Hi All!
Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile
Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format should my output be for mri_vol2surf?
many thanks!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
I'm not sure what identity.nofile is or what you are trying to do (no previous info in the email). If whatever you are trying to map to the surface is already in anatomical space (so no registration necessary), then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume format as input (ie, mgz, nii.gz ,etc)
On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
Hi All!
Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile
Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format should my output be for mri_vol2surf?
many thanks!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug
below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the transformation since my labels and T1s are already in the same space and I just want to resample my labels to the surfaces.
*I will try, as you suggest, --regheader *
When I do "mri_cor2label --help" it says it uses surface overlays or volumes. *I am not sure why I want to generate a volume with mri_vol2surf* - shouldn't I generate a surface overlay that I can then create as a label using mri_cor2label?
many thanks
Trisanna
thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/ mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I'm not sure what identity.nofile is or what you are trying to do (no previous info in the email). If whatever you are trying to map to the surface is already in anatomical space (so no registration necessary), then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume format as input (ie, mgz, nii.gz ,etc)
On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
Hi All!
Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile
Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format should my output be for mri_vol2surf?
many thanks!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
sorry for the confusion. Some of our tools use identity.nofile, but these use --regheader
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the transformation since my labels and T1s are already in the same space and I just want to resample my labels to the surfaces.
I will try, as you suggest, --regheader
When I do "mri_cor2label --help" it says it uses surface overlays or volumes. I am not sure why I want to generate a volume with mri_vol2surf - shouldn't I generate a surface overlay that I can then create as a label using mri_cor2label?
many thanks
Trisanna
thanks Bruce I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile[cleardot.gif]
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: I'm not sure what identity.nofile is or what you are trying to do (no previous info in the email). If whatever you are trying to map to the surface is already in anatomical space (so no registration necessary), then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume format as input (ie, mgz, nii.gz ,etc)
On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surf using > identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes, what format > should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
Hi Doug
below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the transformation since my labels and T1s are already in the same space and I just want to resample my labels to the surfaces.
*I will try, as you suggest, --regheader *
When I do "mri_cor2label --help" it says it uses surface overlays or volumes. *I am not sure why I want to generate a volume with mri_vol2surf* - shouldn't I generate a surface overlay that I can then create as a label using mri_cor2label?
many thanks
Trisanna
thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use mrivol2surf to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure what identity.nofile is or what you are trying to do (no previous info in the email). If whatever you are trying to map to the surface is already in anatomical space (so no registration necessary), then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surf using > identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes, what format > should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
many thanks - will give this a go!
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
Hi Doug
below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the transformation since my labels and T1s are already in the same space and I just want to resample my labels to the surfaces.
*I will try, as you suggest, --regheader *
When I do "mri_cor2label --help" it says it uses surface overlays or volumes. *I am not sure why I want to generate a volume with mri_vol2surf* - shouldn't I generate a surface overlay that I can then create as a label using mri_cor2label?
many thanks
Trisanna
thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use
mrivol2surf
to resample the surface such that the vertices carry the label info? What output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure what identity.nofile is or what you are trying to do (no previous info in the email). If whatever you are trying to map to the surface is already in anatomical space (so no registrationnecessary),
then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surf using > identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes, what format > should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer 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 Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. *However, when I then try to open the pial surface and the corresponding new label in freeview, it says it cannot read the label. *Below is what I ran. I tried the same thing for the inflated surface.
I put labelid as "1" as I was unsure as to what to put. Could this have affected the label creation?
Trisanna
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader icbm-102 --hemi lh --surf pial srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 85413 Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz Dim: 169941 1 1
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest No such file or directory freeview.bin: could not open label file labeltest.label No such file or directory LabelRead failedNo such file or directory en label file labeltest.label
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
many thanks - will give this a go!
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
Hi Doug
below is the email I had written last Friday. I thought it got lost in the mix. I was told by Bruce to use identity.nofile as the transformation since my labels and T1s are already in the same space and I just want to resample my labels to the surfaces.
*I will try, as you suggest, --regheader *
When I do "mri_cor2label --help" it says it uses surface overlays or volumes. *I am not sure why I want to generate a volume with mri_vol2surf* - shouldn't I generate a surface overlay that I can then create as a label using mri_cor2label?
many thanks
Trisanna
thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the following error
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz srcreg = identity.nofile srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): No such file or directory Could not open identity.nofile
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it
with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no transformations have been performed) I get the following snapshot #1. Clearly, my original labels are aligned with the surface, as they should be since Freesurfer did not alter the space. So, how can I use
mrivol2surf
to resample the surface such that the vertices carry the label info?
What
output format should I use in mrivol2surf? How can I open this output in Freeview?
For instance, when I try a .dat that creates no transformation and save the output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something is going wrong in my mrivol2surf command.
My apologies for the questions Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure what identity.nofile is or what you are trying to do(no
previous info in the email). If whatever you are trying to map tothe
surface is already in anatomical space (so no registrationnecessary),
then you can use --regheader with mri_vol2surf. mri_cor2label will take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surf using > identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes, whatformat
> should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-- 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/
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Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label names and are text files. The .mgz is a scalar field over the surface (that is, a vector with a single value at each surface location). In freeview you can view it as:
freeview -f lh.inflated:overlay=surfaceoverlay.mgz
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. However, when I then try to open the pial surface and the corresponding new label in freeview, it says it cannot read the label. Below is what I ran. I tried the same thing for the inflated surface.
I put labelid as "1" as I was unsure as to what to put. Could this have affected the label creation?
Trisanna
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader icbm-102 --hemi lh --surf pial srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 85413 Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz Dim: 169941 1 1
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest No such file or directory freeview.bin: could not open label file labeltest.label No such file or directory LabelRead failedNo such file or directory en label file labeltest.label
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: many thanks - will give this a go!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and T1s are already in the same space > and I just want to resample my labels to the surfaces. > > *I will try, as you suggest, --regheader * > > When I do "mri_cor2label --help" it says it uses surface overlays or > volumes. *I am not sure why I want to generate a volume with > mri_vol2surf* - shouldn't I generate a surface overlay that I can then > create as a label using mri_cor2label? > > many thanks > > Trisanna > > > > thanks Bruce > > I could not find identity.nofile anywhere, when I ran mri_vol2surf I > got the following error > > trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz > srcreg = identity.nofile > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): No such file or directory > Could not open identity.nofile > > > > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi Trisanna > > you can give the transformation "file" named identity.nofile and it > will assume that the transform is the identity. You can then use > mri_vol2label to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: > > Hi there > > Just to reiterate my point above, when I open a surface created in > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no > transformations have been performed) I get the following snapshot > #1. Clearly, my original labels are aligned with the surface, as they > should > be since Freesurfer did not alter the space. So, how can I use mrivol2surf > to resample the surface such that the vertices carry the label info? What > output format should I use in mrivol2surf? How can I open this output in > Freeview? > > For instance, when I try a .dat that creates no transformation and > save the > output as .mgz and use Overlay in Freeview, I get snapshot #2. So, > something > is going wrong in my mrivol2surf command. > > My apologies for the questions > Trisanna > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
wrote:
I'm not sure what identity.nofile is or what you are
trying to do (no
previous info in the email). If whatever you are trying to
map to the
surface is already in anatomical space (so no registration
necessary),
then you can use --regheader with mri_vol2surf.
mri_cor2label will
take a volume format as input (ie, mgz, nii.gz ,etc)
On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surf
using
> identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes,
what format
> should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > 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
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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
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The information in this e-mail is intended only for the
person to
whom it is addressed. If you believe this e-mail was sent to you in
error and
the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was
sent to
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the
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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/
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I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote:
Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label names and are text files. The .mgz is a scalar field over the surface (that is, a vector with a single value at each surface location). In freeview you can view it as:
freeview -f lh.inflated:overlay=surfaceoverlay.mgz
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. However, when I then try to open the pial surface and the corresponding new label in freeview, it says it cannot read the label. Below is what I ran. I tried the same thing for the inflated surface.
I put labelid as "1" as I was unsure as to what to put. Could this have affected the label creation?
Trisanna
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader icbm-102 --hemi lh --surf pial srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 85413 Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz Dim: 169941 1 1
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest No such file or directory freeview.bin: could not open label file labeltest.label No such file or directory LabelRead failedNo such file or directory en label file labeltest.label
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: many thanks - will give this a go!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and T1s are already in the same space > and I just want to resample my labels to the surfaces. > > *I will try, as you suggest, --regheader * > > When I do "mri_cor2label --help" it says it uses surface overlays or > volumes. *I am not sure why I want to generate a volume with > mri_vol2surf* - shouldn't I generate a surface overlay that I can then > create as a label using mri_cor2label? > > many thanks > > Trisanna > > > > thanks Bruce > > I could not find identity.nofile anywhere, when I ran mri_vol2surf I > got the following error > > trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz > srcreg = identity.nofile > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): No such file or directory > Could not open identity.nofile > > > > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi Trisanna > > you can give the transformation "file" named identity.nofile and it > will assume that the transform is the identity. You can then use > mri_vol2label to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: > > Hi there > > Just to reiterate my point above, when I open a surface created in > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no > transformations have been performed) I get the following snapshot > #1. Clearly, my original labels are aligned with the surface, as they > should > be since Freesurfer did not alter the space. So, how can I use mrivol2surf > to resample the surface such that the vertices carry the label info? What > output format should I use in mrivol2surf? How can I open this output in > Freeview? > > For instance, when I try a .dat that creates no transformation and > save the > output as .mgz and use Overlay in Freeview, I get snapshot #2. So, > something > is going wrong in my mrivol2surf command. > > My apologies for the questions > Trisanna > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
wrote:
I'm not sure what identity.nofile is or what you aretrying to do (no
previous info in the email). If whatever you are trying tomap to the
surface is already in anatomical space (so no registrationnecessary),
then you can use --regheader with mri_vol2surf.mri_cor2label will
take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surfusing
> identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes,what format
> should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > 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.edumailto: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/BugReportinghttp://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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for theperson to
whom it is addressed. If you believe this e-mail was sent to you inerror and
the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail wassent to
you in error but does not contain patient information, please contactthe
sender and properly dispose of the e-mail.
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/
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Hi Doug
I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal:
trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped)
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote:
Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label names and are text files. The .mgz is a scalar field over the surface (that is, a vector with a single value at each surface location). In freeview you can view it as:
freeview -f lh.inflated:overlay=surfaceoverlay.mgz
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. However, when I then try to open the pial surface and the corresponding new label in freeview, it says it cannot read the label. Below is what I ran. I tried the same thing for the inflated surface.
I put labelid as "1" as I was unsure as to what to put. Could this have affected the label creation?
Trisanna
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader icbm-102 --hemi lh --surf pial srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 85413 Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz Dim: 169941 1 1
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest No such file or directory freeview.bin: could not open label file labeltest.label No such file or directory LabelRead failedNo such file or directory en label file labeltest.label
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: many thanks - will give this a go!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and T1s are already in the same space > and I just want to resample my labels to the surfaces. > > *I will try, as you suggest, --regheader * > > When I do "mri_cor2label --help" it says it uses surface overlays or > volumes. *I am not sure why I want to generate a volume with > mri_vol2surf* - shouldn't I generate a surface overlay that I can then > create as a label using mri_cor2label? > > many thanks > > Trisanna > > > > thanks Bruce > > I could not find identity.nofile anywhere, when I ran mri_vol2surf I > got the following error > > trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz > srcreg = identity.nofile > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): No such file or directory > Could not open identity.nofile > > > > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi Trisanna > > you can give the transformation "file" named identity.nofile and it > will assume that the transform is the identity. You can then use > mri_vol2label to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: > > Hi there > > Just to reiterate my point above, when I open a surface created in > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no > transformations have been performed) I get the following snapshot > #1. Clearly, my original labels are aligned with the surface, as they > should > be since Freesurfer did not alter the space. So, how can I use mrivol2surf > to resample the surface such that the vertices carry the label info? What > output format should I use in mrivol2surf? How can I open this output in > Freeview? > > For instance, when I try a .dat that creates no transformation and > save the > output as .mgz and use Overlay in Freeview, I get snapshot #2. So, > something > is going wrong in my mrivol2surf command. > > My apologies for the questions > Trisanna > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
wrote:
I'm not sure what identity.nofile is or what you aretrying to do (no
previous info in the email). If whatever you are trying tomap to the
surface is already in anatomical space (so no registrationnecessary),
then you can use --regheader with mri_vol2surf.mri_cor2label will
take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surfusing
> identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes,what format
> should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > 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.edumailto: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/BugReportinghttp://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.edumailto:Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for theperson to
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the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail wassent to
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-- 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/
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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 Doug
I tried again in the terminal and got this:
*trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue Apr 19 21:13:58 2016 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Doug
I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal:
trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped)
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote:
Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label names and are text files. The .mgz is a scalar field over the surface (that is, a vector with a single value at each surface location). In freeview you can view it as:
freeview -f lh.inflated:overlay=surfaceoverlay.mgz
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. However, when I then try to open the pial surface and the corresponding new label in freeview, it says it cannot read the label. Below is what I ran. I tried the same thing for the inflated surface.
I put labelid as "1" as I was unsure as to what to put. Could this have affected the label creation?
Trisanna
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader icbm-102 --hemi lh --surf pial srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 85413 Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz Dim: 169941 1 1
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file
/data-01/trisanna/freesurfer/icbm-102/label/labeltest
Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest No such file or directory freeview.bin: could not open label file labeltest.label No such file or directory LabelRead failedNo such file or directory en label file labeltest.label
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: many thanks - will give this a go!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and T1s are already in the same space > and I just want to resample my labels to the surfaces. > > *I will try, as you suggest, --regheader * > > When I do "mri_cor2label --help" it says it uses surface overlays or > volumes. *I am not sure why I want to generate a volume with > mri_vol2surf* - shouldn't I generate a surface overlay that I can then > create as a label using mri_cor2label? > > many thanks > > Trisanna > > > > thanks Bruce > > I could not find identity.nofile anywhere, when I ran mri_vol2surf I > got the following error > > trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz > srcreg = identity.nofile > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): No such file or directory > Could not open identity.nofile > > > > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > Hi Trisanna > > you can give the transformation "file" named identity.nofile and it > will assume that the transform is the identity. You can then use > mri_vol2label to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: > > Hi there > > Just to reiterate my point above, when I open a surface created in > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no > transformations have been performed) I get the following snapshot > #1. Clearly, my original labels are aligned with the surface, as they > should > be since Freesurfer did not alter the space. So, how can I use mrivol2surf > to resample the surface such that the vertices carry the label info? What > output format should I use in mrivol2surf? How can I open this output in > Freeview? > > For instance, when I try a .dat that creates no transformation and > save the > output as .mgz and use Overlay in Freeview, I get snapshot #2. So, > something > is going wrong in my mrivol2surf command. > > My apologies for the questions > Trisanna > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
wrote:
I'm not sure what identity.nofile is or what you aretrying to do (no
previous info in the email). If whatever you are trying tomap to the
surface is already in anatomical space (so no registrationnecessary),
then you can use --regheader with mri_vol2surf.mri_cor2label will
take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surfusing
> identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes,what format
> should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > 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.edumailto: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/BugReportinghttp://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.edumailto:Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for theperson to
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the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail wassent to
you in error but does not contain patient information, please contactthe
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-- 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/
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-- 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 Trisanna
can you run:
head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
and send us the output?
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
I tried again in the terminal and got this:
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue Apr 19 21:13:58 2016 [0]PETSC ERROR: Libraries linked from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src /petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: Hi Doug
I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal:
trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped)
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote: > Hi Trisanna > > if your output is .mgz it isn't a label file. Labels are stored in > .label names and are text files. The .mgz is a scalar field over the > surface (that is, a vector with a single value at each surface > location). In freeview you can view it as: > > freeview -f lh.inflated:overlay=surfaceoverlay.mgz > > > cheers > Bruce > > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: > >> Hi Doug >> >> So I ran mri_vol2surf and generated my .mgz surface overlay using >> --regheader as you suggested. I than ran mri_cor2label using that >> .mgz file. >> This also completed successfully. However, when I then try to open >> the pial >> surface and the corresponding new label in freeview, it says it >> cannot read >> the label. Below is what I ran. I tried the same thing for the inflated >> surface. >> >> I put labelid as "1" as I was unsure as to what to put. Could this have >> affected the label creation? >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader >> icbm-102 --hemi lh --surf pial >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> srcreg unspecified >> srcregold = 0 >> srcwarp unspecified >> surf = pial >> hemi = lh >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Computing registration from header. >> Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> reference. >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 0 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 85413 >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> Dim: 169941 1 1 >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> ------- Vox2RAS of input volume ----------- >> -1.000 0.000 0.000 84970.500; >> 0.000 0.000 1.000 -0.500; >> 0.000 -1.000 0.000 0.500; >> 0.000 0.000 0.000 1.000; >> Scanning the volume >> Found 1651 label voxels >> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> Centroid: -56170.34 -0.50 0.50 >> mri_cor2label completed SUCCESSFULLY >> >> >> trisanna@kaplan:~$ freeview -f >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest >> No such file or directory >> freeview.bin: could not open label file labeltest.label >> No such file or directory >> LabelRead failedNo such file or directory >> en label file labeltest.label >> >> >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca> wrote: >> many thanks - will give this a go! >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu> wrote: >> yes, but the surface overlay is in mgz (or nii.gz) format >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> > Hi Doug >> > >> > below is the email I had written last Friday. I thought >> it got lost in >> > the mix. I was told by Bruce to use identity.nofile as >> the >> > transformation since my labels and T1s are already in >> the same space >> > and I just want to resample my labels to the surfaces. >> > >> > *I will try, as you suggest, --regheader * >> > >> > When I do "mri_cor2label --help" it says it uses surface >> overlays or >> > volumes. *I am not sure why I want to generate a volume >> with >> > mri_vol2surf* - shouldn't I generate a surface overlay >> that I can then >> > create as a label using mri_cor2label? >> > >> > many thanks >> > >> > Trisanna >> > >> > >> > >> > thanks Bruce >> > >> > I could not find identity.nofile anywhere, when I ran >> mri_vol2surf I >> > got the following error >> > >> > trisanna@kaplan:~$ mri_vol2surf --mov >> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> --o >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> identity.nofile --hemi lh >> > srcvol = >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> > srcreg = identity.nofile >> > srcregold = 0 >> > srcwarp unspecified >> > surf = white >> > hemi = lh >> > reshape = 0 >> > interp = nearest >> > float2int = round >> > GetProjMax = 0 >> > INFO: float2int code = 0 >> > INFO: changing type to float >> > Done loading volume >> > regio_read_register(): No such file or directory >> > Could not open identity.nofile >> > >> > >> > >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu >> <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> > Hi Trisanna >> > >> > you can give the transformation "file" named >> identity.nofile and it >> > will assume that the transform is the identity. You can >> then use >> > mri_vol2label to sample the label onto the surface and >> visualize it with: >> > >> > freeview -f lh.inflated:label=lh.labels.label >> > >> > or some such >> > >> > cheers >> > Bruce >> > >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> > >> > Hi there >> > >> > Just to reiterate my point above, when I open a surface >> created in >> > Freesurfer with my labels.mgz (converted from minc) in >> Freeview (i.e. no >> > transformations have been performed) I get the following >> snapshot >> > #1. Clearly, my original labels are aligned with the >> surface, as they >> > should >> > be since Freesurfer did not alter the space. So, how can >> I use mrivol2surf >> > to resample the surface such that the vertices carry the >> label info? What >> > output format should I use in mrivol2surf? How can I >> open this output in >> > Freeview? >> > >> > For instance, when I try a .dat that creates no >> transformation and >> > save the >> > output as .mgz and use Overlay in Freeview, I get >> snapshot #2. So, >> > something >> > is going wrong in my mrivol2surf command. >> > >> > My apologies for the questions >> > Trisanna >> > >> > >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve >> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> wrote: >> > >> > I'm not sure what identity.nofile is or what you are >> trying to do (no >> > previous info in the email). If whatever you are trying to >> map to the >> > surface is already in anatomical space (so no registration >> necessary), >> > then you can use --regheader with mri_vol2surf. >> mri_cor2label will >> > take >> > a volume format as input (ie, mgz, nii.gz ,etc) >> > >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> > > >> > > Hi All! >> > > >> > > Could someone please tell me how to run mri_vol2surf >> using >> > > identity.nofile as the transformation? I cannot find any >> > documentation >> > > on identity.nofile >> > > >> > > Additionally, if my next step is to use the output of >> > mri_vol2surf in >> > > mri_cor2label, which takes surface overlays OR volumes, >> what format >> > > should my output be for mri_vol2surf? >> > > >> > > many thanks! >> > > >> > > Trisanna >> > > >> > > -- >> > > Ph.D. Candidate >> > > McGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the >> person to >> > whom it is >> > addressed. If you believe this e-mail was sent to you in >> error and >> > the e-mail >> > contains patient information, please contact the Partners >> > Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was >> sent to >> > you in error >> > but does not contain patient information, please contact >> the >> > sender and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer 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 >> >> >> >> >> > > > _______________________________________________ > 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 load another label, eg, lh.cortex.label? Also, I noticed that there is a space between "label=" and "/data/..." in the command line below. That space should not be there, so if it was there when you ran the command try again without the space.
On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote:
Hi Doug
I tried again in the terminal and got this:
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue Apr 19 21:13:58 2016 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca mailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Doug I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal: trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped) -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path On 04/19/2016 05:45 PM, Bruce Fischl wrote: > Hi Trisanna > > if your output is .mgz it isn't a label file. Labels are stored in > .label names and are text files. The .mgz is a scalar field over the > surface (that is, a vector with a single value at each surface > location). In freeview you can view it as: > > freeview -f lh.inflated:overlay=surfaceoverlay.mgz > > > cheers > Bruce > > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: > >> Hi Doug >> >> So I ran mri_vol2surf and generated my .mgz surface overlay using >> --regheader as you suggested. I than ran mri_cor2label using that >> .mgz file. >> This also completed successfully. However, when I then try to open >> the pial >> surface and the corresponding new label in freeview, it says it >> cannot read >> the label. Below is what I ran. I tried the same thing for the inflated >> surface. >> >> I put labelid as "1" as I was unsure as to what to put. Could this have >> affected the label creation? >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader >> icbm-102 --hemi lh --surf pial >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> srcreg unspecified >> srcregold = 0 >> srcwarp unspecified >> surf = pial >> hemi = lh >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Computing registration from header. >> Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> reference. >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 0 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 85413 >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> Dim: 169941 1 1 >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> ------- Vox2RAS of input volume ----------- >> -1.000 0.000 0.000 84970.500; >> 0.000 0.000 1.000 -0.500; >> 0.000 -1.000 0.000 0.500; >> 0.000 0.000 0.000 1.000; >> Scanning the volume >> Found 1651 label voxels >> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> Centroid: -56170.34 -0.50 0.50 >> mri_cor2label completed SUCCESSFULLY >> >> >> trisanna@kaplan:~$ freeview -f >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest >> No such file or directory >> freeview.bin: could not open label file labeltest.label >> No such file or directory >> LabelRead failedNo such file or directory >> en label file labeltest.label >> >> >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote: >> many thanks - will give this a go! >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> yes, but the surface overlay is in mgz (or nii.gz) format >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> > Hi Doug >> > >> > below is the email I had written last Friday. I thought >> it got lost in >> > the mix. I was told by Bruce to use identity.nofile as >> the >> > transformation since my labels and T1s are already in >> the same space >> > and I just want to resample my labels to the surfaces. >> > >> > *I will try, as you suggest, --regheader * >> > >> > When I do "mri_cor2label --help" it says it uses surface >> overlays or >> > volumes. *I am not sure why I want to generate a volume >> with >> > mri_vol2surf* - shouldn't I generate a surface overlay >> that I can then >> > create as a label using mri_cor2label? >> > >> > many thanks >> > >> > Trisanna >> > >> > >> > >> > thanks Bruce >> > >> > I could not find identity.nofile anywhere, when I ran >> mri_vol2surf I >> > got the following error >> > >> > trisanna@kaplan:~$ mri_vol2surf --mov >> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> --o >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> identity.nofile --hemi lh >> > srcvol = >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> > srcreg = identity.nofile >> > srcregold = 0 >> > srcwarp unspecified >> > surf = white >> > hemi = lh >> > reshape = 0 >> > interp = nearest >> > float2int = round >> > GetProjMax = 0 >> > INFO: float2int code = 0 >> > INFO: changing type to float >> > Done loading volume >> > regio_read_register(): No such file or directory >> > Could not open identity.nofile >> > >> > >> > >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: >> > Hi Trisanna >> > >> > you can give the transformation "file" named >> identity.nofile and it >> > will assume that the transform is the identity. You can >> then use >> > mri_vol2label to sample the label onto the surface and >> visualize it with: >> > >> > freeview -f lh.inflated:label=lh.labels.label >> > >> > or some such >> > >> > cheers >> > Bruce >> > >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> > >> > Hi there >> > >> > Just to reiterate my point above, when I open a surface >> created in >> > Freesurfer with my labels.mgz (converted from minc) in >> Freeview (i.e. no >> > transformations have been performed) I get the following >> snapshot >> > #1. Clearly, my original labels are aligned with the >> surface, as they >> > should >> > be since Freesurfer did not alter the space. So, how can >> I use mrivol2surf >> > to resample the surface such that the vertices carry the >> label info? What >> > output format should I use in mrivol2surf? How can I >> open this output in >> > Freeview? >> > >> > For instance, when I try a .dat that creates no >> transformation and >> > save the >> > output as .mgz and use Overlay in Freeview, I get >> snapshot #2. So, >> > something >> > is going wrong in my mrivol2surf command. >> > >> > My apologies for the questions >> > Trisanna >> > >> > >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Tue, Apr 19, 2016 at 1:23 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: >> > >> > I'm not sure what identity.nofile is or what you are >> trying to do (no >> > previous info in the email). If whatever you are trying to >> map to the >> > surface is already in anatomical space (so no registration >> necessary), >> > then you can use --regheader with mri_vol2surf. >> mri_cor2label will >> > take >> > a volume format as input (ie, mgz, nii.gz ,etc) >> > >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> > > >> > > Hi All! >> > > >> > > Could someone please tell me how to run mri_vol2surf >> using >> > > identity.nofile as the transformation? I cannot find any >> > documentation >> > > on identity.nofile >> > > >> > > Additionally, if my next step is to use the output of >> > mri_vol2surf in >> > > mri_cor2label, which takes surface overlays OR volumes, >> what format >> > > should my output be for mri_vol2surf? >> > > >> > > many thanks! >> > > >> > > Trisanna >> > > >> > > -- >> > > Ph.D. Candidate >> > > McGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > >> > > _______________________________________________ >> > > 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 >> > >> > >> > The information in this e-mail is intended only for the >> person to >> > whom it is >> > addressed. If you believe this e-mail was sent to you in >> error and >> > the e-mail >> > contains patient information, please contact the Partners >> > Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was >> sent to >> > you in error >> > but does not contain patient information, please contact >> the >> > sender and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@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 >> >> >> >> >> > > > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug and Bruce
*This what I get when I run the head command on the label:*
trisanna@kaplan:~$ head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label #!ascii label , from subject lh.pial vox2ras=TkReg 1651 -1 -29437.500 -0.500 0.500 0.0000000000 -1 -30660.500 -0.500 0.500 0.0000000000 -1 -30675.500 -0.500 0.500 0.0000000000 -1 -30676.500 -0.500 0.500 0.0000000000 -1 -30748.500 -0.500 0.500 0.0000000000 -1 -30760.500 -0.500 0.500 0.0000000000 -1 -30798.500 -0.500 0.500 0.0000000000 -1 -30815.500 -0.500 0.500 0.0000000000
*When I re-run freeview without the space you pointed out, I get the following:*
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
*** Error in `freeview.bin': double free or corruption (out): 0x0000000028604a50 *** Abort (core dumped)
*If I try an already exiting label in the terminal, it works perfectly:* trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/lh.BA44.label
best
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 11:11 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Can you load another label, eg, lh.cortex.label? Also, I noticed that there is a space between "label=" and "/data/..." in the command line below. That space should not be there, so if it was there when you ran the command try again without the space.
On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote:
Hi Doug
I tried again in the terminal and got this:
- trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue Apr 19 21:13:58 2016 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.catrisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Doug
I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal:
trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped)
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve < greve@nmr.mgh.harvard.edugreve@nmr.mgh.harvard.edu> wrote:
I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote:
Hi Trisanna
if your output is .mgz it isn't a label file. Labels are stored in .label names and are text files. The .mgz is a scalar field over the surface (that is, a vector with a single value at each surface location). In freeview you can view it as:
freeview -f lh.inflated:overlay=surfaceoverlay.mgz
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
So I ran mri_vol2surf and generated my .mgz surface overlay using --regheader as you suggested. I than ran mri_cor2label using that .mgz file. This also completed successfully. However, when I then try to open the pial surface and the corresponding new label in freeview, it says it cannot read the label. Below is what I ran. I tried the same thing for the
inflated
surface.
I put labelid as "1" as I was unsure as to what to put. Could this
have
affected the label creation?
Trisanna
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader icbm-102 --hemi lh --surf pial srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 85413 Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz Dim: 169941 1 1
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file
/data-01/trisanna/freesurfer/icbm-102/label/labeltest
Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest No such file or directory freeview.bin: could not open label file labeltest.label No such file or directory LabelRead failedNo such file or directory en label file labeltest.label
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca wrote: many thanks - will give this a go!
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and T1s are already in the same space > and I just want to resample my labels to the surfaces. > > *I will try, as you suggest, --regheader * > > When I do "mri_cor2label --help" it says it uses surface overlays or > volumes. *I am not sure why I want to generate a volume with > mri_vol2surf* - shouldn't I generate a surface overlay that I can then > create as a label using mri_cor2label? > > many thanks > > Trisanna > > > > thanks Bruce > > I could not find identity.nofile anywhere, when I ran mri_vol2surf I > got the following error > > trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz > srcreg = identity.nofile > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): No such file or directory > Could not open identity.nofile > > > > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl > < <fischl@nmr.mgh.harvard.edu>fischl@nmr.mgh.harvard.edu <mailto: <fischl@nmr.mgh.harvard.edu>fischl@nmr.mgh.harvard.edu>>wrote:
> Hi Trisanna > > you can give the transformation "file" named identity.nofile and it > will assume that the transform is the identity. You can then use > mri_vol2label to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: > > Hi there > > Just to reiterate my point above, when I open a surface created in > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no > transformations have been performed) I get the following snapshot > #1. Clearly, my original labels are aligned with the surface, as they > should > be since Freesurfer did not alter the space. So, how can I use mrivol2surf > to resample the surface such that the vertices carry the label info? What > output format should I use in mrivol2surf? How can I open this output in > Freeview? > > For instance, when I try a .dat that creates no transformation and > save the > output as .mgz and use Overlay in Freeview, I get snapshot #2. So, > something > is going wrong in my mrivol2surf command. > > My apologies for the questions > Trisanna > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
wrote:
I'm not sure what identity.nofile is or what you aretrying to do (no
previous info in the email). If whatever you are trying tomap to the
surface is already in anatomical space (so no registrationnecessary),
then you can use --regheader with mri_vol2surf.mri_cor2label will
take a volume format as input (ie, mgz, nii.gz ,etc) On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > Hi All! > > Could someone please tell me how to run mri_vol2surfusing
> identity.nofile as the transformation? I cannot find any documentation > on identity.nofile > > Additionally, if my next step is to use the output of mri_vol2surf in > mri_cor2label, which takes surface overlays OR volumes,what format
> should my output be for mri_vol2surf? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ > Freesurfer mailing list > <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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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/BugReportinghttp://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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for theperson to
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the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail wassent to
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-- 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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I think the problem is that this is being interpreted as a volume label. The first column is the surface vertex number which you can see is all -1s indicating no vertex. To create a surface label, run mri_cor2label with the --surf subject hemi option. Ruopeng, can you add something to freeview to handle this case more elegantly? doug
On 04/20/2016 10:42 AM, Trisanna Sprung-Much wrote:
Hi Doug and Bruce
*This what I get when I run the head command on the label:*
trisanna@kaplan:~$ head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label #!ascii label , from subject lh.pial vox2ras=TkReg 1651 -1 -29437.500 -0.500 0.500 0.0000000000 -1 -30660.500 -0.500 0.500 0.0000000000 -1 -30675.500 -0.500 0.500 0.0000000000 -1 -30676.500 -0.500 0.500 0.0000000000 -1 -30748.500 -0.500 0.500 0.0000000000 -1 -30760.500 -0.500 0.500 0.0000000000 -1 -30798.500 -0.500 0.500 0.0000000000 -1 -30815.500 -0.500 0.500 0.0000000000
*When I re-run freeview without the space you pointed out, I get the following:*
trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
*** Error in `freeview.bin': double free or corruption (out): 0x0000000028604a50 *** Abort (core dumped)
*If I try an already exiting label in the terminal, it works perfectly:
*trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/lh.BA44.label
best
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 11:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you load another label, eg, lh.cortex.label? Also, I noticed that there is a space between "label=" and "/data/..." in the command line below. That space should not be there, so if it was there when you ran the command try again without the space. On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote:Hi Doug I tried again in the terminal and got this: * trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue Apr 19 21:13:58 2016 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote: Hi Doug I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal: trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped) -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path On 04/19/2016 05:45 PM, Bruce Fischl wrote: > Hi Trisanna > > if your output is .mgz it isn't a label file. Labels are stored in > .label names and are text files. The .mgz is a scalar field over the > surface (that is, a vector with a single value at each surface > location). In freeview you can view it as: > > freeview -f lh.inflated:overlay=surfaceoverlay.mgz > > > cheers > Bruce > > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: > >> Hi Doug >> >> So I ran mri_vol2surf and generated my .mgz surface overlay using >> --regheader as you suggested. I than ran mri_cor2label using that >> .mgz file. >> This also completed successfully. However, when I then try to open >> the pial >> surface and the corresponding new label in freeview, it says it >> cannot read >> the label. Below is what I ran. I tried the same thing for the inflated >> surface. >> >> I put labelid as "1" as I was unsure as to what to put. Could this have >> affected the label creation? >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader >> icbm-102 --hemi lh --surf pial >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> srcreg unspecified >> srcregold = 0 >> srcwarp unspecified >> surf = pial >> hemi = lh >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Computing registration from header. >> Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> reference. >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 0 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 85413 >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> Dim: 169941 1 1 >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> ------- Vox2RAS of input volume ----------- >> -1.000 0.000 0.000 84970.500; >> 0.000 0.000 1.000 -0.500; >> 0.000 -1.000 0.000 0.500; >> 0.000 0.000 0.000 1.000; >> Scanning the volume >> Found 1651 label voxels >> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> Centroid: -56170.34 -0.50 0.50 >> mri_cor2label completed SUCCESSFULLY >> >> >> trisanna@kaplan:~$ freeview -f >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest >> No such file or directory >> freeview.bin: could not open label file labeltest.label >> No such file or directory >> LabelRead failedNo such file or directory >> en label file labeltest.label >> >> >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote: >> many thanks - will give this a go! >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> yes, but the surface overlay is in mgz (or nii.gz) format >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> > Hi Doug >> > >> > below is the email I had written last Friday. I thought >> it got lost in >> > the mix. I was told by Bruce to use identity.nofile as >> the >> > transformation since my labels and T1s are already in >> the same space >> > and I just want to resample my labels to the surfaces. >> > >> > *I will try, as you suggest, --regheader * >> > >> > When I do "mri_cor2label --help" it says it uses surface >> overlays or >> > volumes. *I am not sure why I want to generate a volume >> with >> > mri_vol2surf* - shouldn't I generate a surface overlay >> that I can then >> > create as a label using mri_cor2label? >> > >> > many thanks >> > >> > Trisanna >> > >> > >> > >> > thanks Bruce >> > >> > I could not find identity.nofile anywhere, when I ran >> mri_vol2surf I >> > got the following error >> > >> > trisanna@kaplan:~$ mri_vol2surf --mov >> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> --o >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> identity.nofile --hemi lh >> > srcvol = >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> > srcreg = identity.nofile >> > srcregold = 0 >> > srcwarp unspecified >> > surf = white >> > hemi = lh >> > reshape = 0 >> > interp = nearest >> > float2int = round >> > GetProjMax = 0 >> > INFO: float2int code = 0 >> > INFO: changing type to float >> > Done loading volume >> > regio_read_register(): No such file or directory >> > Could not open identity.nofile >> > >> > >> > >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: >> > Hi Trisanna >> > >> > you can give the transformation "file" named >> identity.nofile and it >> > will assume that the transform is the identity. You can >> then use >> > mri_vol2label to sample the label onto the surface and >> visualize it with: >> > >> > freeview -f lh.inflated:label=lh.labels.label >> > >> > or some such >> > >> > cheers >> > Bruce >> > >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> > >> > Hi there >> > >> > Just to reiterate my point above, when I open a surface >> created in >> > Freesurfer with my labels.mgz (converted from minc) in >> Freeview (i.e. no >> > transformations have been performed) I get the following >> snapshot >> > #1. Clearly, my original labels are aligned with the >> surface, as they >> > should >> > be since Freesurfer did not alter the space. So, how can >> I use mrivol2surf >> > to resample the surface such that the vertices carry the >> label info? What >> > output format should I use in mrivol2surf? How can I >> open this output in >> > Freeview? >> > >> > For instance, when I try a .dat that creates no >> transformation and >> > save the >> > output as .mgz and use Overlay in Freeview, I get >> snapshot #2. So, >> > something >> > is going wrong in my mrivol2surf command. >> > >> > My apologies for the questions >> > Trisanna >> > >> > >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Tue, Apr 19, 2016 at 1:23 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: >> > >> > I'm not sure what identity.nofile is or what you are >> trying to do (no >> > previous info in the email). If whatever you are trying to >> map to the >> > surface is already in anatomical space (so no registration >> necessary), >> > then you can use --regheader with mri_vol2surf. >> mri_cor2label will >> > take >> > a volume format as input (ie, mgz, nii.gz ,etc) >> > >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> > > >> > > Hi All! >> > > >> > > Could someone please tell me how to run mri_vol2surf >> using >> > > identity.nofile as the transformation? I cannot find any >> > documentation >> > > on identity.nofile >> > > >> > > Additionally, if my next step is to use the output of >> > mri_vol2surf in >> > > mri_cor2label, which takes surface overlays OR volumes, >> what format >> > > should my output be for mri_vol2surf? >> > > >> > > many thanks! >> > > >> > > Trisanna >> > > >> > > -- >> > > Ph.D. Candidate >> > > McGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > >> > > _______________________________________________ >> > > 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 >> > >> > >> > The information in this e-mail is intended only for the >> person to >> > whom it is >> > addressed. If you believe this e-mail was sent to you in >> error and >> > the e-mail >> > contains patient information, please contact the Partners >> > Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was >> sent to >> > you in error >> > but does not contain patient information, please contact >> the >> > sender and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@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 >> >> >> >> >> > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug
I had run mri_cor2label using the --surf option. Is what I did below correct?
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 20, 2016 at 11:18 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
I think the problem is that this is being interpreted as a volume label. The first column is the surface vertex number which you can see is all -1s indicating no vertex. To create a surface label, run mri_cor2label with the --surf subject hemi option. Ruopeng, can you add something to freeview to handle this case more elegantly? doug
On 04/20/2016 10:42 AM, Trisanna Sprung-Much wrote:
Hi Doug and Bruce
*This what I get when I run the head command on the label:*
trisanna@kaplan:~$ head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label #!ascii label , from subject lh.pial vox2ras=TkReg 1651 -1 -29437.500 -0.500 0.500 0.0000000000 -1 -30660.500 -0.500 0.500 0.0000000000 -1 -30675.500 -0.500 0.500 0.0000000000 -1 -30676.500 -0.500 0.500 0.0000000000 -1 -30748.500 -0.500 0.500 0.0000000000 -1 -30760.500 -0.500 0.500 0.0000000000 -1 -30798.500 -0.500 0.500 0.0000000000 -1 -30815.500 -0.500 0.500 0.0000000000
*When I re-run freeview without the space you pointed out, I get the following:*
trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
*** Error in `freeview.bin': double free or corruption (out): 0x0000000028604a50 *** Abort (core dumped)
*If I try an already exiting label in the terminal, it works perfectly:
*trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/lh.BA44.label
best
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 11:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you load another label, eg, lh.cortex.label? Also, I noticed that there is a space between "label=" and "/data/..." in the command line below. That space should not be there, so if it was there when you ran the command try again without the space. On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote:Hi Doug I tried again in the terminal and got this: * trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR:
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:
[0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue Apr 19 21:13:58 2016 [0]PETSC ERROR: Libraries linked from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote: Hi Doug I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal: trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped) -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path On 04/19/2016 05:45 PM, Bruce Fischl wrote: > Hi Trisanna > > if your output is .mgz it isn't a label file. Labels are stored in > .label names and are text files. The .mgz is a scalar field over the > surface (that is, a vector with a single value at each surface > location). In freeview you can view it as: > > freeview -f lh.inflated:overlay=surfaceoverlay.mgz > > > cheers > Bruce > > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: > >> Hi Doug >> >> So I ran mri_vol2surf and generated my .mgz surface overlay using >> --regheader as you suggested. I than ran mri_cor2label using that >> .mgz file. >> This also completed successfully. However, when I then try to open >> the pial >> surface and the corresponding new label in freeview, it says it >> cannot read >> the label. Below is what I ran. I tried the same thing for the inflated >> surface. >> >> I put labelid as "1" as I was unsure as to what to put. Could this have >> affected the label creation? >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader >> icbm-102 --hemi lh --surf pial >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> srcreg unspecified >> srcregold = 0 >> srcwarp unspecified >> surf = pial >> hemi = lh >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Computing registration from header. >> Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> reference. >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 0 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 85413 >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> Dim: 169941 1 1 >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> ------- Vox2RAS of input volume ----------- >> -1.000 0.000 0.000 84970.500; >> 0.000 0.000 1.000 -0.500; >> 0.000 -1.000 0.000 0.500; >> 0.000 0.000 0.000 1.000; >> Scanning the volume >> Found 1651 label voxels >> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> Centroid: -56170.34 -0.50 0.50 >> mri_cor2label completed SUCCESSFULLY >> >> >> trisanna@kaplan:~$ freeview -f >>/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
>> No such file or directory >> freeview.bin: could not open label file labeltest.label >> No such file or directory >> LabelRead failedNo such file or directory >> en label file labeltest.label >> >> >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote: >> many thanks - will give this a go! >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> yes, but the surface overlay is in mgz (or nii.gz) format >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> > Hi Doug >> > >> > below is the email I had written last Friday. I thought >> it got lost in >> > the mix. I was told by Bruce to use identity.nofile as >> the >> > transformation since my labels and T1s are already in >> the same space >> > and I just want to resample my labels to the surfaces. >> > >> > *I will try, as you suggest, --regheader * >> > >> > When I do "mri_cor2label --help" it says it uses surface >> overlays or >> > volumes. *I am not sure why I want to generate a volume >> with >> > mri_vol2surf* - shouldn't I generate a surface overlay >> that I can then >> > create as a label using mri_cor2label? >> > >> > many thanks >> > >> > Trisanna >> > >> > >> > >> > thanks Bruce >> > >> > I could not find identity.nofile anywhere, when I ran >> mri_vol2surf I >> > got the following error >> > >> > trisanna@kaplan:~$ mri_vol2surf --mov >> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> --o >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> identity.nofile --hemi lh >> > srcvol = >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> > srcreg = identity.nofile >> > srcregold = 0 >> > srcwarp unspecified >> > surf = white >> > hemi = lh >> > reshape = 0 >> > interp = nearest >> > float2int = round >> > GetProjMax = 0 >> > INFO: float2int code = 0 >> > INFO: changing type to float >> > Done loading volume >> > regio_read_register(): No such file or directory >> > Could not open identity.nofile >> > >> > >> > >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: >> > Hi Trisanna >> > >> > you can give the transformation "file" named >> identity.nofile and it >> > will assume that the transform is the identity. You can >> then use >> > mri_vol2label to sample the label onto the surface and >> visualize it with: >> > >> > freeview -f lh.inflated:label=lh.labels.label >> > >> > or some such >> > >> > cheers >> > Bruce >> > >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> > >> > Hi there >> > >> > Just to reiterate my point above, when I open a surface >> created in >> > Freesurfer with my labels.mgz (converted from minc) in >> Freeview (i.e. no >> > transformations have been performed) I get the following >> snapshot >> > #1. Clearly, my original labels are aligned with the >> surface, as they >> > should >> > be since Freesurfer did not alter the space. So, how can >> I use mrivol2surf >> > to resample the surface such that the vertices carry the >> label info? What >> > output format should I use in mrivol2surf? How can I >> open this output in >> > Freeview? >> > >> > For instance, when I try a .dat that creates no >> transformation and >> > save the >> > output as .mgz and use Overlay in Freeview, I get >> snapshot #2. So, >> > something >> > is going wrong in my mrivol2surf command. >> > >> > My apologies for the questions >> > Trisanna >> > >> > >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Tue, Apr 19, 2016 at 1:23 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: >> > >> > I'm not sure what identity.nofile is or what youare
>> trying to do (no >> > previous info in the email). If whatever you are trying to >> map to the >> > surface is already in anatomical space (so no registration >> necessary), >> > then you can use --regheader with mri_vol2surf. >> mri_cor2label will >> > take >> > a volume format as input (ie, mgz, nii.gz ,etc) >> > >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> > > >> > > Hi All! >> > > >> > > Could someone please tell me how to run mri_vol2surf >> using >> > > identity.nofile as the transformation? I cannot find any >> > documentation >> > > on identity.nofile >> > > >> > > Additionally, if my next step is to use the output of >> > mri_vol2surf in >> > > mri_cor2label, which takes surface overlays OR volumes, >> what format >> > > should my output be for mri_vol2surf? >> > > >> > > many thanks! >> > > >> > > Trisanna >> > > >> > > -- >> > > Ph.D. Candidate >> > > McGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > >> > > _______________________________________________ >> > > 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%3E
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>> > >> > >> > The information in this e-mail is intended only for the >> person to >> > whom it is >> > addressed. If you believe this e-mail was sent to you in >> error and >> > the e-mail >> > contains patient information, please contact the Partners >> > Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was >> sent to >> > you in error >> > but does not contain patient information, please contact >> the >> > sender and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > _______________________________________________ >> > 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%3E
>> Outgoing: >>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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nope, you need to give it just the name of the subject and the hemisphere. Run it with --help for more info
On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote:
Hi Doug
I had run mri_cor2label using the --surf option. Is what I did below correct?
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 20, 2016 at 11:18 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think the problem is that this is being interpreted as a volume label. The first column is the surface vertex number which you can see is all -1s indicating no vertex. To create a surface label, run mri_cor2label with the --surf subject hemi option. Ruopeng, can you add something to freeview to handle this case more elegantly? doug On 04/20/2016 10:42 AM, Trisanna Sprung-Much wrote: > Hi Doug and Bruce > > *This what I get when I run the head command on the label:* > > trisanna@kaplan:~$ head > /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label > #!ascii label , from subject lh.pial vox2ras=TkReg > 1651 > -1 -29437.500 -0.500 0.500 0.0000000000 > -1 -30660.500 -0.500 0.500 0.0000000000 > -1 -30675.500 -0.500 0.500 0.0000000000 > -1 -30676.500 -0.500 0.500 0.0000000000 > -1 -30748.500 -0.500 0.500 0.0000000000 > -1 -30760.500 -0.500 0.500 0.0000000000 > -1 -30798.500 -0.500 0.500 0.0000000000 > -1 -30815.500 -0.500 0.500 0.0000000000 > > > *When I re-run freeview without the space you pointed out, I get the > following:* > > trisanna@kaplan:~$ freeview -f > /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label > > *** Error in `freeview.bin': double free or corruption (out): > 0x0000000028604a50 *** > Abort (core dumped) > > > *If I try an already exiting label in the terminal, it works perfectly: > > *trisanna@kaplan:~$ freeview -f > /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/lh.BA44.label > > * > * > best > > Trisanna > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 11:11 PM, Douglas 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: > > Can you load another label, eg, lh.cortex.label? Also, I noticed > that there is a space between "label=" and "/data/..." in the > command line below. That space should not be there, so if it was > there when you ran the command try again without the space. > > > On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote: >> Hi Doug >> >> I tried again in the terminal and got this: >> * >> trisanna@kaplan:~$ freeview -f >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >> Violation, probably memory access out of range >> [0]PETSC ERROR: Try option -start_in_debugger or >> -on_error_attach_debugger >> [0]PETSC ERROR: or see >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC >> ERROR: or try http://valgrind.org on linux or man libgmalloc on >> Apple to find memory corruption errors >> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >> link, and run >> [0]PETSC ERROR: to get more information on the crash. >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Signal received! >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 >> 17:29:26 CDT 2008 HG revision: >> 4466c6289a0922df26e20626fd4a0b4dd03c8124 >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> [0]PETSC ERROR: See docs/index.html for manual pages. >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by >> trisanna Tue Apr 19 21:13:58 2016 >> [0]PETSC ERROR: Libraries linked from >> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt >> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 >> [0]PETSC ERROR: Configure options --with-debugging=no >> --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 >> --download-mpich=1 --with-mpi=1 --with-x=0 >> --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: User provided function() line 0 in unknown >> directory unknown file >> [unset]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> >> <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>>> wrote: >> >> Hi Doug >> >> I thought this was the case as well but when I try manually >> in Freeview and select the correct label, Freeview crashes >> and gives this error in the terminal: >> >> trisanna@kaplan:~$ freeview >> *** Error in `freeview.bin': double free or corruption (out): >> 0x0000000029080920 *** >> Abort (core dumped) >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 6:17 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: >> >> I don't think that is the problem. The problem is that it >> cannot find >> the file. Try giving it the whole path >> >> On 04/19/2016 05:45 PM, Bruce Fischl wrote: >> > Hi Trisanna >> > >> > if your output is .mgz it isn't a label file. Labels >> are stored in >> > .label names and are text files. The .mgz is a scalar >> field over the >> > surface (that is, a vector with a single value at each >> surface >> > location). In freeview you can view it as: >> > >> > freeview -f lh.inflated:overlay=surfaceoverlay.mgz >> > >> > >> > cheers >> > Bruce >> > >> > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: >> > >> >> Hi Doug >> >> >> >> So I ran mri_vol2surf and generated my .mgz surface >> overlay using >> >> --regheader as you suggested. I than ran mri_cor2label >> using that >> >> .mgz file. >> >> This also completed successfully. However, when I then >> try to open >> >> the pial >> >> surface and the corresponding new label in freeview, >> it says it >> >> cannot read >> >> the label. Below is what I ran. I tried the same thing >> for the inflated >> >> surface. >> >> >> >> I put labelid as "1" as I was unsure as to what to >> put. Could this have >> >> affected the label creation? >> >> >> >> Trisanna >> >> >> >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> >> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> --regheader >> >> icbm-102 --hemi lh --surf pial >> >> srcvol = >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> >> srcreg unspecified >> >> srcregold = 0 >> >> srcwarp unspecified >> >> surf = pial >> >> hemi = lh >> >> reshape = 0 >> >> interp = nearest >> >> float2int = round >> >> GetProjMax = 0 >> >> INFO: float2int code = 0 >> >> INFO: changing type to float >> >> Done loading volume >> >> Computing registration from header. >> >> Using >> /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> >> reference. >> >> Reading surface >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> >> Done reading source surface >> >> Mapping Source Volume onto Source Subject Surface >> >> 1 0 0 0 >> >> using old >> >> Done mapping volume to surface >> >> Number of source voxels hit = 85413 >> >> Writing to >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> >> Dim: 169941 1 1 >> >> >> >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> >> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> --id 1 --l >> >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> --surf lh.pial >> >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks >> Exp $ >> >> Loading mri >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> >> ------- Vox2RAS of input volume ----------- >> >> -1.000 0.000 0.000 84970.500; >> >> 0.000 0.000 1.000 -0.500; >> >> 0.000 -1.000 0.000 0.500; >> >> 0.000 0.000 0.000 1.000; >> >> Scanning the volume >> >> Found 1651 label voxels >> >> Writing label file >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> >> Centroid: -56170.34 -0.50 0.50 >> >> mri_cor2label completed SUCCESSFULLY >> >> >> >> >> >> trisanna@kaplan:~$ freeview -f >> >> >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest >> >> No such file or directory >> >> freeview.bin: could not open label file labeltest.label >> >> No such file or directory >> >> LabelRead failedNo such file or directory >> >> en label file labeltest.label >> >> >> >> >> >> >> >> -- >> >> Ph.D. CandidateMcGill University >> >> Integrated Program in Neuroscience >> >> Psychology >> >> >> >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> >> <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>>> wrote: >> >> many thanks - will give this a go! >> >> >> >> -- >> >> Ph.D. CandidateMcGill University >> >> Integrated Program in Neuroscience >> >> Psychology >> >> >> >> >> >> On Tue, Apr 19, 2016 at 3:48 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: >> >> yes, but the surface overlay is in mgz (or >> nii.gz) format >> >> >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> >> > Hi Doug >> >> > >> >> > below is the email I had written last Friday. >> I thought >> >> it got lost in >> >> > the mix. I was told by Bruce to use >> identity.nofile as >> >> the >> >> > transformation since my labels and T1s are >> already in >> >> the same space >> >> > and I just want to resample my labels to the >> surfaces. >> >> > >> >> > *I will try, as you suggest, --regheader * >> >> > >> >> > When I do "mri_cor2label --help" it says it >> uses surface >> >> overlays or >> >> > volumes. *I am not sure why I want to generate >> a volume >> >> with >> >> > mri_vol2surf* - shouldn't I generate a surface >> overlay >> >> that I can then >> >> > create as a label using mri_cor2label? >> >> > >> >> > many thanks >> >> > >> >> > Trisanna >> >> > >> >> > >> >> > >> >> > thanks Bruce >> >> > >> >> > I could not find identity.nofile anywhere, >> when I ran >> >> mri_vol2surf I >> >> > got the following error >> >> > >> >> > trisanna@kaplan:~$ mri_vol2surf --mov >> >> > >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> >> --o >> >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> >> identity.nofile --hemi lh >> >> > srcvol = >> >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> >> > srcreg = identity.nofile >> >> > srcregold = 0 >> >> > srcwarp unspecified >> >> > surf = white >> >> > hemi = lh >> >> > reshape = 0 >> >> > interp = nearest >> >> > float2int = round >> >> > GetProjMax = 0 >> >> > INFO: float2int code = 0 >> >> > INFO: changing type to float >> >> > Done loading volume >> >> > regio_read_register(): No such file or directory >> >> > Could not open identity.nofile >> >> > >> >> > >> >> > >> >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> >> <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 Trisanna >> >> > >> >> > you can give the transformation "file" named >> >> identity.nofile and it >> >> > will assume that the transform is the >> identity. You can >> >> then use >> >> > mri_vol2label to sample the label onto the >> surface and >> >> visualize it with: >> >> > >> >> > freeview -f lh.inflated:label=lh.labels.label >> >> > >> >> > or some such >> >> > >> >> > cheers >> >> > Bruce >> >> > >> >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> >> > >> >> > Hi there >> >> > >> >> > Just to reiterate my point above, when I open >> a surface >> >> created in >> >> > Freesurfer with my labels.mgz (converted from >> minc) in >> >> Freeview (i.e. no >> >> > transformations have been performed) I get the >> following >> >> snapshot >> >> > #1. Clearly, my original labels are aligned >> with the >> >> surface, as they >> >> > should >> >> > be since Freesurfer did not alter the space. >> So, how can >> >> I use mrivol2surf >> >> > to resample the surface such that the vertices >> carry the >> >> label info? What >> >> > output format should I use in mrivol2surf? How >> can I >> >> open this output in >> >> > Freeview? >> >> > >> >> > For instance, when I try a .dat that creates no >> >> transformation and >> >> > save the >> >> > output as .mgz and use Overlay in Freeview, I get >> >> snapshot #2. So, >> >> > something >> >> > is going wrong in my mrivol2surf command. >> >> > >> >> > My apologies for the questions >> >> > Trisanna >> >> > >> >> > >> >> > >> >> > -- >> >> > Ph.D. Candidate >> >> > McGill University >> >> > Integrated Program in Neuroscience >> >> > Psychology >> >> > >> >> > >> >> > On Tue, Apr 19, 2016 at 1:23 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: >> >> > >> >> > I'm not sure what identity.nofile is or what you are >> >> trying to do (no >> >> > previous info in the email). If whatever you are >> trying to >> >> map to the >> >> > surface is already in anatomical space (so no >> registration >> >> necessary), >> >> > then you can use --regheader with mri_vol2surf. >> >> mri_cor2label will >> >> > take >> >> > a volume format as input (ie, mgz, nii.gz ,etc) >> >> > >> >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> >> > > >> >> > > Hi All! >> >> > > >> >> > > Could someone please tell me how to run >> mri_vol2surf >> >> using >> >> > > identity.nofile as the transformation? I >> cannot find any >> >> > documentation >> >> > > on identity.nofile >> >> > > >> >> > > Additionally, if my next step is to use the >> output of >> >> > mri_vol2surf in >> >> > > mri_cor2label, which takes surface overlays OR >> volumes, >> >> what format >> >> > > should my output be for mri_vol2surf? >> >> > > >> >> > > many thanks! >> >> > > >> >> > > Trisanna >> >> > > >> >> > > -- >> >> > > Ph.D. Candidate >> >> > > McGill University >> >> > > Integrated Program in Neuroscience >> >> > > Psychology >> >> > > >> >> > > >> >> > > >> >> > > _______________________________________________ >> >> > > 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 >> >> > >> >> > >> >> > The information in this e-mail is intended only >> for the >> >> person to >> >> > whom it is >> >> > addressed. If you believe this e-mail was sent >> to you in >> >> error and >> >> > the e-mail >> >> > contains patient information, please contact the >> Partners >> >> > Compliance HelpLine at >> >> > http://www.partners.org/complianceline . If the >> e-mail was >> >> sent to >> >> > you in error >> >> > but does not contain patient information, please >> contact >> >> the >> >> > sender and properly >> >> > dispose of the e-mail. >> >> > >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@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 >> >> >> >> >> >> >> >> >> >> >> > >> > >> > _______________________________________________ >> > 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> >> Fax: 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 >> >> >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks, Doug! sorry, I had misinterpreted the --surf argument when I had originally checked --help. Got the proper label created AND got the overlay.mgz to work as well. All my labels are there in the overlay.mgz created using mri_vol2surf once I change the thresholds of the overlay - I can then isolate a particular label by creating a .label. am SUPER pleased!!!! Thank you so much :)
Out of curiosity, is there any particular reason why I should be using an overlay.mgz versus a .label text file?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 20, 2016 at 12:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
nope, you need to give it just the name of the subject and the hemisphere. Run it with --help for more info
On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote:
Hi Doug
I had run mri_cor2label using the --surf option. Is what I did below correct?
trisanna@kaplan:~$ mri_cor2label --i /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz ------- Vox2RAS of input volume ----------- -1.000 0.000 0.000 84970.500; 0.000 0.000 1.000 -0.500; 0.000 -1.000 0.000 0.500; 0.000 0.000 0.000 1.000; Scanning the volume Found 1651 label voxels Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest Centroid: -56170.34 -0.50 0.50 mri_cor2label completed SUCCESSFULLY
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 20, 2016 at 11:18 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think the problem is that this is being interpreted as a volume label. The first column is the surface vertex number which you can see isall
-1s indicating no vertex. To create a surface label, runmri_cor2label
with the --surf subject hemi option. Ruopeng, can you add somethingto
freeview to handle this case more elegantly? doug On 04/20/2016 10:42 AM, Trisanna Sprung-Much wrote: > Hi Doug and Bruce > > *This what I get when I run the head command on the label:* > > trisanna@kaplan:~$ head > /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label > #!ascii label , from subject lh.pial vox2ras=TkReg > 1651 > -1 -29437.500 -0.500 0.500 0.0000000000 > -1 -30660.500 -0.500 0.500 0.0000000000 > -1 -30675.500 -0.500 0.500 0.0000000000 > -1 -30676.500 -0.500 0.500 0.0000000000 > -1 -30748.500 -0.500 0.500 0.0000000000 > -1 -30760.500 -0.500 0.500 0.0000000000 > -1 -30798.500 -0.500 0.500 0.0000000000 > -1 -30815.500 -0.500 0.500 0.0000000000 > > > *When I re-run freeview without the space you pointed out, I getthe
> following:* > > trisanna@kaplan:~$ freeview -f >/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
> > *** Error in `freeview.bin': double free or corruption (out): > 0x0000000028604a50 *** > Abort (core dumped) > > > *If I try an already exiting label in the terminal, it works perfectly: > > *trisanna@kaplan:~$ freeview -f >/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/lh.BA44.label
> > * > * > best > > Trisanna > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 11:11 PM, Douglas 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: > > Can you load another label, eg, lh.cortex.label? Also, Inoticed
> that there is a space between "label=" and "/data/..." in the > command line below. That space should not be there, so if itwas
> there when you ran the command try again without the space. > > > On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote: >> Hi Doug >> >> I tried again in the terminal and got this: >> * >> trisanna@kaplan:~$ freeview -f >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * >> [0]PETSC ERROR: >>
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >> Violation, probably memory access out of range >> [0]PETSC ERROR: Try option -start_in_debugger or >> -on_error_attach_debugger >> [0]PETSC ERROR: or see >>http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...
>> ERROR: or try http://valgrind.org on linux or man libgmallocon
>> Apple to find memory corruption errors >> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >> link, and run >> [0]PETSC ERROR: to get more information on the crash. >> [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [0]PETSC ERROR: Signal received! >> [0]PETSC ERROR: >>
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 >> 17:29:26 CDT 2008 HG revision: >> 4466c6289a0922df26e20626fd4a0b4dd03c8124 >> [0]PETSC ERROR: See docs/changes/index.html for recentupdates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> [0]PETSC ERROR: See docs/index.html for manual pages. >> [0]PETSC ERROR: >>
>> [0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by >> trisanna Tue Apr 19 21:13:58 2016 >> [0]PETSC ERROR: Libraries linked from >>/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
>> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 >> [0]PETSC ERROR: Configure options --with-debugging=no >> --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 >> --download-mpich=1 --with-mpi=1 --with-x=0 >> --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >> [0]PETSC ERROR: >>
>> [0]PETSC ERROR: User provided function() line 0 in unknown >> directory unknown file >> [unset]: aborting job: >> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> >> <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>>> wrote: >> >> Hi Doug >> >> I thought this was the case as well but when I trymanually
>> in Freeview and select the correct label, Freeview crashes >> and gives this error in the terminal: >> >> trisanna@kaplan:~$ freeview >> *** Error in `freeview.bin': double free or corruption (out): >> 0x0000000029080920 *** >> Abort (core dumped) >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 6:17 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: >> >> I don't think that is the problem. The problem is that it >> cannot find >> the file. Try giving it the whole path >> >> On 04/19/2016 05:45 PM, Bruce Fischl wrote: >> > Hi Trisanna >> > >> > if your output is .mgz it isn't a label file. Labels >> are stored in >> > .label names and are text files. The .mgz is ascalar
>> field over the >> > surface (that is, a vector with a single value at each >> surface >> > location). In freeview you can view it as: >> > >> > freeview -f lh.inflated:overlay=surfaceoverlay.mgz >> > >> > >> > cheers >> > Bruce >> > >> > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: >> > >> >> Hi Doug >> >> >> >> So I ran mri_vol2surf and generated my .mgz surface >> overlay using >> >> --regheader as you suggested. I than ran mri_cor2label >> using that >> >> .mgz file. >> >> This also completed successfully. However, when I then >> try to open >> >> the pial >> >> surface and the corresponding new label infreeview,
>> it says it >> >> cannot read >> >> the label. Below is what I ran. I tried the same thing >> for the inflated >> >> surface. >> >> >> >> I put labelid as "1" as I was unsure as to what to >> put. Could this have >> >> affected the label creation? >> >> >> >> Trisanna >> >> >> >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> >> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> --regheader >> >> icbm-102 --hemi lh --surf pial >> >> srcvol = >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> >> srcreg unspecified >> >> srcregold = 0 >> >> srcwarp unspecified >> >> surf = pial >> >> hemi = lh >> >> reshape = 0 >> >> interp = nearest >> >> float2int = round >> >> GetProjMax = 0 >> >> INFO: float2int code = 0 >> >> INFO: changing type to float >> >> Done loading volume >> >> Computing registration from header. >> >> Using >> /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> >> reference. >> >> Reading surface >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> >> Done reading source surface >> >> Mapping Source Volume onto Source Subject Surface >> >> 1 0 0 0 >> >> using old >> >> Done mapping volume to surface >> >> Number of source voxels hit = 85413 >> >> Writing to >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> >> Dim: 169941 1 1 >> >> >> >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> >> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> --id 1 --l >> >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> --surf lh.pial >> >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks >> Exp $ >> >> Loading mri >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> >> ------- Vox2RAS of input volume ----------- >> >> -1.000 0.000 0.000 84970.500; >> >> 0.000 0.000 1.000 -0.500; >> >> 0.000 -1.000 0.000 0.500; >> >> 0.000 0.000 0.000 1.000; >> >> Scanning the volume >> >> Found 1651 label voxels >> >> Writing label file >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> >> Centroid: -56170.34 -0.50 0.50 >> >> mri_cor2label completed SUCCESSFULLY >> >> >> >> >> >> trisanna@kaplan:~$ freeview -f >> >> >>/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
>> >> No such file or directory >> >> freeview.bin: could not open label file labeltest.label >> >> No such file or directory >> >> LabelRead failedNo such file or directory >> >> en label file labeltest.label >> >> >> >> >> >> >> >> -- >> >> Ph.D. CandidateMcGill University >> >> Integrated Program in Neuroscience >> >> Psychology >> >> >> >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> >> <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca> >> <mailto:trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>>> wrote: >> >> many thanks - will give this a go! >> >> >> >> -- >> >> Ph.D. CandidateMcGill University >> >> Integrated Program in Neuroscience >> >> Psychology >> >> >> >> >> >> On Tue, Apr 19, 2016 at 3:48 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: >> >> yes, but the surface overlay is in mgz (or >> nii.gz) format >> >> >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> >> > Hi Doug >> >> > >> >> > below is the email I had written last Friday. >> I thought >> >> it got lost in >> >> > the mix. I was told by Bruce to use >> identity.nofile as >> >> the >> >> > transformation since my labels and T1s are >> already in >> >> the same space >> >> > and I just want to resample my labels tothe
>> surfaces. >> >> > >> >> > *I will try, as you suggest, --regheader * >> >> > >> >> > When I do "mri_cor2label --help" it says it >> uses surface >> >> overlays or >> >> > volumes. *I am not sure why I want to generate >> a volume >> >> with >> >> > mri_vol2surf* - shouldn't I generate a surface >> overlay >> >> that I can then >> >> > create as a label using mri_cor2label? >> >> > >> >> > many thanks >> >> > >> >> > Trisanna >> >> > >> >> > >> >> > >> >> > thanks Bruce >> >> > >> >> > I could not find identity.nofile anywhere, >> when I ran >> >> mri_vol2surf I >> >> > got the following error >> >> > >> >> > trisanna@kaplan:~$ mri_vol2surf --mov >> >> > >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> >> --o >> >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> >> identity.nofile --hemi lh >> >> > srcvol = >> >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> >> > srcreg = identity.nofile >> >> > srcregold = 0 >> >> > srcwarp unspecified >> >> > surf = white >> >> > hemi = lh >> >> > reshape = 0 >> >> > interp = nearest >> >> > float2int = round >> >> > GetProjMax = 0 >> >> > INFO: float2int code = 0 >> >> > INFO: changing type to float >> >> > Done loading volume >> >> > regio_read_register(): No such file or directory >> >> > Could not open identity.nofile >> >> > >> >> > >> >> > >> >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> >> <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 Trisanna >> >> > >> >> > you can give the transformation "file"named
>> >> identity.nofile and it >> >> > will assume that the transform is the >> identity. You can >> >> then use >> >> > mri_vol2label to sample the label onto the >> surface and >> >> visualize it with: >> >> > >> >> > freeview -f lh.inflated:label=lh.labels.label >> >> > >> >> > or some such >> >> > >> >> > cheers >> >> > Bruce >> >> > >> >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> >> > >> >> > Hi there >> >> > >> >> > Just to reiterate my point above, when I open >> a surface >> >> created in >> >> > Freesurfer with my labels.mgz (converted from >> minc) in >> >> Freeview (i.e. no >> >> > transformations have been performed) I get the >> following >> >> snapshot >> >> > #1. Clearly, my original labels are aligned >> with the >> >> surface, as they >> >> > should >> >> > be since Freesurfer did not alter thespace.
>> So, how can >> >> I use mrivol2surf >> >> > to resample the surface such that the vertices >> carry the >> >> label info? What >> >> > output format should I use in mrivol2surf? How >> can I >> >> open this output in >> >> > Freeview? >> >> > >> >> > For instance, when I try a .dat that creates no >> >> transformation and >> >> > save the >> >> > output as .mgz and use Overlay in Freeview, I get >> >> snapshot #2. So, >> >> > something >> >> > is going wrong in my mrivol2surf command. >> >> > >> >> > My apologies for the questions >> >> > Trisanna >> >> > >> >> > >> >> > >> >> > -- >> >> > Ph.D. Candidate >> >> > McGill University >> >> > Integrated Program in Neuroscience >> >> > Psychology >> >> > >> >> > >> >> > On Tue, Apr 19, 2016 at 1:23 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: >> >> > >> >> > I'm not sure what identity.nofile is or what you are >> >> trying to do (no >> >> > previous info in the email). If whatever you are >> trying to >> >> map to the >> >> > surface is already in anatomical space (so no >> registration >> >> necessary), >> >> > then you can use --regheader with mri_vol2surf. >> >> mri_cor2label will >> >> > take >> >> > a volume format as input (ie, mgz, nii.gz ,etc) >> >> > >> >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> >> > > >> >> > > Hi All! >> >> > > >> >> > > Could someone please tell me how to run >> mri_vol2surf >> >> using >> >> > > identity.nofile as the transformation? I >> cannot find any >> >> > documentation >> >> > > on identity.nofile >> >> > > >> >> > > Additionally, if my next step is to use the >> output of >> >> > mri_vol2surf in >> >> > > mri_cor2label, which takes surface overlays OR >> volumes, >> >> what format >> >> > > should my output be for mri_vol2surf? >> >> > > >> >> > > many thanks! >> >> > > >> >> > > Trisanna >> >> > > >> >> > > -- >> >> > > Ph.D. Candidate >> >> > > McGill University >> >> > > Integrated Program in Neuroscience >> >> > > Psychology >> >> > > >> >> > > >> >> > > >> >> > > _______________________________________________ >> >> > > 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%3E
>> >> > <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 >> >> > >> >> > >> >> > The information in this e-mail is intended only >> for the >> >> person to >> >> > whom it is >> >> > addressed. If you believe this e-mail wassent
>> to you in >> >> error and >> >> > the e-mail >> >> > contains patient information, please contact the >> Partners >> >> > Compliance HelpLine at >> >> > http://www.partners.org/complianceline . If the >> e-mail was >> >> sent to >> >> > you in error >> >> > but does not contain patient information, please >> contact >> >> the >> >> > sender and properly >> >> > dispose of the e-mail. >> >> > >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@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%3E
>> >> 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 >> >> >> >> >> >> >> >> >> >> >> > >> > >> > _______________________________________________ >> > 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> >> Fax: 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%3E
>> 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 >> >> >> >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Hi Trisanna
your output is a .mgz file, which is *not* a label. Try loading it as an overlay. The label format is different (ascii for one thing, and only part of the surface for another).
cheers Bruce
On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
Hi Doug
I thought this was the case as well but when I try manually in Freeview and select the correct label, Freeview crashes and gives this error in the terminal:
trisanna@kaplan:~$ freeview *** Error in `freeview.bin': double free or corruption (out): 0x0000000029080920 *** Abort (core dumped)
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: I don't think that is the problem. The problem is that it cannot find the file. Try giving it the whole path
On 04/19/2016 05:45 PM, Bruce Fischl wrote: > Hi Trisanna > > if your output is .mgz it isn't a label file. Labels are stored in > .label names and are text files. The .mgz is a scalar field over the > surface (that is, a vector with a single value at each surface > location). In freeview you can view it as: > > freeview -f lh.inflated:overlay=surfaceoverlay.mgz > > > cheers > Bruce > > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: > >> Hi Doug >> >> So I ran mri_vol2surf and generated my .mgz surface overlay using >> --regheader as you suggested. I than ran mri_cor2label using that >> .mgz file. >> This also completed successfully. However, when I then try to open >> the pial >> surface and the corresponding new label in freeview, it says it >> cannot read >> the label. Below is what I ran. I tried the same thing for the inflated >> surface. >> >> I put labelid as "1" as I was unsure as to what to put. Could this have >> affected the label creation? >> >> Trisanna >> >> >> trisanna@kaplan:~$ mri_vol2surf --mov >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader >> icbm-102 --hemi lh --surf pial >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >> srcreg unspecified >> srcregold = 0 >> srcwarp unspecified >> surf = pial >> hemi = lh >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Computing registration from header. >> Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >> reference. >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 0 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 85413 >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> Dim: 169941 1 1 >> >> >> trisanna@kaplan:~$ mri_cor2label --i >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >> ------- Vox2RAS of input volume ----------- >> -1.000 0.000 0.000 84970.500; >> 0.000 0.000 1.000 -0.500; >> 0.000 -1.000 0.000 0.500; >> 0.000 0.000 0.000 1.000; >> Scanning the volume >> Found 1651 label voxels >> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest >> Centroid: -56170.34 -0.50 0.50 >> mri_cor2label completed SUCCESSFULLY >> >> >> trisanna@kaplan:~$ freeview -f >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest >> No such file or directory >> freeview.bin: could not open label file labeltest.label >> No such file or directory >> LabelRead failedNo such file or directory >> en label file labeltest.label >> >> >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >> <trisanna.sprung-much@mail.mcgill.ca> wrote: >> many thanks - will give this a go! >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu> wrote: >> yes, but the surface overlay is in mgz (or nii.gz) format >> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >> > Hi Doug >> > >> > below is the email I had written last Friday. I thought >> it got lost in >> > the mix. I was told by Bruce to use identity.nofile as >> the >> > transformation since my labels and T1s are already in >> the same space >> > and I just want to resample my labels to the surfaces. >> > >> > *I will try, as you suggest, --regheader * >> > >> > When I do "mri_cor2label --help" it says it uses surface >> overlays or >> > volumes. *I am not sure why I want to generate a volume >> with >> > mri_vol2surf* - shouldn't I generate a surface overlay >> that I can then >> > create as a label using mri_cor2label? >> > >> > many thanks >> > >> > Trisanna >> > >> > >> > >> > thanks Bruce >> > >> > I could not find identity.nofile anywhere, when I ran >> mri_vol2surf I >> > got the following error >> > >> > trisanna@kaplan:~$ mri_vol2surf --mov >> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> --o >> > /data-01/trisanna/freesurfer/icbm-112 --reg >> identity.nofile --hemi lh >> > srcvol = >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >> > srcreg = identity.nofile >> > srcregold = 0 >> > srcwarp unspecified >> > surf = white >> > hemi = lh >> > reshape = 0 >> > interp = nearest >> > float2int = round >> > GetProjMax = 0 >> > INFO: float2int code = 0 >> > INFO: changing type to float >> > Done loading volume >> > regio_read_register(): No such file or directory >> > Could not open identity.nofile >> > >> > >> > >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu >> <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> > Hi Trisanna >> > >> > you can give the transformation "file" named >> identity.nofile and it >> > will assume that the transform is the identity. You can >> then use >> > mri_vol2label to sample the label onto the surface and >> visualize it with: >> > >> > freeview -f lh.inflated:label=lh.labels.label >> > >> > or some such >> > >> > cheers >> > Bruce >> > >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >> > >> > Hi there >> > >> > Just to reiterate my point above, when I open a surface >> created in >> > Freesurfer with my labels.mgz (converted from minc) in >> Freeview (i.e. no >> > transformations have been performed) I get the following >> snapshot >> > #1. Clearly, my original labels are aligned with the >> surface, as they >> > should >> > be since Freesurfer did not alter the space. So, how can >> I use mrivol2surf >> > to resample the surface such that the vertices carry the >> label info? What >> > output format should I use in mrivol2surf? How can I >> open this output in >> > Freeview? >> > >> > For instance, when I try a .dat that creates no >> transformation and >> > save the >> > output as .mgz and use Overlay in Freeview, I get >> snapshot #2. So, >> > something >> > is going wrong in my mrivol2surf command. >> > >> > My apologies for the questions >> > Trisanna >> > >> > >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve >> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> wrote: >> > >> > I'm not sure what identity.nofile is or what you are >> trying to do (no >> > previous info in the email). If whatever you are trying to >> map to the >> > surface is already in anatomical space (so no registration >> necessary), >> > then you can use --regheader with mri_vol2surf. >> mri_cor2label will >> > take >> > a volume format as input (ie, mgz, nii.gz ,etc) >> > >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >> > > >> > > Hi All! >> > > >> > > Could someone please tell me how to run mri_vol2surf >> using >> > > identity.nofile as the transformation? I cannot find any >> > documentation >> > > on identity.nofile >> > > >> > > Additionally, if my next step is to use the output of >> > mri_vol2surf in >> > > mri_cor2label, which takes surface overlays OR volumes, >> what format >> > > should my output be for mri_vol2surf? >> > > >> > > many thanks! >> > > >> > > Trisanna >> > > >> > > -- >> > > Ph.D. Candidate >> > > McGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the >> person to >> > whom it is >> > addressed. If you believe this e-mail was sent to you in >> error and >> > the e-mail >> > contains patient information, please contact the Partners >> > Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was >> sent to >> > you in error >> > but does not contain patient information, please contact >> the >> > sender and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer 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 >> >> >> >> >> > > > _______________________________________________ > 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
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Douglas N Greve
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Trisanna Sprung-Much