Hi,
I am trying to compare my volume maps (negative_allsocial_proportion.nii) to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface (mni152_subject). So I used the steps for mri_vol2surf command as follows:
Commands: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5
Then to view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
Everything ran fine and we didn't get any error but then while viewing the files we could not see our map (neg_allsocail_lh.nii) on the surface. This file seemed to work fine as it is not an empty file when I checked the file size. However, when we view it using tksurfer it does not show up as a highlighted portion on the surface. The SN_like_cortical_lh.nii.gz file shows up just fine.
Could someone please help me figure out what might have gone wrong here.
Thanks so much!
Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote:
Hi,
I am trying to compare my volume maps (negative_allsocial_proportion.nii) to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface (mni152_subject). So I used the steps for mri_vol2surf command as follows:
Commands: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 Then to view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
Everything ran fine and we didn't get any error but then while viewing the files we could not see our map (neg_allsocail_lh.nii) on the surface. This file seemed to work fine as it is not an empty file when I checked the file size. However, when we view it using tksurfer it does not show up as a highlighted portion on the surface. The SN_like_cortical_lh.nii.gz file shows up just fine.
Could someone please help me figure out what might have gone wrong here.
Thanks so much!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
When I type this command: tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote:
Hi,
I am trying to compare my volume maps (negative_allsocial_proportion.nii) to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface (mni152_subject). So I used the steps for mri_vol2surf command as follows:
Commands: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 Then to view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
Everything ran fine and we didn't get any error but then while viewing the files we could not see our map (neg_allsocail_lh.nii) on the surface. This file seemed to work fine as it is not an empty file when I checked the file size. However, when we view it using tksurfer it does not show up as a highlighted portion on the surface. The SN_like_cortical_lh.nii.gz file shows up just fine.
Could someone please help me figure out what might have gone wrong here.
Thanks so much!
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 dispose of the e-mail.
Hi Srishti
the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do
cheers Bruce
On Sun, 8 Apr 2018, srishti goel wrote:
When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > >
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 dispose of the e-mail.
Hi Bruce,
Thanks so much for pointing that out, I totally missed that part.
Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Srishti
the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do
cheers Bruce
On Sun, 8 Apr 2018, srishti goel wrote:
When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii
--regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader--s mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce
On Apr 8, 2018, at 2:55 PM, srishti goel 23srishtigoel@gmail.com wrote:
Hi Bruce,
Thanks so much for pointing that out, I totally missed that part.
Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.
<Screen Shot 2018-04-08 at 2.53.33 PM.png>
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Srishti
the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do
cheers Bruce
On Sun, 8 Apr 2018, srishti goel wrote:
When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > >
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 dispose of the e-mail.
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader
On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce
On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtigoel@gmail.com mailto:23srishtigoel@gmail.com> wrote:
Hi Bruce,
Thanks so much for pointing that out, I totally missed that part.
Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.
<Screen Shot 2018-04-08 at 2.53.33 PM.png>
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do cheers Bruce On Sun, 8 Apr 2018, srishti goel wrote: When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc. I am unsure what is happening here. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error:
reading source './tmp.bbregister.91068/template.nii'...
mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii.
No such file or directory
Any help is greatly appreciated!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader
On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce
On Apr 8, 2018, at 2:55 PM, srishti goel 23srishtigoel@gmail.com wrote:
Hi Bruce,
Thanks so much for pointing that out, I totally missed that part.
Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.
<Screen Shot 2018-04-08 at 2.53.33 PM.png>
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Srishti
the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do
cheers Bruce
On Sun, 8 Apr 2018, srishti goel wrote:
When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii
--regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve < dgreve@mgh.harvard.edu> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader--s mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > >
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
don't use --init-rr ( you don't need to spec an init in version 6)
On 4/10/18 9:48 PM, srishti goel wrote:
When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error:
reading source './tmp.bbregister.91068/template.nii'...
mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii.
No such file or directory
Any help is greatly appreciated!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader On 4/9/18 11:49 PM, Bruce Fischl wrote:How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com>> wrote:Hi Bruce, Thanks so much for pointing that out, I totally missed that part. Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently. <Screen Shot 2018-04-08 at 2.53.33 PM.png> Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do cheers Bruce On Sun, 8 Apr 2018, srishti goel wrote: When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc. I am unsure what is happening here. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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Hi,
I used bbregister to register: bbregister --mov negative_allsocial_proportion.nii --s mni152_subject --bold --lta register.lta
and then viewed it using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs
It doesn't look great but it still looks okay (Screenshot attached).
Then I also used lta in tkregisterfv, as: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --s mni152_subject --surfs --reg reg.deleteme.dat
In this file, the volume map still lies outside the surface. Could you please help me resolve this issue.
I tried using register.lta file in the mri_vol2surf but the overlay map doesn't show up again.
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
don't use --init-rr ( you don't need to spec an init in version 6)
On 4/10/18 9:48 PM, srishti goel wrote:
When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error:
reading source './tmp.bbregister.91068/template.nii'...
mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii.
No such file or directory
Any help is greatly appreciated!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader
On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce
On Apr 8, 2018, at 2:55 PM, srishti goel 23srishtigoel@gmail.com wrote:
Hi Bruce,
Thanks so much for pointing that out, I totally missed that part.
Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.
<Screen Shot 2018-04-08 at 2.53.33 PM.png>
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Hi Srishti
the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do
cheers Bruce
On Sun, 8 Apr 2018, srishti goel wrote:
When I type this command:tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve < dgreve@mgh.harvard.edu> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader--s mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf commandas > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > >
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
how was negative_allsocial_proportion.nii created?
On 4/11/18 9:14 PM, srishti goel wrote:
Hi,
I used bbregister to register: bbregister --mov negative_allsocial_proportion.nii --s mni152_subject --bold --lta register.lta and then viewed it using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs It doesn't look great but it still looks okay (Screenshot attached). Then I also used lta in tkregisterfv, as: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --s mni152_subject --surfs --reg reg.deleteme.dat In this file, the volume map still lies outside the surface. Could you please help me resolve this issue. I tried using register.lta file in the mri_vol2surf but the overlay map doesn't show up again. Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
don't use --init-rr ( you don't need to spec an init in version 6) On 4/10/18 9:48 PM, srishti goel wrote:When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error: reading source './tmp.bbregister.91068/template.nii'... mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii. No such file or directory Any help is greatly appreciated! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader On 4/9/18 11:49 PM, Bruce Fischl wrote:How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com>> wrote:Hi Bruce, Thanks so much for pointing that out, I totally missed that part. Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently. <Screen Shot 2018-04-08 at 2.53.33 PM.png> Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do cheers Bruce On Sun, 8 Apr 2018, srishti goel wrote: When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc. I am unsure what is happening here. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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Hi Douglas,
The negative_allsocial_proportion.nii file has actually been converted from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to convert the vmp file, option - 'export to analze' and 'export to nifti'. The original vmp file represent the results of a meta-analysis.
Let me know if that helps or you would need more information.
Thanks!
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
how was negative_allsocial_proportion.nii created?
On 4/11/18 9:14 PM, srishti goel wrote:
Hi,
I used bbregister to register: bbregister --mov negative_allsocial_proportion.nii --s mni152_subject --bold --lta register.lta and then viewed it using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs It doesn't look great but it still looks okay (Screenshot attached). Then I also used lta in tkregisterfv, as: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --s mni152_subject --surfs --reg reg.deleteme.dat In this file, the volume map still lies outside the surface. Could you please help me resolve this issue. I tried using register.lta file in the mri_vol2surf but the overlay map doesn't show up again. Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
don't use --init-rr ( you don't need to spec an init in version 6)
On 4/10/18 9:48 PM, srishti goel wrote:
When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error:
reading source './tmp.bbregister.91068/template.nii'...
mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii.
No such file or directory
Any help is greatly appreciated!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader
On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce
On Apr 8, 2018, at 2:55 PM, srishti goel 23srishtigoel@gmail.com wrote:
Hi Bruce,
Thanks so much for pointing that out, I totally missed that part.
Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.
<Screen Shot 2018-04-08 at 2.53.33 PM.png>
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
Hi Srishti
the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do
cheers Bruce
On Sun, 8 Apr 2018, srishti goel wrote:
When I type this command:tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat
It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc.
I am unsure what is happening here.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve < dgreve@mgh.harvard.edu> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii--regheader --s mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf commandas > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > >
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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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
When you use bbregister, it is expecting the input nii file to represent the actual anatomy of the subject, so it does not surprise me that it does not work that well. I'm not sure what to do about this because a meta analysis image will never have decent anatomy. In theory, it should be already in alignment with the mni152, but this is trickier than it seems. How do you usually view the results? In FSL or SPM? Do you view them on an anatomical image?
On 04/12/2018 09:03 AM, srishti goel wrote:
Hi Douglas,
The negative_allsocial_proportion.nii file has actually been converted from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to convert the vmp file, option - 'export to analze' and 'export to nifti'. The original vmp file represent the results of a meta-analysis.
Let me know if that helps or you would need more information.
Thanks!
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
how was negative_allsocial_proportion.nii created? On 4/11/18 9:14 PM, srishti goel wrote:Hi, I used bbregister to register: bbregister --mov negative_allsocial_proportion.nii --s mni152_subject --bold --lta register.lta and then viewed it using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs It doesn't look great but it still looks okay (Screenshot attached). Then I also used lta in tkregisterfv, as: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --s mni152_subject --surfs --reg reg.deleteme.dat In this file, the volume map still lies outside the surface. Could you please help me resolve this issue. I tried using register.lta file in the mri_vol2surf but the overlay map doesn't show up again. Thanks! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: don't use --init-rr ( you don't need to spec an init in version 6) On 4/10/18 9:48 PM, srishti goel wrote:When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error: reading source './tmp.bbregister.91068/template.nii'... mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii. No such file or directory Any help is greatly appreciated! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader On 4/9/18 11:49 PM, Bruce Fischl wrote:How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com>> wrote:Hi Bruce, Thanks so much for pointing that out, I totally missed that part. Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently. <Screen Shot 2018-04-08 at 2.53.33 PM.png> Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do cheers Bruce On Sun, 8 Apr 2018, srishti goel wrote: When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot find mni152_subject. Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc. I am unsure what is happening here. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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. 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Yeah, I am unsure where to go from here as well. So the results can be viewed in SPM and on the MNI template space itself, since SPM typically does not have a problem showing multiple images in different sizes.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
When you use bbregister, it is expecting the input nii file to represent the actual anatomy of the subject, so it does not surprise me that it does not work that well. I'm not sure what to do about this because a meta analysis image will never have decent anatomy. In theory, it should be already in alignment with the mni152, but this is trickier than it seems. How do you usually view the results? In FSL or SPM? Do you view them on an anatomical image?
On 04/12/2018 09:03 AM, srishti goel wrote:
Hi Douglas,
The negative_allsocial_proportion.nii file has actually been converted from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to convert the vmp file, option - 'export to analze' and 'export to nifti'. The original vmp file represent the results of a meta-analysis.
Let me know if that helps or you would need more information.
Thanks!
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
how was negative_allsocial_proportion.nii created? On 4/11/18 9:14 PM, srishti goel wrote:Hi, I used bbregister to register: bbregister --mov negative_allsocial_proportion.nii --s mni152_subject --bold --lta register.lta and then viewed it using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs It doesn't look great but it still looks okay (Screenshot attached). Then I also used lta in tkregisterfv, as: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --s mni152_subject --surfs --reg reg.deleteme.dat In this file, the volume map still lies outside the surface. Could you please help me resolve this issue. I tried using register.lta file in the mri_vol2surf but the overlay map doesn't show up again. Thanks! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: don't use --init-rr ( you don't need to spec an init in version 6) On 4/10/18 9:48 PM, srishti goel wrote:When I run bbregister, it gives me an error. Attached is the register.dat.log file for it. Error: reading source './tmp.bbregister.91068/template.nii'... mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii. No such file or directory Any help is greatly appreciated! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>wrote:
They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader On 4/9/18 11:49 PM, Bruce Fischl wrote:How did you generate the registration? And give us the details of what you are trying to register Cheers Bruce On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com>> wrote:Hi Bruce, Thanks so much for pointing that out, I totally missed that part. Also, the registration definitely isn't appropriate. Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently. <Screen Shot 2018-04-08 at 2.53.33 PM.png> Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to specifythe
directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this stuff better than I do cheers Bruce On Sun, 8 Apr 2018, srishti goel wrote: When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii --regheader--s
mni152_subject --surfs --reg reg.deleteme.dat It gives me the error: cannot findmni152_subject.
Although I clearly checked that the directory from which I am submitting this command has the mni152_subject directory within which there are all the other required directories such as: mri, stats, surf, scripts, etc. I am unsure what is happening here. Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Those commands look ok. My suspicion goes to the use of --regheader. See whether the registration is ok with tkregisterfv --mov negative_allsocial_proportion.nii --regheader--s
mni152_subject --surfs --reg reg.deleteme.dat On 04/05/2018 08:34 AM, srishti goel wrote: > Hi, > > I am trying to compare my volume maps > (negative_allsocial_proportion.nii) to someone else's > (SN_like_cortical_lh.nii.gz) who have it on a surface > (mni152_subject). So I used the steps for mri_vol2surf command as > follows: > > Commands: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 > Then to view it: > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 > > Everything ran fine and we didn't get any error but then while viewing > the files we could not see our map (neg_allsocail_lh.nii) on the > surface. This file seemed to work fine as it is not an empty file when > I checked the file size. However, when we view it using tksurfer it > does not show up as a highlighted portion on the surface. The > SN_like_cortical_lh.nii.gz file shows up just fine. > > Could someone please help me figure out what might have gone wrong here. > > Thanks so much! > > > > ______________________________
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What is the "MNI template" that you are using. I mean an exact file used. Did you use this file when you ran recon-all?
On 04/12/2018 10:23 AM, srishti goel wrote:
Yeah, I am unsure where to go from here as well. So the results can be viewed in SPM and on the MNI template space itself, since SPM typically does not have a problem showing multiple images in different sizes.
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
When you use bbregister, it is expecting the input nii file to represent the actual anatomy of the subject, so it does not surprise me that it does not work that well. I'm not sure what to do about this because a meta analysis image will never have decent anatomy. In theory, it should be already in alignment with the mni152, but this is trickier than it seems. How do you usually view the results? In FSL or SPM? Do you view them on an anatomical image? On 04/12/2018 09:03 AM, srishti goel wrote: > Hi Douglas, > > The negative_allsocial_proportion.nii file has actually been converted > from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to > convert the vmp file, option - 'export to analze' and 'export to > nifti'. The original vmp file represent the results of a meta-analysis. > > Let me know if that helps or you would need more information. > > Thanks! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> > skype: srishti.goel12 > > > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve > <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>> wrote: > > how was negative_allsocial_proportion.nii created? > > > On 4/11/18 9:14 PM, srishti goel wrote: >> Hi, >> >> I used bbregister to register: >> bbregister --mov negative_allsocial_proportion.nii --s >> mni152_subject --bold --lta register.lta >> and then viewed it using: >> tkregisterfv --mov negative_allsocial_proportion.nii --reg >> register.lta --surfs >> It doesn't look great but it still looks okay (Screenshot attached). >> Then I also used lta in tkregisterfv, as: >> tkregisterfv --mov negative_allsocial_proportion.nii --reg >> register.lta --s mni152_subject --surfs --reg reg.deleteme.dat >> In this file, the volume map still lies outside the surface. >> Could you please help me resolve this issue. >> I tried using register.lta file in the mri_vol2surf but the >> overlay map doesn't show up again. >> Thanks! >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> >> skype: srishti.goel12 >> >> >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve >> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>> wrote: >> >> don't use --init-rr ( you don't need to spec an init in >> version 6) >> >> >> On 4/10/18 9:48 PM, srishti goel wrote: >>> When I run bbregister, it gives me an error. Attached is the >>> register.dat.log file for it. >>> Error: >>> >>> reading source './tmp.bbregister.91068/template.nii'... >>> >>> mri_robust_register.bin: only pass single frame MRI source >>> ./tmp.bbregister.91068/template.nii. >>> >>> >>> No such file or directory >>> >>> >>> Any help is greatly appreciated! >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> >>> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> >>> skype: srishti.goel12 >>> >>> >>> On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve >>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>> wrote: >>> >>> They are not in registration. Try running bbregister to >>> create a registration file (lta), then pass the lta to >>> tkregisterfv instead of --regheader >>> >>> >>> On 4/9/18 11:49 PM, Bruce Fischl wrote: >>>> How did you generate the registration? And give us the >>>> details of what you are trying to register >>>> Cheers >>>> Bruce >>>> >>>> On Apr 8, 2018, at 2:55 PM, srishti goel >>>> <23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com> >>>> <mailto:23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com>>> wrote: >>>> >>>>> Hi Bruce, >>>>> >>>>> Thanks so much for pointing that out, I totally missed >>>>> that part. >>>>> >>>>> Also, the registration definitely isn't appropriate. >>>>> Could someone please guide me how to correct this >>>>> problem. I have attached a screenshot of how it looks >>>>> like currently. >>>>> >>>>> >>>>> <Screen Shot 2018-04-08 at 2.53.33 PM.png> >>>>> >>>>> Best, >>>>> Srishti >>>>> Social/Clinical Research Specialist >>>>> Child Imaging Research and Life Experiences Lab >>>>> University of North Carolina at Chapel Hill >>>>> email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> >>>>> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> >>>>> skype: srishti.goel12 >>>>> >>>>> >>>>> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl >>>>> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>>>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: >>>>> >>>>> Hi Srishti >>>>> >>>>> the directory you are in doesn't matter. YOu >>>>> either need to set SUBJECTS_DIR in the >>>>> environment, or use --sd <SUBJECTS_DIR> to specify the >>>>> directory that contains your subjects. I think you >>>>> can also give it the full path to a target volume >>>>> if you want, but maybe Doug can comment as he >>>>> knows this stuff better than I do >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> >>>>> On Sun, 8 Apr 2018, srishti goel wrote: >>>>> >>>>> When I type this command:tkregisterfv --mov >>>>> negative_allsocial_proportion.nii --regheader --s >>>>> mni152_subject --surfs --reg reg.deleteme.dat >>>>> >>>>> It gives me the error: cannot find mni152_subject. >>>>> Although I clearly checked that the directory >>>>> from which I am submitting this command has the >>>>> mni152_subject directory within which there >>>>> are all the other required directories such >>>>> as: mri, >>>>> stats, surf, scripts, etc. >>>>> >>>>> I am unsure what is happening here. >>>>> >>>>> >>>>> Best, >>>>> Srishti >>>>> Social/Clinical Research Specialist >>>>> Child Imaging Research and Life Experiences Lab >>>>> University of North Carolina at Chapel Hill >>>>> email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> >>>>> <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> >>>>> skype: srishti.goel12 >>>>> >>>>> >>>>> On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. >>>>> Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> >>>>> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>> wrote: >>>>> Those commands look ok. My suspicion >>>>> goes to the use of --regheader. See >>>>> whether the registration is ok with >>>>> >>>>> tkregisterfv --mov >>>>> negative_allsocial_proportion.nii --regheader --s >>>>> mni152_subject --surfs --reg reg.deleteme.dat >>>>> >>>>> >>>>> On 04/05/2018 08:34 AM, srishti goel wrote: >>>>> > Hi, >>>>> > >>>>> > I am trying to compare my volume maps >>>>> > (negative_allsocial_proportion.nii) to >>>>> someone else's >>>>> > (SN_like_cortical_lh.nii.gz) who have >>>>> it on a surface >>>>> > (mni152_subject). So I used the steps >>>>> for mri_vol2surf command as >>>>> > follows: >>>>> > >>>>> > Commands: >>>>> > mri_vol2surf --src >>>>> negative_allsocial_proportion.nii --regheader >>>>> > mni152_subject --hemi lh --o >>>>> ./neg_allsocial_lh.nii --projfrac 0.5 >>>>> > Then to view it: >>>>> > tksurfer mni152_subject lh inflated >>>>> -overlay ./neg_allsocial_lh.nii >>>>> > -overlay SN_like_cortical_lh.nii.gz >>>>> -fthresh 0.5 >>>>> > >>>>> > Everything ran fine and we didn't get >>>>> any error but then while viewing >>>>> > the files we could not see our map >>>>> (neg_allsocail_lh.nii) on the >>>>> > surface. This file seemed to work fine >>>>> as it is not an empty file when >>>>> > I checked the file size. However, when >>>>> we view it using tksurfer it >>>>> > does not show up as a highlighted >>>>> portion on the surface. The >>>>> > SN_like_cortical_lh.nii.gz file shows >>>>> up just fine. >>>>> > >>>>> > Could someone please help me figure >>>>> out what might have gone wrong here. >>>>> > >>>>> > Thanks so much! >>>>> > >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > Freesurfer mailing list >>>>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> >>>>> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . 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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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Bruce Fischl -
Douglas Greve -
Douglas N. Greve
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srishti goel