Message: 17 Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Combined parcellation of the left and right hemispheres To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210931470.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Varsha
try using mri_aparc2aseg
Hi Bruce,
I tried using mri_aparc2aseg. While it gives me one volume file as I wanted, the indices on the volume don't seem to correspond to the look-up table that I created. I created the look-up table from the annotation files for the left and right hemispheres, appropriately changing the indices to make it a continuous list of ROIs.
Regards, Varsha
cheers Bruce On Thu, 21 Jul 2016, varshas@cns.iisc.ernet.in wrote:
Hi,
I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of the ROIs from both hemispheres. I tried using mri_label2vol. However, this gives me two separate volumes for the left and right hemispheres. Is there a way to combine these volumes into one? Alternatively, can one generate such a volume form an annotation file that has information of both hemispheres?
Any help is greatly appreciated!
Regards, Varsha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 18 Date: Thu, 21 Jul 2016 09:33:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer build stamps do not match To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210932310.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Subin
it looks more likely that you just don't have write access to your SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set it and it still points to the one we distribute? Typically you want to set the SUBJECTS_DIR env variable to some other directory where you will store all the subjects in a study.
cheers Bruce
On Thu, 21 Jul 2016, Lee Subin Kristine wrote:
Hi FreeSurfer Team,
After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand:
mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or directory.
recon-all used to work fine when I used the stable 5.3 version. I think it may have something to do with the fact that I previously ran recon-all in v.5.3, and so the current subject directory's stamp is still 5.3 (or blank..) and it does not match the current stamp of the dev version? I am not sure.. Could anyone tell me how I can fix this problem?
Thanks in advance, Subin
Message: 19 Date: Thu, 21 Jul 2016 09:35:35 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210933500.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi,? Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file?? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz.?
Thank you for the help!?
Kind regards, Tobias ? _________________________________________? Tobias Granberg, MD, PhD?
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging? Massachusetts General Hospital | Harvard Medical School
Resident in Radiology? Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
Message: 20 Date: Thu, 21 Jul 2016 13:42:48 +0000 From: "Granberg, Erik Tobias" EGRANBERG@mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 9294313C-F63A-420D-BF9C-D568A9A7B21D@mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
Hi Bruce,
Great, thanks for the quick reply! That worked beautifully. I was apparently using the wrong output option. Much appreciated!
Kind regards, Tobias
Tobias Granberg, MD, PhD
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School
Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
On 21 jul 2016, at 09:35, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias
Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thank you for your suggestion. I managed to figure out how to generate the right look-up table. I realised that the indices for the left and right hemispheres have 1000 and 2000 added to them. I created a look-up table with the right indices and it worked fine. Thank you.
Regards, Varsha
Message: 17 Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Combined parcellation of the left and right hemispheres To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210931470.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Varsha
try using mri_aparc2aseg
Hi Bruce,
I tried using mri_aparc2aseg. While it gives me one volume file as I wanted, the indices on the volume don't seem to correspond to the look-up table that I created. I created the look-up table from the annotation files for the left and right hemispheres, appropriately changing the indices to make it a continuous list of ROIs.
Regards, Varsha
cheers Bruce On Thu, 21 Jul 2016, varshas@cns.iisc.ernet.in wrote:
Hi,
I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of the ROIs from both hemispheres. I tried using mri_label2vol. However, this gives me two separate volumes for the left and right hemispheres. Is there a way to combine these volumes into one? Alternatively, can one generate such a volume form an annotation file that has information of both hemispheres?
Any help is greatly appreciated!
Regards, Varsha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 18 Date: Thu, 21 Jul 2016 09:33:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer build stamps do not match To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210932310.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Subin
it looks more likely that you just don't have write access to your SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set it and it still points to the one we distribute? Typically you want to set the SUBJECTS_DIR env variable to some other directory where you will store all the subjects in a study.
cheers Bruce
On Thu, 21 Jul 2016, Lee Subin Kristine wrote:
Hi FreeSurfer Team,
After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand:
mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or directory.
recon-all used to work fine when I used the stable 5.3 version. I think it may have something to do with the fact that I previously ran recon-all in v.5.3, and so the current subject directory's stamp is still 5.3 (or blank..) and it does not match the current stamp of the dev version? I am not sure.. Could anyone tell me how I can fix this problem?
Thanks in advance, Subin
Message: 19 Date: Thu, 21 Jul 2016 09:35:35 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210933500.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi,? Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file?? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz.?
Thank you for the help!?
Kind regards, Tobias ? _________________________________________? Tobias Granberg, MD, PhD?
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging? Massachusetts General Hospital | Harvard Medical School
Resident in Radiology? Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
Message: 20 Date: Thu, 21 Jul 2016 13:42:48 +0000 From: "Granberg, Erik Tobias" EGRANBERG@mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 9294313C-F63A-420D-BF9C-D568A9A7B21D@mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
Hi Bruce,
Great, thanks for the quick reply! That worked beautifully. I was apparently using the wrong output option. Much appreciated!
Kind regards, Tobias
Tobias Granberg, MD, PhD
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School
Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
On 21 jul 2016, at 09:35, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias
Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
glad it worked out Bruce On Fri, 22 Jul 2016, varshas@cns.iisc.ernet.in wrote:
Hi Bruce,
Thank you for your suggestion. I managed to figure out how to generate the right look-up table. I realised that the indices for the left and right hemispheres have 1000 and 2000 added to them. I created a look-up table with the right indices and it worked fine. Thank you.
Regards, Varsha
Message: 17 Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Combined parcellation of the left and right hemispheres To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210931470.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Varsha
try using mri_aparc2aseg
Hi Bruce,
I tried using mri_aparc2aseg. While it gives me one volume file as I wanted, the indices on the volume don't seem to correspond to the look-up table that I created. I created the look-up table from the annotation files for the left and right hemispheres, appropriately changing the indices to make it a continuous list of ROIs.
Regards, Varsha
cheers Bruce On Thu, 21 Jul 2016, varshas@cns.iisc.ernet.in wrote:
Hi,
I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of the ROIs from both hemispheres. I tried using mri_label2vol. However, this gives me two separate volumes for the left and right hemispheres. Is there a way to combine these volumes into one? Alternatively, can one generate such a volume form an annotation file that has information of both hemispheres?
Any help is greatly appreciated!
Regards, Varsha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 18 Date: Thu, 21 Jul 2016 09:33:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer build stamps do not match To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210932310.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Subin
it looks more likely that you just don't have write access to your SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set it and it still points to the one we distribute? Typically you want to set the SUBJECTS_DIR env variable to some other directory where you will store all the subjects in a study.
cheers Bruce
On Thu, 21 Jul 2016, Lee Subin Kristine wrote:
Hi FreeSurfer Team,
After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand:
mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or directory.
recon-all used to work fine when I used the stable 5.3 version. I think it may have something to do with the fact that I previously ran recon-all in v.5.3, and so the current subject directory's stamp is still 5.3 (or blank..) and it does not match the current stamp of the dev version? I am not sure.. Could anyone tell me how I can fix this problem?
Thanks in advance, Subin
Message: 19 Date: Thu, 21 Jul 2016 09:35:35 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210933500.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi,? Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file?? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz.?
Thank you for the help!?
Kind regards, Tobias ? _________________________________________? Tobias Granberg, MD, PhD?
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging? Massachusetts General Hospital | Harvard Medical School
Resident in Radiology? Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
Message: 20 Date: Thu, 21 Jul 2016 13:42:48 +0000 From: "Granberg, Erik Tobias" EGRANBERG@mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 9294313C-F63A-420D-BF9C-D568A9A7B21D@mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
Hi Bruce,
Great, thanks for the quick reply! That worked beautifully. I was apparently using the wrong output option. Much appreciated!
Kind regards, Tobias
Tobias Granberg, MD, PhD
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School
Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
On 21 jul 2016, at 09:35, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias
Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
HI Varsha
we need more information - what was the explicit list of commands you ran and what was their output? You probably have to change all the indices first if you want them to be different.
cheers Bruce
On Fri, 22 Jul 2016, varshas@cns.iisc.ernet.in wrote:
Message: 17 Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Combined parcellation of the left and right hemispheres To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210931470.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Varsha
try using mri_aparc2aseg
Hi Bruce,
I tried using mri_aparc2aseg. While it gives me one volume file as I wanted, the indices on the volume don't seem to correspond to the look-up table that I created. I created the look-up table from the annotation files for the left and right hemispheres, appropriately changing the indices to make it a continuous list of ROIs.
Regards, Varsha
cheers Bruce On Thu, 21 Jul 2016, varshas@cns.iisc.ernet.in wrote:
Hi,
I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of the ROIs from both hemispheres. I tried using mri_label2vol. However, this gives me two separate volumes for the left and right hemispheres. Is there a way to combine these volumes into one? Alternatively, can one generate such a volume form an annotation file that has information of both hemispheres?
Any help is greatly appreciated!
Regards, Varsha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 18 Date: Thu, 21 Jul 2016 09:33:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer build stamps do not match To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210932310.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Subin
it looks more likely that you just don't have write access to your SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set it and it still points to the one we distribute? Typically you want to set the SUBJECTS_DIR env variable to some other directory where you will store all the subjects in a study.
cheers Bruce
On Thu, 21 Jul 2016, Lee Subin Kristine wrote:
Hi FreeSurfer Team,
After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand:
mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or directory.
recon-all used to work fine when I used the stable 5.3 version. I think it may have something to do with the fact that I previously ran recon-all in v.5.3, and so the current subject directory's stamp is still 5.3 (or blank..) and it does not match the current stamp of the dev version? I am not sure.. Could anyone tell me how I can fix this problem?
Thanks in advance, Subin
Message: 19 Date: Thu, 21 Jul 2016 09:35:35 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607210933500.14081@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi,? Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file?? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz.?
Thank you for the help!?
Kind regards, Tobias ? _________________________________________? Tobias Granberg, MD, PhD?
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging? Massachusetts General Hospital | Harvard Medical School
Resident in Radiology? Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
Message: 20 Date: Thu, 21 Jul 2016 13:42:48 +0000 From: "Granberg, Erik Tobias" EGRANBERG@mgh.harvard.edu Subject: Re: [Freesurfer] Subtracting overlays To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 9294313C-F63A-420D-BF9C-D568A9A7B21D@mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
Hi Bruce,
Great, thanks for the quick reply! That worked beautifully. I was apparently using the wrong output option. Much appreciated!
Kind regards, Tobias
Tobias Granberg, MD, PhD
Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School
Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology
On 21 jul 2016, at 09:35, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay)
cheers Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias
Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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