Re: [Freesurfer] mri_convert documentation error
Hi Doug, Thanks for clarifying this. My data is in Nifti-Format and looks fine in FSLview, meaning that left is on the right-hand side of the screen and vice versa. There is no qform orientation information in the header. When I convert my data without --in_orientation LAS, it ends up looking the wrong way round in tkmedit. When I convert as in mri_convert --in_orientation LAS mydata.nii 001.mgz it looks alright again, i.e. left is on the right-hand side of the screen in tkmedit. Now - having changed the orientation info, does that mean that I can rely on the lh.* surfaces truly being the left hemisphere, as long as I make sure that the 001.mgz input looks correct in tkmedit? Or is there some more intricate problem with the orientation info that I am missing? Thanks again, Johannes Doug Greve schrieb: I think this has been fixed. BTW, be very careful changing the orientation describtion. Note that it is the description that is being chaanged, NOT the pixel data. If your pixel data were oriented one way and the description was correct, changing the description will make the description wrong. doug Johannes Klein wrote: Hi folks, There's a small bug in the online help for mri_convert I found when trying to get my input Nifti's left/right to match with freesurfer conventions. When run without any parameters, the last paragraph describes the use of the --in-orientation switch. That must read --in_orientation (probably same for out-/out_). Took me a while to figure that one out ;) Cheers, Johannes ___ 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
Re: [Freesurfer] mri_convert documentation error
I've recently changed the way we handle nifti to read and write both the qform and sform, so it should be (more) comptatible with fsl. If it "looks right" in tkmedit, then you have the geometry correct, and freesurfer will respect that. But you have to make sure that you know which side is left/right in your image, which is very difficult to do if you did not use a fiducial. The subject's left side should show up on the right side of the image in tkmedit. You may want to use mri_convert to convert from your dicom into nifti or mgz for further processing in freesurfer. doug Johannes Klein wrote: Hi Doug, Thanks for clarifying this. My data is in Nifti-Format and looks fine in FSLview, meaning that left is on the right-hand side of the screen and vice versa. There is no qform orientation information in the header. When I convert my data without --in_orientation LAS, it ends up looking the wrong way round in tkmedit. When I convert as in mri_convert --in_orientation LAS mydata.nii 001.mgz it looks alright again, i.e. left is on the right-hand side of the screen in tkmedit. Now - having changed the orientation info, does that mean that I can rely on the lh.* surfaces truly being the left hemisphere, as long as I make sure that the 001.mgz input looks correct in tkmedit? Or is there some more intricate problem with the orientation info that I am missing? Thanks again, Johannes Doug Greve schrieb: I think this has been fixed. BTW, be very careful changing the orientation describtion. Note that it is the description that is being chaanged, NOT the pixel data. If your pixel data were oriented one way and the description was correct, changing the description will make the description wrong. doug Johannes Klein wrote: Hi folks, There's a small bug in the online help for mri_convert I found when trying to get my input Nifti's left/right to match with freesurfer conventions. When run without any parameters, the last paragraph describes the use of the --in-orientation switch. That must read --in_orientation (probably same for out-/out_). Took me a while to figure that one out ;) Cheers, Johannes ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem in curv surface
recon-all -s maryam -finalsurfs Reza Rajimehr wrote: Hi, I have recently reconstructed a brain using "recon-all -autorecon" in dev environment. First I converted anatomicals to mgz format and then I ran the following commands sequentially: recon-all -subjid subject -autorecon1 -legacy recon-all -subjid subject -autorecon2 The reconstruction has been done successfully without error. The inflated surface is almost fine (without topological defects) but the "curv" surfaces (curv.lh and curv.rh) do not look normal. They have only red boundaries (sulci); the green boundaries (gyri) are absent. The sulc surfaces look fine though. on machine monkeylove source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/ship/3/users/reza/mvp022106/3danat which recon-all /usr/local/freesurfer/dev/bin//recon-all cd /space/ship/3/users/reza/mvp022106/MYSTUDY Thanks for any comments, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] autorecon3 parcellations and corresponding lists of labels
Hello, I'm hoping someone can help me clear something up about the different parcellations now performed as part of autorecon3. In tksurfer, when I select file-->Label-->Import Annotation, I can choose from (for the lh, for example) lh.aparc.annot or lh.aparc.a2005s.annot. I understand that one of these is the "old" parcellation and one is the newer one done in (for the moment) the dev version of Freesurfer. My question is which of the aseg.mgz's correspond to which parcellation, and also which list in FREESUFER_HOME contains the list of labels created by which parcellation. When I look in $FREESURFER_HOME, there are several texts with numbered lists of cortical and subcortical areas. Having the correct "match" between aseg and $FREESURFER_HOME/ seems to be necessary in the sense that, to load a segmentation in tkmedit, the aseg volume that is loaded must correspond to the appropriate color list in order to get the segmentation labeled properly. My experience has been that aparc+aseg.mgz and FreeSurferColorLUT.txt match one another and that these correspond to the annotation lh.aparc.annot when loaded upon a surface. It has also been my experience that the labels/regions in lh.aparc.a2005s.annot correspond to the list contained in $FREESURFER_HOME/Simple_surface_labels2005.txt. I am hoping someone can help me figure out which aseg volume, if any, contains this particular parcellation. As it happens, my area of interest is the superior temporal gyrus, which is subdivided in this aparc.a2005s.annot but not in the aparc.annot, and because I will be extracting functional and volumetric data about these ROI, I would like to work with as small anatomical areas as possible. The way that this ROI extraction works (as the scripts I am using are set up) involves inputing a particular aseg volume and the number of a given label as it appears on the appropriate corresponding list, and I have been unable to find a way to use the cortical areas identified in the aparc.a2005s.annot annotation. Sorry this email is long, and likely not using the most accurate terminology, but I hope I got my question across. Thanks so much! Best, Eli Diamond ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] autorecon3 parcellations and corresponding lists of labels
So you want aparc.a2005s mapped into the volume? You can use mri_label2vol. It will take an annotation as an input. You can also use it to map directly to functional space. Eli Diamond wrote: Hello, I'm hoping someone can help me clear something up about the different parcellations now performed as part of autorecon3. In tksurfer, when I select file-->Label-->Import Annotation, I can choose from (for the lh, for example) lh.aparc.annot or lh.aparc.a2005s.annot. I understand that one of these is the "old" parcellation and one is the newer one done in (for the moment) the dev version of Freesurfer. My question is which of the aseg.mgz's correspond to which parcellation, and also which list in FREESUFER_HOME contains the list of labels created by which parcellation. When I look in $FREESURFER_HOME, there are several texts with numbered lists of cortical and subcortical areas. Having the correct "match" between aseg and $FREESURFER_HOME/ seems to be necessary in the sense that, to load a segmentation in tkmedit, the aseg volume that is loaded must correspond to the appropriate color list in order to get the segmentation labeled properly. My experience has been that aparc+aseg.mgz and FreeSurferColorLUT.txt match one another and that these correspond to the annotation lh.aparc.annot when loaded upon a surface. It has also been my experience that the labels/regions in lh.aparc.a2005s.annot correspond to the list contained in $FREESURFER_HOME/Simple_surface_labels2005.txt. I am hoping someone can help me figure out which aseg volume, if any, contains this particular parcellation. As it happens, my area of interest is the superior temporal gyrus, which is subdivided in this aparc.a2005s.annot but not in the aparc.annot, and because I will be extracting functional and volumetric data about these ROI, I would like to work with as small anatomical areas as possible. The way that this ROI extraction works (as the scripts I am using are set up) involves inputing a particular aseg volume and the number of a given label as it appears on the appropriate corresponding list, and I have been unable to find a way to use the cortical areas identified in the aparc.a2005s.annot annotation. Sorry this email is long, and likely not using the most accurate terminology, but I hope I got my question across. Thanks so much! Best, Eli Diamond ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] autorecon3 parcellations and corresponding lists of labels
Hi Eli, the .annot files have the proper colortable embedded in them (and have for a long time), so they'll never be wrong. For the aseg just use the FreeSurferColorLUT.txt file. cheers, Bruce On Thu, 2 Mar 2006, Eli Diamond wrote: Hello, I'm hoping someone can help me clear something up about the different parcellations now performed as part of autorecon3. In tksurfer, when I select file-->Label-->Import Annotation, I can choose from (for the lh, for example) lh.aparc.annot or lh.aparc.a2005s.annot. I understand that one of these is the "old" parcellation and one is the newer one done in (for the moment) the dev version of Freesurfer. My question is which of the aseg.mgz's correspond to which parcellation, and also which list in FREESUFER_HOME contains the list of labels created by which parcellation. When I look in $FREESURFER_HOME, there are several texts with numbered lists of cortical and subcortical areas. Having the correct "match" between aseg and $FREESURFER_HOME/ seems to be necessary in the sense that, to load a segmentation in tkmedit, the aseg volume that is loaded must correspond to the appropriate color list in order to get the segmentation labeled properly. My experience has been that aparc+aseg.mgz and FreeSurferColorLUT.txt match one another and that these correspond to the annotation lh.aparc.annot when loaded upon a surface. It has also been my experience that the labels/regions in lh.aparc.a2005s.annot correspond to the list contained in $FREESURFER_HOME/Simple_surface_labels2005.txt. I am hoping someone can help me figure out which aseg volume, if any, contains this particular parcellation. As it happens, my area of interest is the superior temporal gyrus, which is subdivided in this aparc.a2005s.annot but not in the aparc.annot, and because I will be extracting functional and volumetric data about these ROI, I would like to work with as small anatomical areas as possible. The way that this ROI extraction works (as the scripts I am using are set up) involves inputing a particular aseg volume and the number of a given label as it appears on the appropriate corresponding list, and I have been unable to find a way to use the cortical areas identified in the aparc.a2005s.annot annotation. Sorry this email is long, and likely not using the most accurate terminology, but I hope I got my question across. Thanks so much! Best, Eli Diamond ___ 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
