000001pixdim4 1.000000cal_max 1.0000cal_min 0.0000file_type NIFTI-1+ Specifically I have 1. Registered FreeSurfer conformed structural space to diffusion spacenet della T1 e rinominarla come struct_brain struct<->freesufertkregister2 --mov $SUBJECTS_DIR/mri/orig.mgz --targ $SUBJECTS_DIR/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat fa<-->freesurferflirt -in $SUBJECTS_DIR/dmri/dtifit_FA.nii.gz -ref struct_brain -omat fa2struct.mat convert_xfm -omat struct2fa.mat -inverse fa2struct.mat convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat 2. Creating a label file from FreeSurfer mri_binarize --i aparc+aseg.mgz --match 49 --o Right_Thalamus.nii.gz mri_annotation2label --subject Control02 --hemi rh --outdir $SUBJECTS_DIR/label --lobesStrict --lobesStrictmri_annotation2label --subject Control02 --annotation lobesStrict --hemi rh --outdir $SUBJECTS_DIR/labelproducerh.frontal.labelrh.occipital.labelrh.parietal.labelrh.temporal.label cd $SUBJECTS_DIR/surfmris_convert rh.white rh.white.giimris_convert lh.white lh.white.giiecho $SUBJECTS_DIR/label/rh.frontal.label $SUBJECTS_DIR/label/rh.occipital.label $SUBJECTS_DIR/label/rh.parietal.label $SUBJECTS_DIR/label/rh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.frontal.gii -l listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.occipital.gii -l listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.parietal.gii -l listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.temporal.gii -l listOfAreas_right.txtlabel2surf -s rh.white.gii -o rh.Right_Thalamus.gii -l listOfAreas_right.txt echo $SUBJECTS_DIR/label/lh.frontal.label $SUBJECTS_DIR/label/lh.occipital.label $SUBJECTS_DIR/label/lh.parietal.label $SUBJECTS_DIR/label/lh.temporal.label $SUBJECTS_DIR/label/Right_Thalamus.label > listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.frontal.gii -l listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.occipital.gii -l listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.parietal.gii -l listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.temporal.gii -l listOfAreas_right.txtlabel2surf -s lh.white.gii -o lh.Right_Thalamus.gii -l listOfAreas_right.txt ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 20.56 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Harms, Michael"<mharms(a)wustl.edu>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL You need to overlay the thalamus ROI on the T1 from which it was derived, so that I have a reference for the anatomy. It is very unlikely that FSLview is ignoring the orientation information. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Date: Tuesday, April 29, 2014 1:52 PM To: "Harms, Michael" <mharms(a)wustl.edu>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: R: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Michael, please, see the file attached. They are reffered to FS and FSL visualization of the same file (R_thalamus overlapped on T1). Thanks, Stefano ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 20.32 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Is the brain merely shown "sideways" in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 29, 2014 1:19 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL How do you know the orientation is wrong? Is it right in tkmedit? On 04/29/2014 10:23 AM, stdp82(a)virgilio.it wrote: > My apologies, how can I visualize mri_binarize output? I tried in > fslview but orientation is wrong. Different orientation is a file's > feature or swapdim is request? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: fischl(a)nmr.mgh.harvard.edu > Data: 29-apr-2014 16.01 > A: <stdp82(a)virgilio.it>, "Freesurfer support > list"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL > > Hi Stefano > > you can use either mri_binarize --match or mri_extract_label with labels > 10 and 49 (which I got from FreeSurferColorLUT.txt) > > cheers > Bruce > On Tue, 29 Apr 2014, > stdp82(a)virgilio.it wrote: > > > Hi list, > > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it > as seed > > mask in probtrackx. > > > > Thanks, > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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R: Re: R: Re: R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

Hi Michael, please, see the file attached. They are reffered to FS and FSL visualization of the same file (R_thalamus overlapped on T1). Thanks, Stefano ----Messaggio originale---- Da: mharms(a)wustl.edu Data: 29-apr-2014 20.32 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Is the brain merely shown "sideways" in FSLview? What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it> Reply-To: "stdp82(a)virgilio.it" <stdp82(a)virgilio.it>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, April 29, 2014 1:19 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL How do you know the orientation is wrong? Is it right in tkmedit? On 04/29/2014 10:23 AM, stdp82(a)virgilio.it wrote: > My apologies, how can I visualize mri_binarize output? I tried in > fslview but orientation is wrong. Different orientation is a file's > feature or swapdim is request? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: fischl(a)nmr.mgh.harvard.edu > Data: 29-apr-2014 16.01 > A: <stdp82(a)virgilio.it>, "Freesurfer support > list"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL > > Hi Stefano > > you can use either mri_binarize --match or mri_extract_label with labels > 10 and 49 (which I got from FreeSurferColorLUT.txt) > > cheers > Bruce > On Tue, 29 Apr 2014, > stdp82(a)virgilio.it wrote: > > > Hi list, > > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it > as seed > > mask in probtrackx. > > > > Thanks, > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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R: Re: R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

Hi Bruce, in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results. Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 29-apr-2014 17.52 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: thalami mask (nii.gz) to import in FSL How do you know the orientation is wrong? Is it right in tkmedit? On 04/29/2014 10:23 AM, stdp82(a)virgilio.it wrote: > My apologies, how can I visualize mri_binarize output? I tried in > fslview but orientation is wrong. Different orientation is a file's > feature or swapdim is request? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: fischl(a)nmr.mgh.harvard.edu > Data: 29-apr-2014 16.01 > A: <stdp82(a)virgilio.it>, "Freesurfer support > list"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL > > Hi Stefano > > you can use either mri_binarize --match or mri_extract_label with labels > 10 and 49 (which I got from FreeSurferColorLUT.txt) > > cheers > Bruce > On Tue, 29 Apr 2014, > stdp82(a)virgilio.it wrote: > > > Hi list, > > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it > as seed > > mask in probtrackx. > > > > Thanks, > > > > > > Stefano > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Problem with Monte Carlo Simulation
by Jacqueline Elaine Fitzgerald 29 Apr '14

29 Apr '14

Hi, I am having problem when running the Monte Carlo script. The script seems to fail after only a few simulations but it does not give me any error message, it just says 'killed'. I am running it on 126 participants (2 groups of 63) and I have tried it on a number of different measures (sulc, area etc.). I thought it may be an space issue but I cleared all other files but that did not seem to make any difference. This is what is printed out on the terminal: [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwritecmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 --surf fsaverage rh --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat WARNING: unrecognized mri_glmfit cmd option dods SURFACE: fsaverage rh /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim--glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite$Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $Thu Apr 24 18:58:31 IST 2014Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linuxfitzgejesetenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0DoPoll = 0DoPBSubmit = 0DoBackground = 0DiagCluster = 0gd2mtx = dodsfwhm = 21.770250nSimPerJob = 100001/1 Thu Apr 24 18:58:31 IST 2014mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh whiteINFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed reading group avg surface area 822 cm^2 from fileReading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mghreading group avg surface area 822 cm^2 from fileReading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mghsimbase Rh_JacobianW_15/csd/mc-z.negative.j001gdfReadHeader: reading Rh_JacobianW_15/y.fsgdINFO: demeaning continous variablesContinuous Variable Means (all subjects)Class Means of each Continuous Variable1 groupASD2 groupCTRLINFO: gd2mtx_method is dodsReading source surface /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.whiteNumber of vertices 163842Number of faces 327680Total area 65020.765625AvgVtxArea 0.396850AvgVtxDist 0.717994StdVtxDist 0.193566INFO: fwhm2niters: NOT fixing group surface areaSurface smoothing by fwhm=21.770250, niters=441.000000 $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $cwd /projects/pi-lgallagh/HPC_12_00408/qdeccmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white sysname Linuxhostname lonsdale01.clustermachine x86_64user fitzgejeFixVertexAreaFlag = 1UseMaskWithSmoothing 1fwhm 21.770250niters 441.000000OneSampleGroupMean 0y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mghlogyflag 0usedti 0FSGD Rh_JacobianW_15/y.fsgdlabelmask /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.labelmask Rh_JacobianW_15/mask.mghmaskinv 0glmdir (null)IllCondOK 0DoFFx 0Loading y from /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mghINFO: gd2mtx_method is dodsMatrix condition is 1/projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.labelFound 149926 points in label.Found 149926 voxels in masksearch space = 75188.6DOF = 124thresh = 1.3, threshadj = 0.99897 Starting simulation sim over 10000 trialsSmoothing done, nsteps = 441, tsec = 69.733Smoothing done, nsteps = 441, tsec = 69.799Smoothing done, nsteps = 441, tsec = 69.754Smoothing done, nsteps = 441, tsec = 69.749Smoothing done, nsteps = 441, tsec = 69.743Smoothing done, nsteps = 441, tsec = 69.749Smoothing done, nsteps = 441, tsec = 69.737Smoothing done, nsteps = 441, tsec = 69.738Smoothing done, nsteps = 441, tsec = 69.734Smoothing done, nsteps = 441, tsec = 69.806Smoothing done, nsteps = 441, tsec = 70.012Smoothing done, nsteps = 441, tsec = 70.139 Killed Any suggestions that may help? Kind regards, Jackie

2 7

Xhemi: vertex-wise volume asymmetry analysis?
by Yizhou Ma 29 Apr '14

29 Apr '14

Dear freesurfer experts, I am working on a project on cortical asymmetry and I have analyzed vertex-wise cortical thickness/surface area asymmetry. However, I noticed that Freesurfer doesn't not seem to facilitate such analysis for gray matter volume, as after running surfreg -xhemi there is no ?h.volume file in subject/xhemi/surf. I searched the literature and found studies on gray matter density asymmetry with VBM and ROI-based volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise volume asymmetry analysis? And may I know the rationale? Thanks, Cherry

2 6

FSL registration
by Jones, Richard 29 Apr '14

29 Apr '14

I have T1 data that has been run through freesurfer and I want to apply the subcortical parcellations from that analysis to some QSM data. The mailing list and website refer to using reg-feat2anat but this require an existing feat directory. If I make a "pseudo" feat directory with my QSM data so that I can use reg-feat2anat does it just need to contain the subfolder reg containing the the QSM data as "example_func.nii" and the registration matrix from using FLIRT to register the QSM data to MNI space as "example_func2standard.mat", or is there something else that needs to be included? Thanks, Richard

2 1

incongruent coordinates in freeview and *sig.cluster.summary
by charujing123 29 Apr '14

29 Apr '14

Hi all, I have done group analysis and see it in freeview. Also I can see my sig.cluster.summary file to find clusters those survived. As I know, the MNIX MNIY MNIZ in the cluster summary file is coordinates for the maximum. The coordinate system is MNI305. Also I input the vertex number at the maximum in freeview, but it echo different coordinate for the vertex from that in cluster summary file. Why? Another question. There is "RAS" symbol at the bottom of freeview window. However I see the coordinates : inferior, posterior, left is negtive, superior, anterior,and right is positive. I suspect the coordinate system is LPI. Is that right? Thanks. All the best. Rujing Zha 2014-04-26 charujing123

3 3

R: Re: thalami mask (nii.gz) to import in FSL
by stdp82＠virgilio.it 29 Apr '14

29 Apr '14

My apologies, how can I visualize mri_binarize output? I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request? Thanks, Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 29-apr-2014 16.01 A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL Hi Stefano you can use either mri_binarize --match or mri_extract_label with labels 10 and 49 (which I got from FreeSurferColorLUT.txt) cheers Bruce On Tue, 29 Apr 2014, stdp82(a)virgilio.it wrote: > Hi list, > I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed > mask in probtrackx. > > Thanks, > > > Stefano > >_______________________________________________ Freesurfer mailing list Freesurfer(a)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.

2 1

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