I am having the same problem with a newer version of tcshell and reg-feat2anat as discussed in threads below. Has this been resolved? If not, could a working link to the updated version mentioned previously be reposted.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-June/030473.html
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-September/033521....
Thanks, Greg
use this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat
On 11/15/2013 02:04 PM, Greg Reckless wrote:
I am having the same problem with a newer version of tcshell and reg-feat2anat as discussed in threads below. Has this been resolved? If not, could a working link to the updated version mentioned previously be reposted.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-June/030473.html
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-September/033521....
Thanks, Greg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug, that did the trick.
On 13-11-15 20:13 , Douglas N Greve wrote:
use this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat
On 11/15/2013 02:04 PM, Greg Reckless wrote:
I am having the same problem with a newer version of tcshell and reg-feat2anat as discussed in threads below. Has this been resolved? If not, could a working link to the updated version mentioned previously be reposted.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-June/030473.html
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-September/033521....
Thanks, Greg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble.
The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1).
How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks?
Thanks so much!
Emily
Do you mean the aseg.mgz for an individual? If so, you can run mni152reg to register that subject to mni152space. Next you can run mri_label2vol to map the aseg to the 152 space. doug
On 11/17/2013 07:26 PM, ebelleau@uwm.edu wrote:
Hello,
I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble.
The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1).
How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks?
Thanks so much!
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas,
Thanks for the reply. I am very new to Freesurfer and am more used to scripting with AFNI.
Would you mind giving me a bit of sample code to get used to what this may look like? Can I script this in a .tcsh file?
Also, once I convert the aseg to MNI space, can I simply average or add the individual masks (which could be done in afni) or is there a better way to do this in Freesurfer?
Also, is this a linear or non-linear warp?
Thanks,
Emily
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 21, 2013 12:57:07 PM Subject: Re: [Freesurfer] Warping to MNI space
Do you mean the aseg.mgz for an individual? If so, you can run mni152reg to register that subject to mni152space. Next you can run mri_label2vol to map the aseg to the 152 space. doug
On 11/17/2013 07:26 PM, ebelleau@uwm.edu wrote:
Hello,
I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble.
The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1).
How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks?
Thanks so much!
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Note: you can run each command with --help to get info
something like mni152reg --s subject to create the registration file (it will go into $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat
then something like
mri_label2vol --seg $SUBJECTS_DIR/$subject/mri/aseg.mgz --reg $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat --o aseg.$subject.mni152.nii
doug
On 11/25/2013 11:09 AM, ebelleau@uwm.edu wrote:
Hi Douglas,
Thanks for the reply. I am very new to Freesurfer and am more used to scripting with AFNI.
Would you mind giving me a bit of sample code to get used to what this may look like? Can I script this in a .tcsh file?
Also, once I convert the aseg to MNI space, can I simply average or add the individual masks (which could be done in afni) or is there a better way to do this in Freesurfer?
Also, is this a linear or non-linear warp?
Thanks,
Emily
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 21, 2013 12:57:07 PM Subject: Re: [Freesurfer] Warping to MNI space
Do you mean the aseg.mgz for an individual? If so, you can run mni152reg to register that subject to mni152space. Next you can run mri_label2vol to map the aseg to the 152 space. doug
On 11/17/2013 07:26 PM, ebelleau@uwm.edu wrote:
Hello,
I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble.
The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1).
How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks?
Thanks so much!
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I have a followup question on this topic. I understand the two command you mentioned in this thread to warp a segmentation to the MNI152 space.
In the subjects dir, I see there is an average subject "cvs_avg35_inMNI152" which is already in MNI space (and the volume size is 256^3). I want to just reslice the aparc+aseg.mgz to size of the MNI template (91*109*91)
Since this subject is already in MNI152 space, I can just do the following right?
mri_label2vol --subject cvs_avg35_inMNI152 --aparc+aseg --temp spm-T1.nii --o aparc+aseg2.nii --regheader aparc+aseg.mgz (where spm-T1.nii is the T1 template from spm)
Or would you recommend a different approach ?
Thanks Mehul ps: Earlier I used mri_convert as follows: mri_convert aparc+aseg.mgz -rt nearest -rl spm-T1.nii aparc+aseg1.mgz
But then I recalled your advice (from earlier) to use mri_label2vol convert the segmentation labels and followed it!
On Mon, Nov 25, 2013 at 3:46 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Note: you can run each command with --help to get info
something like mni152reg --s subject to create the registration file (it will go into $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat
then something like
mri_label2vol --seg $SUBJECTS_DIR/$subject/mri/aseg.mgz --reg $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat --o aseg.$subject.mni152.nii
doug
On 11/25/2013 11:09 AM, ebelleau@uwm.edu wrote:
Hi Douglas,
Thanks for the reply. I am very new to Freesurfer and am more used to
scripting with AFNI.
Would you mind giving me a bit of sample code to get used to what this
may look like? Can I script this in a .tcsh file?
Also, once I convert the aseg to MNI space, can I simply average or add
the individual masks (which could be done in afni) or is there a better way to do this in Freesurfer?
Also, is this a linear or non-linear warp?
Thanks,
Emily
----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 21, 2013 12:57:07 PM Subject: Re: [Freesurfer] Warping to MNI space
Do you mean the aseg.mgz for an individual? If so, you can run mni152reg to register that subject to mni152space. Next you can run mri_label2vol to map the aseg to the 152 space. doug
On 11/17/2013 07:26 PM, ebelleau@uwm.edu wrote:
Hello,
I plan on using the aseg.nii to create a grey matter mask. I want to
warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble.
The reason I need this in MNI space is because I plan to make a group
grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1).
How might I go about doing the warping and I wanted to double check the
order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks?
Thanks so much!
Emily _______________________________________________ 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.
Mehul, I'm not sure what you are trying to do? Just get a version of the aparc+aseg into mni152 space? If so, what is the application? In most applications (eg, linear intersubject registration), this is not very useful because the cortical labels are quite small (tailored to surface-based analyses) so they don't usually create good ROIs for volume-based group analyses. Note that even though cvs_avg35_inMNI152 is in "mni152 space" CVS registration was used so applying it to data co-registrered with another technique might not work all that well.
doug
ps. The command line looks right.
On 2/6/14 9:26 PM, Mehul Sampat wrote:
Hi Doug,
I have a followup question on this topic. I understand the two command you mentioned in this thread to warp a segmentation to the MNI152 space.
In the subjects dir, I see there is an average subject "cvs_avg35_inMNI152" which is already in MNI space (and the volume size is 256^3). I want to just reslice the aparc+aseg.mgz to size of the MNI template (91*109*91)
Since this subject is already in MNI152 space, I can just do the following right?
mri_label2vol --subject cvs_avg35_inMNI152 --aparc+aseg --temp spm-T1.nii --o aparc+aseg2.nii --regheader aparc+aseg.mgz (where spm-T1.nii is the T1 template from spm)
Or would you recommend a different approach ?
Thanks Mehul ps: Earlier I used mri_convert as follows: mri_convert aparc+aseg.mgz -rt nearest -rl spm-T1.nii aparc+aseg1.mgz
But then I recalled your advice (from earlier) to use mri_label2vol convert the segmentation labels and followed it!
On Mon, Nov 25, 2013 at 3:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Note: you can run each command with --help to get info something like mni152reg --s subject to create the registration file (it will go into $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat then something like mri_label2vol --seg $SUBJECTS_DIR/$subject/mri/aseg.mgz --reg $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat --o aseg.$subject.mni152.nii doug On 11/25/2013 11:09 AM, ebelleau@uwm.edu <mailto:ebelleau@uwm.edu> wrote: > Hi Douglas, > > Thanks for the reply. I am very new to Freesurfer and am more used to scripting with AFNI. > > Would you mind giving me a bit of sample code to get used to what this may look like? Can I script this in a .tcsh file? > > Also, once I convert the aseg to MNI space, can I simply average or add the individual masks (which could be done in afni) or is there a better way to do this in Freesurfer? > > Also, is this a linear or non-linear warp? > > Thanks, > > Emily > > ----- Original Message ----- > From: "Douglas N Greve" <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Sent: Thursday, November 21, 2013 12:57:07 PM > Subject: Re: [Freesurfer] Warping to MNI space > > > Do you mean the aseg.mgz for an individual? If so, you can run mni152reg > to register that subject to mni152space. Next you can run mri_label2vol > to map the aseg to the 152 space. > doug > > > On 11/17/2013 07:26 PM, ebelleau@uwm.edu <mailto:ebelleau@uwm.edu> wrote: >> Hello, >> >> I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble. >> >> The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1). >> >> How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks? >> >> Thanks so much! >> >> Emily >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
ebelleau＠uwm.edu -
Greg Reckless -
Mehul Sampat