[Freesurfer] produce mgz files from ima files of Siemens Scanner
Hi, i would like to know how i produce the mgz files from dicomfiles with the end ima instead of dcm? Thanks Thomas___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer - temporal lobes not included
did you check the skull stripping? And the talairach? On Wed, 21 Mar 2007, deepa preeti wrote: Hi Bruce, I am trying to do cortical thickness on a few scans. But on many of the subjects after autorecon2, I found temporal regions were not included. When I browsed the archive, it was suggested to add a few control points in the temporal lobe wm, saving the control points and rerunning using the command : recon-all -autorecon2-cp -autorecon3 -subjid subject - which is supposed to do the trick and fix the pial surface as well. Unfortunately, this didn't give me different results when I opened the image using this command : tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white The image was the same, with contol points added, and the temporal regionstillnot included. I have some images for you to look at ( However, I compared the stats ( lh & rh .aparc.2005 and lh & rh aparc ) before adding cp and after adding cp & rerunning eveything --- the values are different. Although the second image still did not include the temporal region, the stats nevertheless gave me different values. I am relatively new to Freesurfer and I appreciate your suggestions and thoughts on this dilemma. Thank you for taking the time to help me with this. Deepa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Complex value color scales.
I am trying to display phase information on the cortical surface using tksurfer, but am running into problems with the scale bar. Specifically when plotting scalar values using a complex color scale (e.g. RYGB Wheel), I am getting nice looking (continulus) cortical maps, with the correct scale values, but the color bar is showing up inconsistent (two colors). Is there any way to correct this problem, or access the actual color values being projected to the cortical mesh? Greg Appelbaum Post-Doctoral Fellow Center for Cognitive Neuroscience Duke University Box 90999 Durham, NC 27708 Office: (919) 668-3608 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer - temporal lobes not included
Deepa, How different were the values? The stats will differ about 0.02% from run-to-run on the same subject due to randomness present in some of the processing algorithms. Nick On Wed, 2007-03-21 at 11:17 -0400, deepa preeti wrote: > Hi Bruce, > > I am trying to do cortical thickness on a few scans. But on many of > the subjects after autorecon2, I found temporal regions were not > included. When I browsed the archive, it was suggested to add a few > control points in the temporal lobe wm, saving the control points and > rerunning using the command : > > recon-all -autorecon2-cp -autorecon3 -subjid subject > - which is supposed to do the trick and fix the pial surface as well. > Unfortunately, this didn't give me different results when I opened the > image using this command : > > tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white > The image was the same, with contol points added, and the temporal > region still not included. I have some images for you to look at ( > > However, I compared the stats ( lh & rh .aparc.2005 and lh & rh > aparc ) before adding cp and after adding cp & rerunning eveything --- > the values are different. Although the second image still did not > include the temporal region, the stats nevertheless gave me different > values. I am relatively new to Freesurfer and I appreciate your > suggestions and thoughts on this dilemma. Thank you for taking the > time to help me with this. > > Deepa. > > -- > Deepa Ramasamy, MD > Research Assistant > Buffalo Neuroimaging Center > The Jacobs Neurological Institute > Department of Neurology > Buffalo General Hospital > 100 High St. Buffalo, NY 14203 > Work: 716-859-7038 > Cell: 716-479- 3050 > E-Mail: [EMAIL PROTECTED] > ___ > 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] produce mgz files from ima files of Siemens Scanner
Thomas, You should be able to just use: mri_convert .ima 001.mgz but if that doesnt work try: mri_convert -it siemens .ima 001.mgz also, the --help flag to mri_convert will display its options. Nick On Wed, 2007-03-21 at 12:21 -0300, Thomas Doering wrote: > > > Hi, > i would like to know how i produce the mgz files from dicomfiles with > the end ima instead of dcm? > > Thanks > Thomas > ___ > 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
[Freesurfer] gray matter misclassified as csf
Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] gray matter misclassified as csf
Hi Binyam, don't worry about the subcortical regions in the wm.mgz (they were actually classified as white matter, but it won't matter) Bruce On Wed, 21 Mar 2007, Binyam Nardos wrote: Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] gray matter misclassified as csf
the wm.mgz is a binary segmentation of white and non-white, so there is no distinction between CSF and gm. There is some autofilling of various structures to get the topology of the gray/white interface close to spherical (e.g. ventricles, basal ganglia, etc...), but you should only bother editing if the final white and pial surfaces are not correct On Wed, 21 Mar 2007, Binyam Nardos wrote: Bruce, thanks for the quick response. I have to bug you one more time, I have attached a screenshot of the wm volume, would you correct the voxels classified as csf (on the top left corner) which, on the brainmask volume, appear as graymatter, or should I altogether stop worrying about gray matter structures misclassified as csf? thanks a lot, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 3/21/2007 4:35 PM To: Binyam Nardos Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] gray matter misclassified as csf Hi Binyam, don't worry about the subcortical regions in the wm.mgz (they were actually classified as white matter, but it won't matter) Bruce On Wed, 21 Mar 2007, Binyam Nardos wrote: Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
