I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy.
The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities).
The values in the table (ie, volumes and intensities) should be exactly the same.
This change only applies to dev (not to stable) and should be live on Tue.
doug
I should have mentioned one more thing. If you want to re-run recon-all so that it only re-creates the stats/aseg.stats table, then run
recon-all -s subject -segstats
doug
On Mon, 31 Jul 2006, Doug Greve wrote:
I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy.
The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities).
The values in the table (ie, volumes and intensities) should be exactly the same.
This change only applies to dev (not to stable) and should be live on Tue.
doug
Hi, So where can I download this update? Would I have to download the whole version of freesurfer? Thanks, HweeLing
On 8/1/06 10:09 AM, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:
I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy.
The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities).
The values in the table (ie, volumes and intensities) should be exactly the same.
This change only applies to dev (not to stable) and should be live on Tue.
doug
Hi Hwee Ling!
In general, we typically post a new stable update on our website every few weeks, and you can check https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes to see what bugs/fixes/changes have been made to each release.
For this change, Doug may be able to make something specific available to you so you can replace a binary and re-run recon-all -segstats -s subjid
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lee HL Sent: Monday, July 31, 2006 10:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aseg.stats
Hi, So where can I download this update? Would I have to download the whole version of freesurfer? Thanks, HweeLing
On 8/1/06 10:09 AM, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:
I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy.
The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities).
The values in the table (ie, volumes and intensities) should be exactly the same.
This change only applies to dev (not to stable) and should be live on Tue.
doug
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think we'd have to get nick to cut a new dev version and put it on the web site.
doug
On Mon, 31 Jul 2006, Jenni Pacheco wrote:
Hi Hwee Ling!
In general, we typically post a new stable update on our website every few weeks, and you can check https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes to see what bugs/fixes/changes have been made to each release.
For this change, Doug may be able to make something specific available to you so you can replace a binary and re-run recon-all -segstats -s subjid
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lee HL Sent: Monday, July 31, 2006 10:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aseg.stats
Hi, So where can I download this update? Would I have to download the whole version of freesurfer? Thanks, HweeLing
On 8/1/06 10:09 AM, "Doug Greve" greve@nmr.mgh.harvard.edu wrote:
I have just changed the way that DEV version recon-all creates the aseg.stats file. Previously, it would report everything that it found in FreeSurferColorLUT.txt. This included a lot of stuff that would never be in the subcortical segmentation, and this made the aseg.stats file very messy.
The new version only reports on segmentations that are part of the subcortical segmentation process (ie, in mri_ca_label). Note that there may still be some segmentations reported in aseg.stats that are not found in a particular aseg.mgz because that segmentation was not found during labeling (eg, hypointensities).
The values in the table (ie, volumes and intensities) should be exactly the same.
This change only applies to dev (not to stable) and should be live on Tue.
doug
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
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz?
-Eric
-----Original Message----- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz?
-Eric
-----Original Message----- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
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
So my images come off the scanner as DICOM.
Steps For Both: 1) Convert DICOM to ANALYZE 2) Align and Average the scans
Steps For Broken: 3) Convert to minc to create a brain mask and do some normalization 4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing monkeys) 5) Use mri_convert to convert MNC to MGZ
Steps for Working: 3) Convert Analyze to AFNI 4) Use 3drefit (AFNI) to fake 1.0mm voxels 5) Use mri_convert to convert BRIK to MGZ
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 8/1/2006 2:27 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems)
can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz?
-Eric
-----Original Message----- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
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
If you're doing a recon, then there should be an mri/orig.mgz which is conformed (ie, the dimension and voxel size will be 256^3 and 1mm^3) regardless of what you start with. This is what you should be doing all of your operations on (not necessarily orig.mgz, but a conformed volume).
doug
Faden, Eric (NIH/NIMH) [F] wrote:
So my images come off the scanner as DICOM.
Steps For Both:
- Convert DICOM to ANALYZE
- Align and Average the scans
Steps For Broken: 3) Convert to minc to create a brain mask and do some normalization 4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing monkeys) 5) Use mri_convert to convert MNC to MGZ
Steps for Working: 3) Convert Analyze to AFNI 4) Use 3drefit (AFNI) to fake 1.0mm voxels 5) Use mri_convert to convert BRIK to MGZ
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 8/1/2006 2:27 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems)
can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz?
-Eric
-----Original Message----- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't. Should I add blank slices to bring it to 256?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 8/1/2006 2:04 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Vanishing Control Points
what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, you should use mri_convert -c to "conform" them. tkmedit is only guaranteed to work with volumes that have been put through this process.
Bruce
On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't. Should I add blank slices to bring it to 256?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 8/1/2006 2:04 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Vanishing Control Points
what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mri_convert -c worked.
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 8/1/2006 2:39 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points
no, you should use mri_convert -c to "conform" them. tkmedit is only guaranteed to work with volumes that have been put through this process.
Bruce
On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't. Should I add blank slices to bring it to 256?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 8/1/2006 2:04 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Vanishing Control Points
what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Faden, Eric (NIH/NIMH) [F] -
Jenni Pacheco -
Lee HL