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