Hi Freesurfers,
I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A.
However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine.
Data from the newer session were coregistered to the older session, so that can't be the problem.
I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'?
Thanks, Bianca
Hi Bianca
how did you coregister the data? Did you map the label so that it is in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce
On Wed, 10 Jul 2013, Bianca van Kemenade wrote:
Hi Freesurfers,
I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A.
However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine.
Data from the newer session were coregistered to the older session, so that can't be the problem.
I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'?
Thanks, Bianca
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in SPM (to the structural of the old session). So I didn't do anything to the label. I displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity data) and loaded the label just by clicking load --> label. Should I add -reassign in this tksurfer command, or is there a way to load the label with a command, to which I have to add -reassign?
Also, I'm not familiar with freeview, I tried starting it by typing 'freeview' but I get the error: freeview.bin: error while loading shared libraries libXss.so.1: cannot open shared object file: No such file or directory. It doesn't seem to depend on which directory I'm in.
Thanks, Bianca
On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Bianca
how did you coregister the data? Did you map the label so that it is in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce
On Wed, 10 Jul 2013, Bianca van Kemenade wrote:
Hi Freesurfers,
I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A.
However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine.
Data from the newer session were coregistered to the older session, so that can't be the problem.
I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'?
Thanks, Bianca
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/**compliancelinehttp://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.
you can try adding -reassign, but the label must be in the same coords as the anatomical for this to work. You'll know right away if it did or not though
cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote:
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in SPM (to the structural of the old session). So I didn't do anything to the label. I displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity data) and loaded the label just by clicking load --> label. Should I add -reassign in this tksurfer command, or is there a way to load the label with a command, to which I have to add -reassign?
Also, I'm not familiar with freeview, I tried starting it by typing 'freeview' but I get the error: freeview.bin: error while loading shared libraries libXss.so.1: cannot open shared object file: No such file or directory. It doesn't seem to depend on which directory I'm in.
Thanks, Bianca
On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Bianca
how did you coregister the data? Did you map the label so that it is in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote: Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, BiancaThe 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.
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Flag -reassign is unrecognised unfortunately when I add it to the tksurfer-sess command I posted before. I tried it with tksurfer P2_BK rh inflated -reassign, there at least it ran. However if I then use the tksurfer-sess command again and load the labels I can only see that the labels changed a bit, but they are still not correct.
I assumed coregistering the new session to the (not inflated) anatomical used in the old session used to create the labels would suffice, but apparently some other transformation needs to take place. Do you have an idea how to put the label in the same coordinates? Sorry for my basic questions.
Best, Bianca
On Wed, Jul 10, 2013 at 6:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
you can try adding -reassign, but the label must be in the same coords as the anatomical for this to work. You'll know right away if it did or not though
cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote:
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in SPM (to the structural of the old session). So I didn't do anything to the label. I displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity data) and loaded the label just by clicking load --> label. Should I add -reassign in this tksurfer command, or is there a way to load the label with a command, to which I have to add -reassign?
Also, I'm not familiar with freeview, I tried starting it by typing 'freeview' but I get the error: freeview.bin: error while loading shared libraries libXss.so.1: cannot open shared object file: No such file or directory. It doesn't seem to depend on which directory I'm in.
Thanks, Bianca
On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Bianca
how did you coregister the data? Did you map the label so that itis in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce
On Wed, 10 Jul 2013, Bianca van Kemenade wrote: Hi Freesurfers, I have some participants of whom I obtained retinotopic polarangle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A.
However, when I load my old V1-3 labels onto the inflatedbrain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine.
Data from the newer session were coregistered to the oldersession, so that can't be the problem.
I looked around on the wiki and found the commandmri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'?
Thanks, BiancaThe 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/**compliancelinehttp://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.
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
mri_label2label is what we would typically use. You can probably use bbregister to generate the registration from the old session to the new anatomicals
On Wed, 10 Jul 2013, Bianca van Kemenade wrote:
Flag -reassign is unrecognised unfortunately when I add it to the tksurfer-sess command I posted before. I tried it with tksurfer P2_BK rh inflated -reassign, there at least it ran. However if I then use the tksurfer-sess command again and load the labels I can only see that the labels changed a bit, but they are still not correct.
I assumed coregistering the new session to the (not inflated) anatomical used in the old session used to create the labels would suffice, but apparently some other transformation needs to take place. Do you have an idea how to put the label in the same coordinates? Sorry for my basic questions.
Best, Bianca
On Wed, Jul 10, 2013 at 6:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can try adding -reassign, but the label must be in the same coords as the anatomical for this to work. You'll know right away if it did or not though
cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote: Hi Bruce, Thank you for your reply. I coregistered the new data beforehand in SPM (to the structural of the old session). So I didn't do anything to the label. I displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity data) and loaded the label just by clicking load --> label. Should I add -reassign in this tksurfer command, or is there a way to load the label with a command, to which I have to add -reassign? Also, I'm not familiar with freeview, I tried starting it by typing 'freeview' but I get the error: freeview.bin: error while loading shared libraries libXss.so.1: cannot open shared object file: No such file or directory. It doesn't seem to depend on which directory I'm in. Thanks, Bianca On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Bianca how did you coregister the data? Did you map the label so that it is in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote: Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, Bianca 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. -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Hi Bianca, I'm a little confused. What do you mean you registered with SPM beforehand? If you're using FSFAST, then the registration is done as part of preproc-sess. The results for both sessions are on the surface, so there is no need to do anything to a label created from one session to show it on another session.
doug
On 07/10/2013 11:55 AM, Bianca van Kemenade wrote:
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in SPM (to the structural of the old session). So I didn't do anything to the label. I displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity data) and loaded the label just by clicking load --> label. Should I add -reassign in this tksurfer command, or is there a way to load the label with a command, to which I have to add -reassign?
Also, I'm not familiar with freeview, I tried starting it by typing 'freeview' but I get the error: freeview.bin: error while loading shared libraries libXss.so.1: cannot open shared object file: No such file or directory. It doesn't seem to depend on which directory I'm in.
Thanks, Bianca
On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Bianca how did you coregister the data? Did you map the label so that it is in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote: Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, Bianca 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.-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Well the situation is as follows:
I had a polar angle session, of which I only have the labels and the anatomical (not inflated) left due to a computer crash. In a different session, I scanned both my main experiment and the eccentricity runs. Since the eccentricity was in the same session as the main experiment, I included those runs in my preprocessing batch in SPM, that is I realigned them and coregistered the data to the anatomical of the polar angle session. I then inflated the anatomical of this newer session (the one with eccentricity) and did my analyses of the eccentricity data without using preproc-sess. Apologies if I wasn't clear.
I thought it should therefore be no problem to overlay the polar angle labels onto the newly inflated anatomical, since this one was coregistered to the one from the polar angle session. However the labels don't look correct. Should I have inflated the 'old' anatomical instead? Or would I then nevertheless have needed some kind of transformation?
I tried mri_label2label, but when I use a command like this:
mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume
then it requires access to the anatomical in mri/orig from the srcsubject (the same subject, old session), which I don't have. Well I do have the .nii anatomical, but it can't read that header either, it probably needs the .mgz one which I don't have. When I try the command like this:
mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume
it does create a new label, which however looks exactly the same as the previous one. When I change --regmethod to surface, it gives this error: ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created.
I'm not sure about using bbregister for the labels, what would be the movable volume? And do I then use the register.dat file to load the labels with? Thanks again for your patience and help.
Best, Bianca
On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Bianca, I'm a little confused. What do you mean you registered with SPM beforehand? If you're using FSFAST, then the registration is done as part of preproc-sess. The results for both sessions are on the surface, so there is no need to do anything to a label created from one session to show it on another session.
doug
On 07/10/2013 11:55 AM, Bianca van Kemenade wrote:
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in SPM (to the structural of the old session). So I didn't do anything to the label. I displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity data) and loaded the label just by clicking load --> label. Should I add -reassign in this tksurfer command, or is there a way to load the label with a command, to which I have to add -reassign?
Also, I'm not familiar with freeview, I tried starting it by typing 'freeview' but I get the error: freeview.bin: error while loading shared libraries libXss.so.1: cannot open shared object file: No such file or directory. It doesn't seem to depend on which directory I'm in.
Thanks, Bianca
On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Bianca how did you coregister the data? Did you map the label so that it is in the coords of the new session? If so, try specifying -reassign on the tksurfer command line. That will discard the vertex indices in the label (which refer to the first session surfaces) and reassign vertex numbers from the current subject. This will *only* work if the label is in the correct coordinate system. You can verify this by loading it in freeview on top of the anatomical from the new session cheers Bruce On Wed, 10 Jul 2013, Bianca van Kemenade wrote: Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity datain
a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricitysession
to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, Bianca 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.-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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
Hi Bianca, I'm still unclear what it is you have done.
You only need to run freesurfer on one of the anatomicals, it does not matter which one.
You should not do anything to the fMRI runs (eg, align with SPM). You should put your eccen and polar data into a single bold folder under your session folder.
Then run preproc-sess.
I'm not sure how this overlaps with what you have done
doug
On 07/11/2013 05:10 AM, Bianca van Kemenade wrote:
Well the situation is as follows:
I had a polar angle session, of which I only have the labels and the anatomical (not inflated) left due to a computer crash. In a different session, I scanned both my main experiment and the eccentricity runs. Since the eccentricity was in the same session as the main experiment, I included those runs in my preprocessing batch in SPM, that is I realigned them and coregistered the data to the anatomical of the polar angle session. I then inflated the anatomical of this newer session (the one with eccentricity) and did my analyses of the eccentricity data without using preproc-sess. Apologies if I wasn't clear.
I thought it should therefore be no problem to overlay the polar angle labels onto the newly inflated anatomical, since this one was coregistered to the one from the polar angle session. However the labels don't look correct. Should I have inflated the 'old' anatomical instead? Or would I then nevertheless have needed some kind of transformation?
I tried mri_label2label, but when I use a command like this:
mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume
then it requires access to the anatomical in mri/orig from the srcsubject (the same subject, old session), which I don't have. Well I do have the .nii anatomical, but it can't read that header either, it probably needs the .mgz one which I don't have. When I try the command like this:
mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume
it does create a new label, which however looks exactly the same as the previous one. When I change --regmethod to surface, it gives this error: ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created.
I'm not sure about using bbregister for the labels, what would be the movable volume? And do I then use the register.dat file to load the labels with? Thanks again for your patience and help.
Best, Bianca
On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I'm a little confused. What do you mean you registered with SPM beforehand? If you're using FSFAST, then the registration is done as part of preproc-sess. The results for both sessions are on the surface, so there is no need to do anything to a label created from one session to show it on another session. doug On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > Hi Bruce, > > Thank you for your reply. I coregistered the new data beforehand in > SPM (to the structural of the old session). So I didn't do anything to > the label. I displayed the structural with tksurfer-sess -c eccen > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my > eccentricity data) and loaded the label just by clicking load --> > label. Should I add -reassign in this tksurfer command, or is there a > way to load the label with a command, to which I have to add -reassign? > > Also, I'm not familiar with freeview, I tried starting it by typing > 'freeview' but I get the error: freeview.bin: error while loading > shared libraries libXss.so.1: cannot open shared object file: No such > file or directory. It doesn't seem to depend on which directory I'm in. > > Thanks, > Bianca > > > On Wed, Jul 10, 2013 at 5:19 PM, 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 Bianca > > how did you coregister the data? Did you map the label so that it > is in the coords of the new session? If so, try specifying > -reassign on the tksurfer command line. That will discard the > vertex indices in the label (which refer to the first session > surfaces) and reassign vertex numbers from the current subject. > This will *only* work if the label is in the correct coordinate > system. You can verify this by loading it in freeview on top of > the anatomical from the new session > cheers > Bruce > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > Hi Freesurfers, > > I have some participants of whom I obtained retinotopic polar > angle data in a previous session, and scanned eccentricity data in > a later session. I used the polar angle data to define V1-3, > and would like to display these labels on the eccentricity session > to help me define V3A. > > However, when I load my old V1-3 labels onto the inflated > brain based on the new session the labels look very strange. I > attached a screenshot of what is supposed to be lh dorsal V1, > as you can see it is scattered all over the cortex. When I load > the .nii based on the label into MRIcron, the ROI looks fine. > > Data from the newer session were coregistered to the older > session, so that can't be the problem. > > I looked around on the wiki and found the command > mri_label2label that seemed useful. However, this command > needs acces to the > 'surf' folders of both sessions. Due to a computer crash I > only have the labels of the previous session, not the 'surf' > folder. > Is there a way to display my old labels onto the new session > without needing access to 'surf'? > > Thanks, > Bianca > > > > > > 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. > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > _______________________________________________ > 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug & Bruce,
It's indeed a confusing situation. What it boils down to is:
- I scanned the polar angle session and the eccentricity session on different days - I had defined V1-3 already based on the polar angle session before scanning eccentricity - All data from the polar angle session were lost, apart from the V1-3 labels I made and the anatomical (not inflated) - Since I now didn't have an inflated brain anymore, I inflated the anatomical from the eccentricity - When I tried to overlay the labels onto this newly inflated brain, the labels were not correctly displayed
I just tried again by inflating the anatomical from the polar angle session (instead of eccentricity), and when I use tksurfer P2_BK lh inflated -reassign the labels are displayed correctly, so that's great news!
However, when I display my eccentricity data, with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are wrong again. Adding -reassign doesn't work in this command (flag not recognised). So at least I could open two terminals, one to display the inflated brain with correct labels, and one to display the eccentricity data. This is of course not ideal if I want to draw labels on the eccentricity screen using the labels displayed in the other screen as a boundary. So if anyone has an idea how to get the labels to be displayed correctly with the tksurfer-sess command please let me know.
In any case, thank you all for your help so far!
Best, Bianca
On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Bianca, I'm still unclear what it is you have done.
You only need to run freesurfer on one of the anatomicals, it does not matter which one.
You should not do anything to the fMRI runs (eg, align with SPM). You should put your eccen and polar data into a single bold folder under your session folder.
Then run preproc-sess.
I'm not sure how this overlaps with what you have done
doug
On 07/11/2013 05:10 AM, Bianca van Kemenade wrote:
Well the situation is as follows:
I had a polar angle session, of which I only have the labels and the anatomical (not inflated) left due to a computer crash. In a different session, I scanned both my main experiment and the eccentricity runs. Since the eccentricity was in the same session as the main experiment, I included those runs in my preprocessing batch in SPM, that is I realigned them and coregistered the data to the anatomical of the polar angle session. I then inflated the anatomical of this newer session (the one with eccentricity) and did my analyses of the eccentricity data without using preproc-sess. Apologies if I wasn't
clear.
I thought it should therefore be no problem to overlay the polar angle labels onto the newly inflated anatomical, since this one was coregistered to the one from the polar angle session. However the labels don't look correct. Should I have inflated the 'old' anatomical instead? Or would I then nevertheless have needed some kind of transformation?
I tried mri_label2label, but when I use a command like this:
mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume
then it requires access to the anatomical in mri/orig from the srcsubject (the same subject, old session), which I don't have. Well I do have the .nii anatomical, but it can't read that header either, it probably needs the .mgz one which I don't have. When I try the command like this:
mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume
it does create a new label, which however looks exactly the same as the previous one. When I change --regmethod to surface, it gives this error: ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created.
I'm not sure about using bbregister for the labels, what would be the movable volume? And do I then use the register.dat file to load the labels with? Thanks again for your patience and help.
Best, Bianca
On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I'm a little confused. What do you mean you registeredwith
SPM beforehand? If you're using FSFAST, then the registration is done as part of preproc-sess. The results for both sessions are on the surface, so there is no need to do anything to a label created from onesession
to show it on another session. doug On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > Hi Bruce, > > Thank you for your reply. I coregistered the new data beforehand in > SPM (to the structural of the old session). So I didn't do anything to > the label. I displayed the structural with tksurfer-sess -c eccen > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to displaymy
> eccentricity data) and loaded the label just by clicking load --> > label. Should I add -reassign in this tksurfer command, or is there a > way to load the label with a command, to which I have to add -reassign? > > Also, I'm not familiar with freeview, I tried starting it by typing > 'freeview' but I get the error: freeview.bin: error while loading > shared libraries libXss.so.1: cannot open shared object file: No such > file or directory. It doesn't seem to depend on which directory I'm in. > > Thanks, > Bianca > > > On Wed, Jul 10, 2013 at 5:19 PM, 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 Bianca > > how did you coregister the data? Did you map the label so that it > is in the coords of the new session? If so, try specifying > -reassign on the tksurfer command line. That will discard the > vertex indices in the label (which refer to the first session > surfaces) and reassign vertex numbers from the current subject. > This will *only* work if the label is in the correct coordinate > system. You can verify this by loading it in freeview on top of > the anatomical from the new session > cheers > Bruce > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > Hi Freesurfers, > > I have some participants of whom I obtained retinotopic polar > angle data in a previous session, and scanned eccentricity data in > a later session. I used the polar angle data to defineV1-3,
> and would like to display these labels on the eccentricity session > to help me define V3A. > > However, when I load my old V1-3 labels onto the inflated > brain based on the new session the labels look very strange. I > attached a screenshot of what is supposed to be lh dorsal V1, > as you can see it is scattered all over the cortex. When I load > the .nii based on the label into MRIcron, the ROI looks fine. > > Data from the newer session were coregistered to the older > session, so that can't be the problem. > > I looked around on the wiki and found the command > mri_label2label that seemed useful. However, this command > needs acces to the > 'surf' folders of both sessions. Due to a computer crash I > only have the labels of the previous session, not the'surf'
> folder. > Is there a way to display my old labels onto the newsession
> without needing access to 'surf'? > > Thanks, > Bianca > > > > > > 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. > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > _______________________________________________ > 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does that mean? doug
On 07/14/2013 09:52 AM, Bianca van Kemenade wrote:
Dear Doug & Bruce,
It's indeed a confusing situation. What it boils down to is:
- I scanned the polar angle session and the eccentricity session on
different days
- I had defined V1-3 already based on the polar angle session before
scanning eccentricity
- All data from the polar angle session were lost, apart from the V1-3
labels I made and the anatomical (not inflated)
- Since I now didn't have an inflated brain anymore, I inflated the
anatomical from the eccentricity
- When I tried to overlay the labels onto this newly inflated brain,
the labels were not correctly displayed
I just tried again by inflating the anatomical from the polar angle session (instead of eccentricity), and when I use tksurfer P2_BK lh inflated -reassign the labels are displayed correctly, so that's great news!
However, when I display my eccentricity data, with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are wrong again. Adding -reassign doesn't work in this command (flag not recognised). So at least I could open two terminals, one to display the inflated brain with correct labels, and one to display the eccentricity data. This is of course not ideal if I want to draw labels on the eccentricity screen using the labels displayed in the other screen as a boundary. So if anyone has an idea how to get the labels to be displayed correctly with the tksurfer-sess command please let me know.
In any case, thank you all for your help so far!
Best, Bianca
On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I'm still unclear what it is you have done. You only need to run freesurfer on one of the anatomicals, it does not matter which one. You should not do anything to the fMRI runs (eg, align with SPM). You should put your eccen and polar data into a single bold folder under your session folder. Then run preproc-sess. I'm not sure how this overlaps with what you have done doug On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > Well the situation is as follows: > > I had a polar angle session, of which I only have the labels and the > anatomical (not inflated) left due to a computer crash. In a different > session, I scanned both my main experiment and the eccentricity runs. > Since the eccentricity was in the same session as the main experiment, > I included those runs in my preprocessing batch in SPM, that is I > realigned them and coregistered the data to the anatomical of the > polar angle session. I then inflated the anatomical of this newer > session (the one with eccentricity) and did my analyses of the > eccentricity data without using preproc-sess. Apologies if I wasn't clear. > > I thought it should therefore be no problem to overlay the polar angle > labels onto the newly inflated anatomical, since this one was > coregistered to the one from the polar angle session. However the > labels don't look correct. Should I have inflated the 'old' anatomical > instead? Or would I then nevertheless have needed some kind of > transformation? > > I tried mri_label2label, but when I use a command like this: > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > then it requires access to the anatomical in mri/orig from the > srcsubject (the same subject, old session), which I don't have. Well I > do have the .nii anatomical, but it can't read that header either, it > probably needs the .mgz one which I don't have. When I try the command > like this: > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > lh_V1_v_new.label --regmethod volume > > it does create a new label, which however looks exactly the same as > the previous one. When I change --regmethod to surface, it gives this > error: > ERROR: there is a vertex in the label that cannot be matched to the > surface. This usually occurs when the label and surface are from > different subjects or hemispheres or the surface has been changed > since the label was created. > > I'm not sure about using bbregister for the labels, what would be the > movable volume? And do I then use the register.dat file to load the > labels with? Thanks again for your patience and help. > > Best, > Bianca > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > Hi Bianca, I'm a little confused. What do you mean you registered with > SPM beforehand? If you're using FSFAST, then the registration is > done as > part of preproc-sess. The results for both sessions are on the > surface, > so there is no need to do anything to a label created from one session > to show it on another session. > > doug > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > Hi Bruce, > > > > Thank you for your reply. I coregistered the new data beforehand in > > SPM (to the structural of the old session). So I didn't do > anything to > > the label. I displayed the structural with tksurfer-sess -c eccen > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my > > eccentricity data) and loaded the label just by clicking load --> > > label. Should I add -reassign in this tksurfer command, or is > there a > > way to load the label with a command, to which I have to add > -reassign? > > > > Also, I'm not familiar with freeview, I tried starting it by typing > > 'freeview' but I get the error: freeview.bin: error while loading > > shared libraries libXss.so.1: cannot open shared object file: No > such > > file or directory. It doesn't seem to depend on which directory > I'm in. > > > > Thanks, > > Bianca > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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>> > <mailto: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 Bianca > > > > how did you coregister the data? Did you map the label so > that it > > is in the coords of the new session? If so, try specifying > > -reassign on the tksurfer command line. That will discard the > > vertex indices in the label (which refer to the first session > > surfaces) and reassign vertex numbers from the current subject. > > This will *only* work if the label is in the correct coordinate > > system. You can verify this by loading it in freeview on top of > > the anatomical from the new session > > cheers > > Bruce > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > Hi Freesurfers, > > > > I have some participants of whom I obtained retinotopic > polar > > angle data in a previous session, and scanned > eccentricity data in > > a later session. I used the polar angle data to define V1-3, > > and would like to display these labels on the > eccentricity session > > to help me define V3A. > > > > However, when I load my old V1-3 labels onto the inflated > > brain based on the new session the labels look very > strange. I > > attached a screenshot of what is supposed to be lh > dorsal V1, > > as you can see it is scattered all over the cortex. When > I load > > the .nii based on the label into MRIcron, the ROI looks > fine. > > > > Data from the newer session were coregistered to the older > > session, so that can't be the problem. > > > > I looked around on the wiki and found the command > > mri_label2label that seemed useful. However, this command > > needs acces to the > > 'surf' folders of both sessions. Due to a computer crash I > > only have the labels of the previous session, not the 'surf' > > folder. > > Is there a way to display my old labels onto the new session > > without needing access to 'surf'? > > > > Thanks, > > Bianca > > > > > > > > > > > > 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. > > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > _______________________________________________ > 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
By that I mean that I only have a normal MPRAGE anatomical scan. By "inflated" I mean that I ran recon-all on this anatomical so that I can display the inflated surface for example. So when I said I inflated the anatomical I meant I ran recon-all. Sorry for the confusing terminology.
On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does that mean? doug
On 07/14/2013 09:52 AM, Bianca van Kemenade wrote:
Dear Doug & Bruce,
It's indeed a confusing situation. What it boils down to is:
- I scanned the polar angle session and the eccentricity session on
different days
- I had defined V1-3 already based on the polar angle session before
scanning eccentricity
- All data from the polar angle session were lost, apart from the V1-3
labels I made and the anatomical (not inflated)
- Since I now didn't have an inflated brain anymore, I inflated the
anatomical from the eccentricity
- When I tried to overlay the labels onto this newly inflated brain,
the labels were not correctly displayed
I just tried again by inflating the anatomical from the polar angle session (instead of eccentricity), and when I use tksurfer P2_BK lh inflated -reassign the labels are displayed correctly, so that's great news!
However, when I display my eccentricity data, with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are wrong again. Adding -reassign doesn't work in this command (flag not recognised). So at least I could open two terminals, one to display the inflated brain with correct labels, and one to display the eccentricity data. This is of course not ideal if I want to draw labels on the eccentricity screen using the labels displayed in the other screen as a boundary. So if anyone has an idea how to get the labels to be displayed correctly with the tksurfer-sess command please let me know.
In any case, thank you all for your help so far!
Best, Bianca
On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I'm still unclear what it is you have done. You only need to run freesurfer on one of the anatomicals, it doesnot
matter which one. You should not do anything to the fMRI runs (eg, align with SPM). You should put your eccen and polar data into a single bold folder under your session folder. Then run preproc-sess. I'm not sure how this overlaps with what you have done doug On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > Well the situation is as follows: > > I had a polar angle session, of which I only have the labels andthe
> anatomical (not inflated) left due to a computer crash. In a different > session, I scanned both my main experiment and the eccentricity runs. > Since the eccentricity was in the same session as the main experiment, > I included those runs in my preprocessing batch in SPM, that is I > realigned them and coregistered the data to the anatomical of the > polar angle session. I then inflated the anatomical of this newer > session (the one with eccentricity) and did my analyses of the > eccentricity data without using preproc-sess. Apologies if I wasn't clear. > > I thought it should therefore be no problem to overlay the polar angle > labels onto the newly inflated anatomical, since this one was > coregistered to the one from the polar angle session. However the > labels don't look correct. Should I have inflated the 'old' anatomical > instead? Or would I then nevertheless have needed some kind of > transformation? > > I tried mri_label2label, but when I use a command like this: > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK --scrlabel > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > then it requires access to the anatomical in mri/orig from the > srcsubject (the same subject, old session), which I don't have. Well I > do have the .nii anatomical, but it can't read that header either, it > probably needs the .mgz one which I don't have. When I try the command > like this: > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > lh_V1_v_new.label --regmethod volume > > it does create a new label, which however looks exactly the same as > the previous one. When I change --regmethod to surface, it gives this > error: > ERROR: there is a vertex in the label that cannot be matched to the > surface. This usually occurs when the label and surface are from > different subjects or hemispheres or the surface has been changed > since the label was created. > > I'm not sure about using bbregister for the labels, what would be the > movable volume? And do I then use the register.dat file to load the > labels with? Thanks again for your patience and help. > > Best, > Bianca > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > Hi Bianca, I'm a little confused. What do you mean you registered with > SPM beforehand? If you're using FSFAST, then the registrationis
> done as > part of preproc-sess. The results for both sessions are on the > surface, > so there is no need to do anything to a label created from one session > to show it on another session. > > doug > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > Hi Bruce, > > > > Thank you for your reply. I coregistered the new data beforehand in > > SPM (to the structural of the old session). So I didn't do > anything to > > the label. I displayed the structural with tksurfer-sess -c eccen > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to display my > > eccentricity data) and loaded the label just by clicking load --> > > label. Should I add -reassign in this tksurfer command, or is > there a > > way to load the label with a command, to which I have to add > -reassign? > > > > Also, I'm not familiar with freeview, I tried starting it by typing > > 'freeview' but I get the error: freeview.bin: error while loading > > shared libraries libXss.so.1: cannot open shared object file: No > such > > file or directory. It doesn't seem to depend on which directory > I'm in. > > > > Thanks, > > Bianca > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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>> > <mailto: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 Bianca > > > > how did you coregister the data? Did you map the label so > that it > > is in the coords of the new session? If so, tryspecifying
> > -reassign on the tksurfer command line. That will discard the > > vertex indices in the label (which refer to the first session > > surfaces) and reassign vertex numbers from the current subject. > > This will *only* work if the label is in the correct coordinate > > system. You can verify this by loading it in freeview on top of > > the anatomical from the new session > > cheers > > Bruce > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > Hi Freesurfers, > > > > I have some participants of whom I obtained retinotopic > polar > > angle data in a previous session, and scanned > eccentricity data in > > a later session. I used the polar angle data to define V1-3, > > and would like to display these labels on the > eccentricity session > > to help me define V3A. > > > > However, when I load my old V1-3 labels onto the inflated > > brain based on the new session the labels look very > strange. I > > attached a screenshot of what is supposed to be lh > dorsal V1, > > as you can see it is scattered all over the cortex. When > I load > > the .nii based on the label into MRIcron, the ROI looks > fine. > > > > Data from the newer session were coregistered to the older > > session, so that can't be the problem. > > > > I looked around on the wiki and found the command > > mri_label2label that seemed useful. However, this command > > needs acces to the > > 'surf' folders of both sessions. Due to a computer crash I > > only have the labels of the previous session, not the 'surf' > > folder. > > Is there a way to display my old labels onto the new session > > without needing access to 'surf'? > > > > Thanks, > > Bianca > > > > > > > > > > > > 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. > > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > _______________________________________________ > 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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
Can you re-run recon-all on the polar anatomical? doug
On 07/15/2013 05:01 PM, Bianca van Kemenade wrote:
By that I mean that I only have a normal MPRAGE anatomical scan. By "inflated" I mean that I ran recon-all on this anatomical so that I can display the inflated surface for example. So when I said I inflated the anatomical I meant I ran recon-all. Sorry for the confusing terminology.
On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does that mean? doug On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > Dear Doug & Bruce, > > It's indeed a confusing situation. What it boils down to is: > > - I scanned the polar angle session and the eccentricity session on > different days > - I had defined V1-3 already based on the polar angle session before > scanning eccentricity > - All data from the polar angle session were lost, apart from the V1-3 > labels I made and the anatomical (not inflated) > - Since I now didn't have an inflated brain anymore, I inflated the > anatomical from the eccentricity > - When I tried to overlay the labels onto this newly inflated brain, > the labels were not correctly displayed > > I just tried again by inflating the anatomical from the polar angle > session (instead of eccentricity), and when I use tksurfer P2_BK lh > inflated -reassign the labels are displayed correctly, so that's great > news! > > However, when I display my eccentricity data, with tksurfer-sess -c > eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > wrong again. Adding -reassign doesn't work in this command (flag not > recognised). So at least I could open two terminals, one to display > the inflated brain with correct labels, and one to display the > eccentricity data. This is of course not ideal if I want to draw > labels on the eccentricity screen using the labels displayed in the > other screen as a boundary. So if anyone has an idea how to get the > labels to be displayed correctly with the tksurfer-sess command please > let me know. > > In any case, thank you all for your help so far! > > Best, > Bianca > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > Well the situation is as follows: > > > > I had a polar angle session, of which I only have the labels and the > > anatomical (not inflated) left due to a computer crash. In a > different > > session, I scanned both my main experiment and the eccentricity > runs. > > Since the eccentricity was in the same session as the main > experiment, > > I included those runs in my preprocessing batch in SPM, that is I > > realigned them and coregistered the data to the anatomical of the > > polar angle session. I then inflated the anatomical of this newer > > session (the one with eccentricity) and did my analyses of the > > eccentricity data without using preproc-sess. Apologies if I > wasn't clear. > > > > I thought it should therefore be no problem to overlay the polar > angle > > labels onto the newly inflated anatomical, since this one was > > coregistered to the one from the polar angle session. However the > > labels don't look correct. Should I have inflated the 'old' > anatomical > > instead? Or would I then nevertheless have needed some kind of > > transformation? > > > > I tried mri_label2label, but when I use a command like this: > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK > --scrlabel > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > > > then it requires access to the anatomical in mri/orig from the > > srcsubject (the same subject, old session), which I don't have. > Well I > > do have the .nii anatomical, but it can't read that header > either, it > > probably needs the .mgz one which I don't have. When I try the > command > > like this: > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > > lh_V1_v_new.label --regmethod volume > > > > it does create a new label, which however looks exactly the same as > > the previous one. When I change --regmethod to surface, it gives > this > > error: > > ERROR: there is a vertex in the label that cannot be matched to the > > surface. This usually occurs when the label and surface are from > > different subjects or hemispheres or the surface has been changed > > since the label was created. > > > > I'm not sure about using bbregister for the labels, what would > be the > > movable volume? And do I then use the register.dat file to load the > > labels with? Thanks again for your patience and help. > > > > Best, > > Bianca > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > Hi Bianca, I'm a little confused. What do you mean you > registered with > > SPM beforehand? If you're using FSFAST, then the registration is > > done as > > part of preproc-sess. The results for both sessions are on the > > surface, > > so there is no need to do anything to a label created from > one session > > to show it on another session. > > > > doug > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > Hi Bruce, > > > > > > Thank you for your reply. I coregistered the new data > beforehand in > > > SPM (to the structural of the old session). So I didn't do > > anything to > > > the label. I displayed the structural with tksurfer-sess > -c eccen > > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to > display my > > > eccentricity data) and loaded the label just by clicking > load --> > > > label. Should I add -reassign in this tksurfer command, or is > > there a > > > way to load the label with a command, to which I have to add > > -reassign? > > > > > > Also, I'm not familiar with freeview, I tried starting it > by typing > > > 'freeview' but I get the error: freeview.bin: error while > loading > > > shared libraries libXss.so.1: cannot open shared object > file: No > > such > > > file or directory. It doesn't seem to depend on which > directory > > I'm in. > > > > > > Thanks, > > > Bianca > > > > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto: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 Bianca > > > > > > how did you coregister the data? Did you map the label so > > that it > > > is in the coords of the new session? If so, try specifying > > > -reassign on the tksurfer command line. That will > discard the > > > vertex indices in the label (which refer to the first > session > > > surfaces) and reassign vertex numbers from the current > subject. > > > This will *only* work if the label is in the correct > coordinate > > > system. You can verify this by loading it in freeview > on top of > > > the anatomical from the new session > > > cheers > > > Bruce > > > > > > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > > > Hi Freesurfers, > > > > > > I have some participants of whom I obtained > retinotopic > > polar > > > angle data in a previous session, and scanned > > eccentricity data in > > > a later session. I used the polar angle data to > define V1-3, > > > and would like to display these labels on the > > eccentricity session > > > to help me define V3A. > > > > > > However, when I load my old V1-3 labels onto the > inflated > > > brain based on the new session the labels look very > > strange. I > > > attached a screenshot of what is supposed to be lh > > dorsal V1, > > > as you can see it is scattered all over the > cortex. When > > I load > > > the .nii based on the label into MRIcron, the ROI > looks > > fine. > > > > > > Data from the newer session were coregistered to > the older > > > session, so that can't be the problem. > > > > > > I looked around on the wiki and found the command > > > mri_label2label that seemed useful. However, this > command > > > needs acces to the > > > 'surf' folders of both sessions. Due to a computer > crash I > > > only have the labels of the previous session, not > the 'surf' > > > folder. > > > Is there a way to display my old labels onto the > new session > > > without needing access to 'surf'? > > > > > > Thanks, > > > Bianca > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > Bianca van Kemenade, MSc > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > Klinik für Psychiatrie und Psychotherapie > > > Campus Charité Mitte > > > Charitéplatz 1 > > > 10117 Berlin > > > http://www.mind-and-brain.de/ > > > > > > > > > _______________________________________________ > > > 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>> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto: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 > > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > > _______________________________________________ > 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 Fax: 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I did, but I only managed to get the labels to be displayed correctly when using tksurfer P2_BK lh inflated -reassign and loading the labels on it. When I want to display my eccentricity data with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK and load the labels, the labels are wrong again.
On Mon, Jul 15, 2013 at 11:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Can you re-run recon-all on the polar anatomical? doug
On 07/15/2013 05:01 PM, Bianca van Kemenade wrote:
By that I mean that I only have a normal MPRAGE anatomical scan. By "inflated" I mean that I ran recon-all on this anatomical so that I can display the inflated surface for example. So when I said I inflated the anatomical I meant I ran recon-all. Sorry for the confusing terminology.
On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does that mean? doug On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > Dear Doug & Bruce, > > It's indeed a confusing situation. What it boils down to is: > > - I scanned the polar angle session and the eccentricity session on > different days > - I had defined V1-3 already based on the polar angle sessionbefore
> scanning eccentricity > - All data from the polar angle session were lost, apart from the V1-3 > labels I made and the anatomical (not inflated) > - Since I now didn't have an inflated brain anymore, I inflated the > anatomical from the eccentricity > - When I tried to overlay the labels onto this newly inflatedbrain,
> the labels were not correctly displayed > > I just tried again by inflating the anatomical from the polar angle > session (instead of eccentricity), and when I use tksurfer P2_BK lh > inflated -reassign the labels are displayed correctly, so that's great > news! > > However, when I display my eccentricity data, with tksurfer-sess -c > eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > wrong again. Adding -reassign doesn't work in this command (flagnot
> recognised). So at least I could open two terminals, one to display > the inflated brain with correct labels, and one to display the > eccentricity data. This is of course not ideal if I want to draw > labels on the eccentricity screen using the labels displayed in the > other screen as a boundary. So if anyone has an idea how to get the > labels to be displayed correctly with the tksurfer-sess command please > let me know. > > In any case, thank you all for your help so far! > > Best, > Bianca > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > Well the situation is as follows: > > > > I had a polar angle session, of which I only have the labels and the > > anatomical (not inflated) left due to a computer crash. In a > different > > session, I scanned both my main experiment and the eccentricity > runs. > > Since the eccentricity was in the same session as the main > experiment, > > I included those runs in my preprocessing batch in SPM, that is I > > realigned them and coregistered the data to the anatomical of the > > polar angle session. I then inflated the anatomical of this newer > > session (the one with eccentricity) and did my analyses ofthe
> > eccentricity data without using preproc-sess. Apologies if I > wasn't clear. > > > > I thought it should therefore be no problem to overlay the polar > angle > > labels onto the newly inflated anatomical, since this one was > > coregistered to the one from the polar angle session. However the > > labels don't look correct. Should I have inflated the 'old' > anatomical > > instead? Or would I then nevertheless have needed some kindof
> > transformation? > > > > I tried mri_label2label, but when I use a command like this: > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK > --scrlabel > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > > > then it requires access to the anatomical in mri/orig fromthe
> > srcsubject (the same subject, old session), which I don't have. > Well I > > do have the .nii anatomical, but it can't read that header > either, it > > probably needs the .mgz one which I don't have. When I trythe
> command > > like this: > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > > lh_V1_v_new.label --regmethod volume > > > > it does create a new label, which however looks exactly the same as > > the previous one. When I change --regmethod to surface, it gives > this > > error: > > ERROR: there is a vertex in the label that cannot be matched to the > > surface. This usually occurs when the label and surface are from > > different subjects or hemispheres or the surface has been changed > > since the label was created. > > > > I'm not sure about using bbregister for the labels, whatwould
> be the > > movable volume? And do I then use the register.dat file to load the > > labels with? Thanks again for your patience and help. > > > > Best, > > Bianca > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > Hi Bianca, I'm a little confused. What do you mean you > registered with > > SPM beforehand? If you're using FSFAST, then the registration is > > done as > > part of preproc-sess. The results for both sessions are on the > > surface, > > so there is no need to do anything to a label createdfrom
> one session > > to show it on another session. > > > > doug > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > Hi Bruce, > > > > > > Thank you for your reply. I coregistered the new data > beforehand in > > > SPM (to the structural of the old session). So I didn't do > > anything to > > > the label. I displayed the structural withtksurfer-sess
> -c eccen > > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to > display my > > > eccentricity data) and loaded the label just byclicking
> load --> > > > label. Should I add -reassign in this tksurfer command, or is > > there a > > > way to load the label with a command, to which I have to add > > -reassign? > > > > > > Also, I'm not familiar with freeview, I tried starting it > by typing > > > 'freeview' but I get the error: freeview.bin: error while > loading > > > shared libraries libXss.so.1: cannot open shared object > file: No > > such > > > file or directory. It doesn't seem to depend on which > directory > > I'm in. > > > > > > Thanks, > > > Bianca > > > > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto: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 Bianca > > > > > > how did you coregister the data? Did you map the label so > > that it > > > is in the coords of the new session? If so, try specifying > > > -reassign on the tksurfer command line. That will > discard the > > > vertex indices in the label (which refer to the first > session > > > surfaces) and reassign vertex numbers from the current > subject. > > > This will *only* work if the label is in thecorrect
> coordinate > > > system. You can verify this by loading it in freeview > on top of > > > the anatomical from the new session > > > cheers > > > Bruce > > > > > > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > > > Hi Freesurfers, > > > > > > I have some participants of whom I obtained > retinotopic > > polar > > > angle data in a previous session, and scanned > > eccentricity data in > > > a later session. I used the polar angle data to > define V1-3, > > > and would like to display these labels on the > > eccentricity session > > > to help me define V3A. > > > > > > However, when I load my old V1-3 labels ontothe
> inflated > > > brain based on the new session the labels look very > > strange. I > > > attached a screenshot of what is supposed to be lh > > dorsal V1, > > > as you can see it is scattered all over the > cortex. When > > I load > > > the .nii based on the label into MRIcron, the ROI > looks > > fine. > > > > > > Data from the newer session were coregisteredto
> the older > > > session, so that can't be the problem. > > > > > > I looked around on the wiki and found the command > > > mri_label2label that seemed useful. However, this > command > > > needs acces to the > > > 'surf' folders of both sessions. Due to a computer > crash I > > > only have the labels of the previous session, not > the 'surf' > > > folder. > > > Is there a way to display my old labels ontothe
> new session > > > without needing access to 'surf'? > > > > > > Thanks, > > > Bianca > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > Bianca van Kemenade, MSc > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > Klinik für Psychiatrie und Psychotherapie > > > Campus Charité Mitte > > > Charitéplatz 1 > > > 10117 Berlin > > > http://www.mind-and-brain.de/ > > > > > > > > > _______________________________________________ > > > 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>> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto: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 > > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > > _______________________________________________ > 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 Fax: 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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
Hi, I was wondering whether anyone would still have a tip for this problem?
So far I'm just using " tksurfer P2_BK lh inflated -reassign" and loading the labels on it in one window, and displaying my functional eccentricity data with "tksurfer-sess ....." in a new window. I can sort of draw V3A on the functional data by closely looking at the other window to see where my previously defined V3 is, but it would be great if I could actually load my previously defined labels on the functional data instead.
Thanks! Bianca
On Tue, Jul 16, 2013 at 10:35 AM, Bianca van Kemenade < biancavankemenade@gmail.com> wrote:
I did, but I only managed to get the labels to be displayed correctly when using tksurfer P2_BK lh inflated -reassign and loading the labels on it. When I want to display my eccentricity data with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK and load the labels, the labels are wrong again.
On Mon, Jul 15, 2013 at 11:19 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Can you re-run recon-all on the polar anatomical? doug
On 07/15/2013 05:01 PM, Bianca van Kemenade wrote:
By that I mean that I only have a normal MPRAGE anatomical scan. By "inflated" I mean that I ran recon-all on this anatomical so that I can display the inflated surface for example. So when I said I inflated the anatomical I meant I ran recon-all. Sorry for the confusing terminology.
On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does thatmean?
doug On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > Dear Doug & Bruce, > > It's indeed a confusing situation. What it boils down to is: > > - I scanned the polar angle session and the eccentricity sessionon
> different days > - I had defined V1-3 already based on the polar angle sessionbefore
> scanning eccentricity > - All data from the polar angle session were lost, apart from the V1-3 > labels I made and the anatomical (not inflated) > - Since I now didn't have an inflated brain anymore, I inflatedthe
> anatomical from the eccentricity > - When I tried to overlay the labels onto this newly inflatedbrain,
> the labels were not correctly displayed > > I just tried again by inflating the anatomical from the polarangle
> session (instead of eccentricity), and when I use tksurfer P2_BKlh
> inflated -reassign the labels are displayed correctly, so that's great > news! > > However, when I display my eccentricity data, with tksurfer-sess-c
> eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > wrong again. Adding -reassign doesn't work in this command (flagnot
> recognised). So at least I could open two terminals, one todisplay
> the inflated brain with correct labels, and one to display the > eccentricity data. This is of course not ideal if I want to draw > labels on the eccentricity screen using the labels displayed inthe
> other screen as a boundary. So if anyone has an idea how to getthe
> labels to be displayed correctly with the tksurfer-sess command please > let me know. > > In any case, thank you all for your help so far! > > Best, > Bianca > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > Well the situation is as follows: > > > > I had a polar angle session, of which I only have the labels and the > > anatomical (not inflated) left due to a computer crash. In a > different > > session, I scanned both my main experiment and the eccentricity > runs. > > Since the eccentricity was in the same session as the main > experiment, > > I included those runs in my preprocessing batch in SPM, that is I > > realigned them and coregistered the data to the anatomical of the > > polar angle session. I then inflated the anatomical of this newer > > session (the one with eccentricity) and did my analyses ofthe
> > eccentricity data without using preproc-sess. Apologies if I > wasn't clear. > > > > I thought it should therefore be no problem to overlay the polar > angle > > labels onto the newly inflated anatomical, since this onewas
> > coregistered to the one from the polar angle session. However the > > labels don't look correct. Should I have inflated the 'old' > anatomical > > instead? Or would I then nevertheless have needed some kindof
> > transformation? > > > > I tried mri_label2label, but when I use a command like this: > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK > --scrlabel > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethodvolume
> > > > then it requires access to the anatomical in mri/orig fromthe
> > srcsubject (the same subject, old session), which I don't have. > Well I > > do have the .nii anatomical, but it can't read that header > either, it > > probably needs the .mgz one which I don't have. When I trythe
> command > > like this: > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label--trglabel
> > lh_V1_v_new.label --regmethod volume > > > > it does create a new label, which however looks exactly the same as > > the previous one. When I change --regmethod to surface, it gives > this > > error: > > ERROR: there is a vertex in the label that cannot be matched to the > > surface. This usually occurs when the label and surface are from > > different subjects or hemispheres or the surface has been changed > > since the label was created. > > > > I'm not sure about using bbregister for the labels, whatwould
> be the > > movable volume? And do I then use the register.dat file to load the > > labels with? Thanks again for your patience and help. > > > > Best, > > Bianca > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > Hi Bianca, I'm a little confused. What do you mean you > registered with > > SPM beforehand? If you're using FSFAST, then the registration is > > done as > > part of preproc-sess. The results for both sessions are on the > > surface, > > so there is no need to do anything to a label createdfrom
> one session > > to show it on another session. > > > > doug > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > Hi Bruce, > > > > > > Thank you for your reply. I coregistered the new data > beforehand in > > > SPM (to the structural of the old session). So I didn't do > > anything to > > > the label. I displayed the structural withtksurfer-sess
> -c eccen > > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to > display my > > > eccentricity data) and loaded the label just byclicking
> load --> > > > label. Should I add -reassign in this tksurfer command, or is > > there a > > > way to load the label with a command, to which I have to add > > -reassign? > > > > > > Also, I'm not familiar with freeview, I tried starting it > by typing > > > 'freeview' but I get the error: freeview.bin: error while > loading > > > shared libraries libXss.so.1: cannot open sharedobject
> file: No > > such > > > file or directory. It doesn't seem to depend on which > directory > > I'm in. > > > > > > Thanks, > > > Bianca > > > > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto: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 Bianca > > > > > > how did you coregister the data? Did you map the label so > > that it > > > is in the coords of the new session? If so, try specifying > > > -reassign on the tksurfer command line. That will > discard the > > > vertex indices in the label (which refer to the first > session > > > surfaces) and reassign vertex numbers from the current > subject. > > > This will *only* work if the label is in thecorrect
> coordinate > > > system. You can verify this by loading it in freeview > on top of > > > the anatomical from the new session > > > cheers > > > Bruce > > > > > > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > > > Hi Freesurfers, > > > > > > I have some participants of whom I obtained > retinotopic > > polar > > > angle data in a previous session, and scanned > > eccentricity data in > > > a later session. I used the polar angle datato
> define V1-3, > > > and would like to display these labels on the > > eccentricity session > > > to help me define V3A. > > > > > > However, when I load my old V1-3 labels ontothe
> inflated > > > brain based on the new session the labels look very > > strange. I > > > attached a screenshot of what is supposed to be lh > > dorsal V1, > > > as you can see it is scattered all over the > cortex. When > > I load > > > the .nii based on the label into MRIcron, the ROI > looks > > fine. > > > > > > Data from the newer session were coregisteredto
> the older > > > session, so that can't be the problem. > > > > > > I looked around on the wiki and found the command > > > mri_label2label that seemed useful. However, this > command > > > needs acces to the > > > 'surf' folders of both sessions. Due to a computer > crash I > > > only have the labels of the previous session, not > the 'surf' > > > folder. > > > Is there a way to display my old labels ontothe
> new session > > > without needing access to 'surf'? > > > > > > Thanks, > > > Bianca > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > Bianca van Kemenade, MSc > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > Klinik für Psychiatrie und Psychotherapie > > > Campus Charité Mitte > > > Charitéplatz 1 > > > 10117 Berlin > > > http://www.mind-and-brain.de/ > > > > > > > > > _______________________________________________ > > > 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>> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto: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
> > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > _______________________________________________ > > 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
> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > > _______________________________________________ > 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 Fax: 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-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Hi Bianca
can you run tksurfer with -reassign, then save the label?
cheers Bruce
On Mon, 29 Jul 2013, Bianca van Kemenade wrote:
Hi, I was wondering whether anyone would still have a tip for this problem?
So far I'm just using " tksurfer P2_BK lh inflated -reassign" and loading the labels on it in one window, and displaying my functional eccentricity data with "tksurfer-sess ....." in a new window. I can sort of draw V3A on the functional data by closely looking at the other window to see where my previously defined V3 is, but it would be great if I could actually load my previously defined labels on the functional data instead.
Thanks! Bianca
On Tue, Jul 16, 2013 at 10:35 AM, Bianca van Kemenade biancavankemenade@gmail.com wrote: I did, but I only managed to get the labels to be displayed correctly when using tksurfer P2_BK lh inflated -reassign and loading the labels on it. When I want to display my eccentricity data with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK and load the labels, the labels are wrong again.
On Mon, Jul 15, 2013 at 11:19 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Can you re-run recon-all on the polar anatomical? doug
On 07/15/2013 05:01 PM, Bianca van Kemenade wrote: > By that I mean that I only have a normal MPRAGE anatomical scan. By > "inflated" I mean that I ran recon-all on this anatomical so that I > can display the inflated surface for example. So when I said I > inflated the anatomical I meant I ran recon-all. Sorry for the > confusing terminology. > > > On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does that mean? doug
On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > Dear Doug & Bruce, > > It's indeed a confusing situation. What it boils down to is: > > - I scanned the polar angle session and the eccentricity session on > different days > - I had defined V1-3 already based on the polar angle session before > scanning eccentricity > - All data from the polar angle session were lost, apart from the V1-3 > labels I made and the anatomical (not inflated) > - Since I now didn't have an inflated brain anymore, I inflated the > anatomical from the eccentricity > - When I tried to overlay the labels onto this newly inflated brain, > the labels were not correctly displayed > > I just tried again by inflating the anatomical from the polar angle > session (instead of eccentricity), and when I use tksurfer P2_BK lh > inflated -reassign the labels are displayed correctly, so that's great > news! > > However, when I display my eccentricity data, with tksurfer-sess -c > eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > wrong again. Adding -reassign doesn't work in this command (flag not > recognised). So at least I could open two terminals, one to display > the inflated brain with correct labels, and one to display the > eccentricity data. This is of course not ideal if I want to draw > labels on the eccentricity screen using the labels displayed in the > other screen as a boundary. So if anyone has an idea how to get the > labels to be displayed correctly with the tksurfer-sess command please > let me know. > > In any case, thank you all for your help so far! > > Best, > Bianca > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > Well the situation is as follows: > > > > I had a polar angle session, of which I only have the labels and the > > anatomical (not inflated) left due to a computer crash. In a > different > > session, I scanned both my main experiment and the eccentricity > runs. > > Since the eccentricity was in the same session as the main > experiment, > > I included those runs in my preprocessing batch in SPM, that is I > > realigned them and coregistered the data to the anatomical of the > > polar angle session. I then inflated the anatomical of this newer > > session (the one with eccentricity) and did my analyses of the > > eccentricity data without using preproc-sess. Apologies if I > wasn't clear. > > > > I thought it should therefore be no problem to overlay the polar > angle > > labels onto the newly inflated anatomical, since this one was > > coregistered to the one from the polar angle session. However the > > labels don't look correct. Should I have inflated the 'old' > anatomical > > instead? Or would I then nevertheless have needed some kind of > > transformation? > > > > I tried mri_label2label, but when I use a command like this: > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK > --scrlabel > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > > > then it requires access to the anatomical in mri/orig from the > > srcsubject (the same subject, old session), which I don't have. > Well I > > do have the .nii anatomical, but it can't read that header > either, it > > probably needs the .mgz one which I don't have. When I try the > command > > like this: > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > > lh_V1_v_new.label --regmethod volume > > > > it does create a new label, which however looks exactly the same as > > the previous one. When I change --regmethod to surface, it gives > this > > error: > > ERROR: there is a vertex in the label that cannot be matched to the > > surface. This usually occurs when the label and surface are from > > different subjects or hemispheres or the surface has been changed > > since the label was created. > > > > I'm not sure about using bbregister for the labels, what would > be the > > movable volume? And do I then use the register.dat file to load the > > labels with? Thanks again for your patience and help. > > > > Best, > > Bianca > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > > > Hi Bianca, I'm a little confused. What do you mean you > registered with > > SPM beforehand? If you're using FSFAST, then the registration is > > done as > > part of preproc-sess. The results for both sessions are on the > > surface, > > so there is no need to do anything to a label created from > one session > > to show it on another session. > > > > doug > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > Hi Bruce, > > > > > > Thank you for your reply. I coregistered the new data > beforehand in > > > SPM (to the structural of the old session). So I didn't do > > anything to > > > the label. I displayed the structural with tksurfer-sess > -c eccen > > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to > display my > > > eccentricity data) and loaded the label just by clicking > load --> > > > label. Should I add -reassign in this tksurfer command, or is > > there a > > > way to load the label with a command, to which I have to add > > -reassign? > > > > > > Also, I'm not familiar with freeview, I tried starting it > by typing > > > 'freeview' but I get the error: freeview.bin: error while > loading > > > shared libraries libXss.so.1: cannot open shared object > file: No > > such > > > file or directory. It doesn't seem to depend on which > directory > > I'm in. > > > > > > Thanks, > > > Bianca > > > > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > > <mailto: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 Bianca > > > > > > how did you coregister the data? Did you map the label so > > that it > > > is in the coords of the new session? If so, try specifying > > > -reassign on the tksurfer command line. That will > discard the > > > vertex indices in the label (which refer to the first > session > > > surfaces) and reassign vertex numbers from the current > subject. > > > This will *only* work if the label is in the correct > coordinate > > > system. You can verify this by loading it in freeview > on top of > > > the anatomical from the new session > > > cheers > > > Bruce > > > > > > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > > > Hi Freesurfers, > > > > > > I have some participants of whom I obtained > retinotopic > > polar > > > angle data in a previous session, and scanned > > eccentricity data in > > > a later session. I used the polar angle data to > define V1-3, > > > and would like to display these labels on the > > eccentricity session > > > to help me define V3A. > > > > > > However, when I load my old V1-3 labels onto the > inflated > > > brain based on the new session the labels look very > > strange. I > > > attached a screenshot of what is supposed to be lh > > dorsal V1, > > > as you can see it is scattered all over the > cortex. When > > I load > > > the .nii based on the label into MRIcron, the ROI > looks > > fine. > > > > > > Data from the newer session were coregistered to > the older > > > session, so that can't be the problem. > > > > > > I looked around on the wiki and found the command > > > mri_label2label that seemed useful. However, this > command > > > needs acces to the > > > 'surf' folders of both sessions. Due to a computer > crash I > > > only have the labels of the previous session, not > the 'surf' > > > folder. > > > Is there a way to display my old labels onto the > new session > > > without needing access to 'surf'? > > > > > > Thanks, > > > Bianca > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > Bianca van Kemenade, MSc > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > Klinik für Psychiatrie und Psychotherapie > > > Campus Charité Mitte > > > Charitéplatz 1 > > > 10117 Berlin > > > http://www.mind-and-brain.de/ > > > > > > > > > _______________________________________________ > > > 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> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 tel:617-724-2358 <tel:617-724-2358 tel:617-724-2358> > <tel:617-724-2358 tel:617-724-2358 <tel:617-724-2358 tel:617-724-2358>> > > Fax: 617-726-7422 tel:617-726-7422 <tel:617-726-7422 tel:617-726-7422> <tel:617-726-7422 tel:617-726-7422 > <tel:617-726-7422 tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > http://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 > http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 tel:617-724-2358 <tel:617-724-2358 tel:617-724-2358> > Fax: 617-726-7422 tel:617-726-7422 <tel:617-726-7422 tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > > _______________________________________________ > 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 Fax: 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
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
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
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
Silly that I didn't think of that, that seems to do the trick! Thank you very much!
Best, Bianca
On Mon, Jul 29, 2013 at 5:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Bianca
can you run tksurfer with -reassign, then save the label?
cheers Bruce
On Mon, 29 Jul 2013, Bianca van Kemenade wrote:
Hi, I was wondering whether anyone would still have a tip for this
problem?
So far I'm just using " tksurfer P2_BK lh inflated -reassign" and loading the labels on it in one window, and displaying my functional eccentricity data with "tksurfer-sess ....." in a new window. I can sort of draw V3A on the functional data by closely looking at the other window to see where my previously defined V3 is, but it would be great if I could actually load my previously defined labels on the functional data instead.
Thanks! Bianca
On Tue, Jul 16, 2013 at 10:35 AM, Bianca van Kemenade < biancavankemenade@gmail.com> wrote: I did, but I only managed to get the labels to be displayed correctly when using tksurfer P2_BK lh inflated -reassign and loading the labels on it. When I want to display my eccentricity data with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK and load the labels, the labels are wrong again.
On Mon, Jul 15, 2013 at 11:19 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote: Can you re-run recon-all on the polar anatomical? doug
On 07/15/2013 05:01 PM, Bianca van Kemenade wrote: > By that I mean that I only have a normal MPRAGE anatomical scan.By > "inflated" I mean that I ran recon-all on this anatomical so that I > can display the inflated surface for example. So when I said I > inflated the anatomical I meant I ran recon-all. Sorry for the > confusing terminology. > > > On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>>
wrote:
Hi Bianca, I still don't understand how you have the anatomical from the polar session but you don't have the "inflated". What does thatmean?
doug On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > Dear Doug & Bruce, > > It's indeed a confusing situation. What it boils down to is: > > - I scanned the polar angle session and the eccentricity sessionon
> different days > - I had defined V1-3 already based on the polar angle sessionbefore
> scanning eccentricity > - All data from the polar angle session were lost, apart from the V1-3 > labels I made and the anatomical (not inflated) > - Since I now didn't have an inflated brain anymore, I inflatedthe
> anatomical from the eccentricity > - When I tried to overlay the labels onto this newly inflatedbrain,
> the labels were not correctly displayed > > I just tried again by inflating the anatomical from the polarangle
> session (instead of eccentricity), and when I use tksurfer P2_BKlh
> inflated -reassign the labels are displayed correctly, so that's great > news! > > However, when I display my eccentricity data, with tksurfer-sess-c
> eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > wrong again. Adding -reassign doesn't work in this command (flagnot
> recognised). So at least I could open two terminals, one todisplay
> the inflated brain with correct labels, and one to display the > eccentricity data. This is of course not ideal if I want to draw > labels on the eccentricity screen using the labels displayed inthe
> other screen as a boundary. So if anyone has an idea how to getthe
> labels to be displayed correctly with the tksurfer-sess command please > let me know. > > In any case, thank you all for your help so far! > > Best, > Bianca > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
> > Hi Bianca, I'm still unclear what it is you have done. > > You only need to run freesurfer on one of the anatomicals, it does not > matter which one. > > You should not do anything to the fMRI runs (eg, align with SPM). You > should put your eccen and polar data into a single bold folder under > your session folder. > > Then run preproc-sess. > > I'm not sure how this overlaps with what you have done > > doug > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > Well the situation is as follows: > > > > I had a polar angle session, of which I only have the labels and the > > anatomical (not inflated) left due to a computer crash. In a > different > > session, I scanned both my main experiment and the eccentricity > runs. > > Since the eccentricity was in the same session as the main > experiment, > > I included those runs in my preprocessing batch in SPM, that is I > > realigned them and coregistered the data to the anatomical of the > > polar angle session. I then inflated the anatomical of this newer > > session (the one with eccentricity) and did my analyses ofthe
> > eccentricity data without using preproc-sess. Apologies if I > wasn't clear. > > > > I thought it should therefore be no problem to overlay the polar > angle > > labels onto the newly inflated anatomical, since this onewas
> > coregistered to the one from the polar angle session. However the > > labels don't look correct. Should I have inflated the 'old' > anatomical > > instead? Or would I then nevertheless have needed some kindof
> > transformation? > > > > I tried mri_label2label, but when I use a command like this: > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK > --scrlabel > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethodvolume
> > > > then it requires access to the anatomical in mri/orig fromthe
> > srcsubject (the same subject, old session), which I don't have. > Well I > > do have the .nii anatomical, but it can't read that header > either, it > > probably needs the .mgz one which I don't have. When I trythe
> command > > like this: > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label--trglabel
> > lh_V1_v_new.label --regmethod volume > > > > it does create a new label, which however looks exactly the same as > > the previous one. When I change --regmethod to surface, it gives > this > > error: > > ERROR: there is a vertex in the label that cannot be matched to the > > surface. This usually occurs when the label and surface are from > > different subjects or hemispheres or the surface has been changed > > since the label was created. > > > > I'm not sure about using bbregister for the labels, whatwould
> be the > > movable volume? And do I then use the register.dat file to load the > > labels with? Thanks again for your patience and help. > > > > Best, > > Bianca > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>wrote:
> > > > > > Hi Bianca, I'm a little confused. What do you mean you > registered with > > SPM beforehand? If you're using FSFAST, then the registration is > > done as > > part of preproc-sess. The results for both sessions are on the > > surface, > > so there is no need to do anything to a label createdfrom
> one session > > to show it on another session. > > > > doug > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > Hi Bruce, > > > > > > Thank you for your reply. I coregistered the new data > beforehand in > > > SPM (to the structural of the old session). So I didn't do > > anything to > > > the label. I displayed the structural withtksurfer-sess
> -c eccen > > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I wanted to > display my > > > eccentricity data) and loaded the label just byclicking
> load --> > > > label. Should I add -reassign in this tksurfer command, or is > > there a > > > way to load the label with a command, to which I have to add > > -reassign? > > > > > > Also, I'm not familiar with freeview, I tried starting it > by typing > > > 'freeview' but I get the error: freeview.bin: error while > loading > > > shared libraries libXss.so.1: cannot open sharedobject
> file: No > > such > > > file or directory. It doesn't seem to depend on which > directory > > I'm in. > > > > > > Thanks, > > > Bianca > > > > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, Bruce Fischl > > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>>> > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>>> > > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>>>>>>wrote:
> > > > > > Hi Bianca > > > > > > how did you coregister the data? Did you map the label so > > that it > > > is in the coords of the new session? If so, try specifying > > > -reassign on the tksurfer command line. That will > discard the > > > vertex indices in the label (which refer to the first > session > > > surfaces) and reassign vertex numbers from the current > subject. > > > This will *only* work if the label is in thecorrect
> coordinate > > > system. You can verify this by loading it in freeview > on top of > > > the anatomical from the new session > > > cheers > > > Bruce > > > > > > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > > > Hi Freesurfers, > > > > > > I have some participants of whom I obtained > retinotopic > > polar > > > angle data in a previous session, and scanned > > eccentricity data in > > > a later session. I used the polar angle datato
> define V1-3, > > > and would like to display these labels on the > > eccentricity session > > > to help me define V3A. > > > > > > However, when I load my old V1-3 labels ontothe
> inflated > > > brain based on the new session the labels look very > > strange. I > > > attached a screenshot of what is supposed to be lh > > dorsal V1, > > > as you can see it is scattered all over the > cortex. When > > I load > > > the .nii based on the label into MRIcron, the ROI > looks > > fine. > > > > > > Data from the newer session were coregisteredto
> the older > > > session, so that can't be the problem. > > > > > > I looked around on the wiki and found the command > > > mri_label2label that seemed useful. However, this > command > > > needs acces to the > > > 'surf' folders of both sessions. Due to a computer > crash I > > > only have the labels of the previous session, not > the 'surf' > > > folder. > > > Is there a way to display my old labels ontothe
> new session > > > without needing access to 'surf'? > > > > > > Thanks, > > > Bianca > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > Bianca van Kemenade, MSc > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > Klinik für Psychiatrie und Psychotherapie > > > Campus Charité Mitte > > > Charitéplatz 1 > > > 10117 Berlin > > > http://www.mind-and-brain.de/ > > > > > > > > > ______________________________**_________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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 <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>>
> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > ______________________________**_________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > ______________________________**_________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
sure, glad it finally worked Bruce On Mon, 29 Jul 2013, Bianca van Kemenade wrote:
Silly that I didn't think of that, that seems to do the trick! Thank you very much!
Best, Bianca
On Mon, Jul 29, 2013 at 5:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Bianca
can you run tksurfer with -reassign, then save the label? cheers Bruce On Mon, 29 Jul 2013, Bianca van Kemenade wrote: Hi, I was wondering whether anyone would still have a tip for this problem? So far I'm just using " tksurfer P2_BK lh inflated -reassign" and loading the labels on it in one window, and displaying my functional eccentricity data with "tksurfer-sess ....." in a new window. I can sort of draw V3A on the functional data by closely looking at the other window to see where my previously defined V3 is, but it would be great if I could actually load my previously defined labels on the functional data instead. Thanks! Bianca On Tue, Jul 16, 2013 at 10:35 AM, Bianca van Kemenade <biancavankemenade@gmail.com> wrote: I did, but I only managed to get the labels to be displayed correctly when using tksurfer P2_BK lh inflated -reassign and loading the labels on it. When I want to display my eccentricity data with tksurfer-sess -c eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK and load the labels, the labels are wrong again. On Mon, Jul 15, 2013 at 11:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: Can you re-run recon-all on the polar anatomical? doug On 07/15/2013 05:01 PM, Bianca van Kemenade wrote: > By that I mean that I only have a normal MPRAGE anatomical scan. By > "inflated" I mean that I ran recon-all on this anatomical so that I > can display the inflated surface for example. So when I said I > inflated the anatomical I meant I ran recon-all. Sorry for the > confusing terminology. > > > On Mon, Jul 15, 2013 at 8:12 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Bianca, I still don't understand how you have the anatomical > from the > polar session but you don't have the "inflated". What does that mean? > doug > > On 07/14/2013 09:52 AM, Bianca van Kemenade wrote: > > Dear Doug & Bruce, > > > > It's indeed a confusing situation. What it boils down to is: > > > > - I scanned the polar angle session and the eccentricity session on > > different days > > - I had defined V1-3 already based on the polar angle session before > > scanning eccentricity > > - All data from the polar angle session were lost, apart from > the V1-3 > > labels I made and the anatomical (not inflated) > > - Since I now didn't have an inflated brain anymore, I inflated the > > anatomical from the eccentricity > > - When I tried to overlay the labels onto this newly inflated brain, > > the labels were not correctly displayed > > > > I just tried again by inflating the anatomical from the polar angle > > session (instead of eccentricity), and when I use tksurfer P2_BK lh > > inflated -reassign the labels are displayed correctly, so that's > great > > news! > > > > However, when I display my eccentricity data, with tksurfer-sess -c > > eccen -fthresh 0.5 -a rtopy.self.lh.eccen -s P2_BK, the labels are > > wrong again. Adding -reassign doesn't work in this command (flag not > > recognised). So at least I could open two terminals, one to display > > the inflated brain with correct labels, and one to display the > > eccentricity data. This is of course not ideal if I want to draw > > labels on the eccentricity screen using the labels displayed in the > > other screen as a boundary. So if anyone has an idea how to get the > > labels to be displayed correctly with the tksurfer-sess command > please > > let me know. > > > > In any case, thank you all for your help so far! > > > > Best, > > Bianca > > > > > > > > > > On Fri, Jul 12, 2013 at 7:47 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > Hi Bianca, I'm still unclear what it is you have done. > > > > You only need to run freesurfer on one of the anatomicals, > it does not > > matter which one. > > > > You should not do anything to the fMRI runs (eg, align with > SPM). You > > should put your eccen and polar data into a single bold > folder under > > your session folder. > > > > Then run preproc-sess. > > > > I'm not sure how this overlaps with what you have done > > > > doug > > > > > > On 07/11/2013 05:10 AM, Bianca van Kemenade wrote: > > > Well the situation is as follows: > > > > > > I had a polar angle session, of which I only have the > labels and the > > > anatomical (not inflated) left due to a computer crash. In a > > different > > > session, I scanned both my main experiment and the > eccentricity > > runs. > > > Since the eccentricity was in the same session as the main > > experiment, > > > I included those runs in my preprocessing batch in SPM, > that is I > > > realigned them and coregistered the data to the anatomical > of the > > > polar angle session. I then inflated the anatomical of > this newer > > > session (the one with eccentricity) and did my analyses of the > > > eccentricity data without using preproc-sess. Apologies if I > > wasn't clear. > > > > > > I thought it should therefore be no problem to overlay the > polar > > angle > > > labels onto the newly inflated anatomical, since this one was > > > coregistered to the one from the polar angle session. > However the > > > labels don't look correct. Should I have inflated the 'old' > > anatomical > > > instead? Or would I then nevertheless have needed some kind of > > > transformation? > > > > > > I tried mri_label2label, but when I use a command like this: > > > > > > mri_label2label --srcsubject P2_BK_test --trgsubject P2_BK > > --scrlabel > > > lh_V1_v.label --trglabel lh_V1_v_new.label --regmethod volume > > > > > > then it requires access to the anatomical in mri/orig from the > > > srcsubject (the same subject, old session), which I don't > have. > > Well I > > > do have the .nii anatomical, but it can't read that header > > either, it > > > probably needs the .mgz one which I don't have. When I try the > > command > > > like this: > > > > > > mri_label2label --s P2_BK --scrlabel lh_V1_v.label --trglabel > > > lh_V1_v_new.label --regmethod volume > > > > > > it does create a new label, which however looks exactly > the same as > > > the previous one. When I change --regmethod to surface, it > gives > > this > > > error: > > > ERROR: there is a vertex in the label that cannot be > matched to the > > > surface. This usually occurs when the label and surface > are from > > > different subjects or hemispheres or the surface has been > changed > > > since the label was created. > > > > > > I'm not sure about using bbregister for the labels, what would > > be the > > > movable volume? And do I then use the register.dat file to > load the > > > labels with? Thanks again for your patience and help. > > > > > > Best, > > > Bianca > > > > > > > > > > > > > > > On Wed, Jul 10, 2013 at 6:24 PM, Douglas N Greve > > > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > > > > Hi Bianca, I'm a little confused. What do you mean you > > registered with > > > SPM beforehand? If you're using FSFAST, then the > registration is > > > done as > > > part of preproc-sess. The results for both sessions > are on the > > > surface, > > > so there is no need to do anything to a label created from > > one session > > > to show it on another session. > > > > > > doug > > > > > > > > > > > > > > > On 07/10/2013 11:55 AM, Bianca van Kemenade wrote: > > > > Hi Bruce, > > > > > > > > Thank you for your reply. I coregistered the new data > > beforehand in > > > > SPM (to the structural of the old session). So I > didn't do > > > anything to > > > > the label. I displayed the structural with tksurfer-sess > > -c eccen > > > > -fthresh 0.5 -a rtopy.self.lh -s P2_BK (since I > wanted to > > display my > > > > eccentricity data) and loaded the label just by clicking > > load --> > > > > label. Should I add -reassign in this tksurfer > command, or is > > > there a > > > > way to load the label with a command, to which I > have to add > > > -reassign? > > > > > > > > Also, I'm not familiar with freeview, I tried > starting it > > by typing > > > > 'freeview' but I get the error: freeview.bin: error > while > > loading > > > > shared libraries libXss.so.1: cannot open shared object > > file: No > > > such > > > > file or directory. It doesn't seem to depend on which > > directory > > > I'm in. > > > > > > > > Thanks, > > > > Bianca > > > > > > > > > > > > On Wed, Jul 10, 2013 at 5:19 PM, 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>> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > > <mailto: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 Bianca > > > > > > > > how did you coregister the data? Did you map the > label so > > > that it > > > > is in the coords of the new session? If so, try > specifying > > > > -reassign on the tksurfer command line. That will > > discard the > > > > vertex indices in the label (which refer to the > first > > session > > > > surfaces) and reassign vertex numbers from the > current > > subject. > > > > This will *only* work if the label is in the correct > > coordinate > > > > system. You can verify this by loading it in > freeview > > on top of > > > > the anatomical from the new session > > > > cheers > > > > Bruce > > > > > > > > > > > > > > > > > > > > On Wed, 10 Jul 2013, Bianca van Kemenade wrote: > > > > > > > > Hi Freesurfers, > > > > > > > > I have some participants of whom I obtained > > retinotopic > > > polar > > > > angle data in a previous session, and scanned > > > eccentricity data in > > > > a later session. I used the polar angle data to > > define V1-3, > > > > and would like to display these labels on the > > > eccentricity session > > > > to help me define V3A. > > > > > > > > However, when I load my old V1-3 labels onto the > > inflated > > > > brain based on the new session the labels > look very > > > strange. I > > > > attached a screenshot of what is supposed to > be lh > > > dorsal V1, > > > > as you can see it is scattered all over the > > cortex. When > > > I load > > > > the .nii based on the label into MRIcron, > the ROI > > looks > > > fine. > > > > > > > > Data from the newer session were coregistered to > > the older > > > > session, so that can't be the problem. > > > > > > > > I looked around on the wiki and found the > command > > > > mri_label2label that seemed useful. However, > this > > command > > > > needs acces to the > > > > 'surf' folders of both sessions. Due to a > computer > > crash I > > > > only have the labels of the previous > session, not > > the 'surf' > > > > folder. > > > > Is there a way to display my old labels onto the > > new session > > > > without needing access to 'surf'? > > > > > > > > Thanks, > > > > Bianca > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > -- > > > > Bianca van Kemenade, MSc > > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > > > Klinik für Psychiatrie und Psychotherapie > > > > Campus Charité Mitte > > > > Charitéplatz 1 > > > > 10117 Berlin > > > > http://www.mind-and-brain.de/ > > > > > > > > > > > > _______________________________________________ > > > > 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>> > > > <mailto: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 > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <http://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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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 > > > > > > > > > > > > > > > -- > > > Bianca van Kemenade, MSc > > > Doctoral Candidate, Berlin School of Mind and Brain > > > > > > Klinik für Psychiatrie und Psychotherapie > > > Campus Charité Mitte > > > Charitéplatz 1 > > > 10117 Berlin > > > http://www.mind-and-brain.de/ > > > > > > > > > _______________________________________________ > > > 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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Bianca van Kemenade, MSc > > Doctoral Candidate, Berlin School of Mind and Brain > > > > Klinik für Psychiatrie und Psychotherapie > > Campus Charité Mitte > > Charitéplatz 1 > > 10117 Berlin > > http://www.mind-and-brain.de/ > > > > > > > > _______________________________________________ > > 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 > Fax: 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 > > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > _______________________________________________ > 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 -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/ -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/-- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain
Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/
freesurfer@nmr.mgh.harvard.edu
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Bianca van Kemenade -
Bruce Fischl -
Douglas N Greve