Re: [Freesurfer] WM volume
Yes (excluding ventricles, of course) On 2/23/2021 3:27 PM, Barletta, Valeria wrote: Thanks a lot. One more thing, is the total brain volume "BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles" ? Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, February 23, 2021 9:10 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] WM volume Yes, that is the right value. We changed the name of it in more recent versions to CerebralWhiteMatter On 2/22/2021 4:12 PM, Barletta, Valeria wrote: Dear Freesurfers, In what file inside the patient_name/stats folder do I find the total white matter volume? In the file "aseg.stats" there is something called lh/rh "cortical white matter volume", is that the right value to look at? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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
Re: [Freesurfer] WM volume
Thanks a lot. One more thing, is the total brain volume "BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles" ? Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, February 23, 2021 9:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM volume Yes, that is the right value. We changed the name of it in more recent versions to CerebralWhiteMatter On 2/22/2021 4:12 PM, Barletta, Valeria wrote: Dear Freesurfers, In what file inside the patient_name/stats folder do I find the total white matter volume? In the file "aseg.stats" there is something called lh/rh "cortical white matter volume", is that the right value to look at? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] WM volume
Yes, that is the right value. We changed the name of it in more recent versions to CerebralWhiteMatter On 2/22/2021 4:12 PM, Barletta, Valeria wrote: Dear Freesurfers, In what file inside the patient_name/stats folder do I find the total white matter volume? In the file "aseg.stats" there is something called lh/rh "cortical white matter volume", is that the right value to look at? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 ___ 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] WM volume
Dear Freesurfers, In what file inside the patient_name/stats folder do I find the total white matter volume? In the file "aseg.stats" there is something called lh/rh "cortical white matter volume", is that the right value to look at? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM Volume
nope, as long as the white surface is accurate you should be all set. cheers Bruce On Mon, 19 Jun 2017, Michael Davies wrote: > > Hello, i am currently looking at the WM Volume in heat mode and am curious > as to if i need to fill in all the small missing voxels located within the > boundary as well as the bigger holes? > > > Kind regards, Michael > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] WM Volume
Hello, i am currently looking at the WM Volume in heat mode and am curious as to if i need to fill in all the small missing voxels located within the boundary as well as the bigger holes? Kind regards, Michael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] wm- volume limitations
Great - just what I was looking for - thanks. Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Tuesday, July 07, 2015 10:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] wm- volume limitations the wmparc gets the cortical parcellation of the closest cortical parcellation (not necessarily normal to the surface). I think it has to be within 5mm of cortex or else it gets Unsegmented White Matter. The method is described here http://www.ncbi.nlm.nih.gov/pubmed/19027860 On 7/7/15 8:36 PM, Krieger, Donald N. wrote: Freesurfer provides ctx- and wm- volumes on either side of the white labelled sheet, all for a particular cortical region. What is the idea which is used to limit the extent of the wm- volume which is adjacent to a particular ctx- volume? Is it as simple as a maximum distance normal to the white matter sheet? I'm sure this is documented somewhere but I haven't been able to find it. Thanks. Don ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] wm- volume limitations
Freesurfer provides ctx- and wm- volumes on either side of the white labelled sheet, all for a particular cortical region. What is the idea which is used to limit the extent of the wm- volume which is adjacent to a particular ctx- volume? Is it as simple as a maximum distance normal to the white matter sheet? I'm sure this is documented somewhere but I haven't been able to find it. Thanks. Don ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] wm- volume limitations
the wmparc gets the cortical parcellation of the closest cortical parcellation (not necessarily normal to the surface). I think it has to be within 5mm of cortex or else it gets Unsegmented White Matter. The method is described here http://www.ncbi.nlm.nih.gov/pubmed/19027860 On 7/7/15 8:36 PM, Krieger, Donald N. wrote: Freesurfer provides ctx- and wm- volumes on either side of the “white” labelled sheet, all for a particular cortical region. What is the idea which is used to limit the extent of the wm- volume which is adjacent to a particular ctx- volume? Is it as simple as a maximum distance normal to the white matter sheet? I’m sure this is documented somewhere but I haven’t been able to find it. Thanks. Don ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] WM volume estimation - image capture
Whilst estimating white matter volume using mris_wm_volume is it possible to save an image for inspection? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM volume estimation - image capture
what kind of image do you mean? On Wed, 30 Apr 2008, Damian Jenkins wrote: Whilst estimating white matter volume using mris_wm_volume is it possible to save an image for inspection? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ 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] WM volume CSF BPF
Hi Bruce, Thanks for your prompt reply. Could you please further clarify some points below ? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thursday, October 25, 2007 8:38 PM To: Gallo, Antonio (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM volume CSF BPF On Thu, 25 Oct 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Dear All, We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5. Images belong to a group of Multiple Sclerosis patients. We would like to ask some questions and we apologize for the fact that we have quite a number of them :-) First, regarding measurements coming from mris_anatomical_stats: 1) What is exactly included in total WM volume? in mris_anatomical_stats this is the total volume occupied by voxels in the wm.mgz volume that are on. We now use mris_wm_volume to compute the volume using the surfaces, which we believe is more accurate. In WM.mgz file I can see on ventricles, deep nuclei, brainstem and off (zeroed) some little spots that don't correspond to WM lesions and are not enclosed by any surface contour (so we didn't correct). Since we would like to stay on FS 3.0.5, at least for now, could you please better clarify what does WM volume refer to? 2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ? there is no lateralization in this calculation, but you could use the aseg.mgz to get lh and rh volumes (in the aseg.stats file) 3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately. it depends whether they were classified as wm in the wm.mgz. If you use the mris_wm_volume method, then the hypointensities *will* be included in the volume. 4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume? just cortical GM. Second, some other questions on the aseg.stat file: 1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF? CSF is sulcal CSF and we don't label very much of it, as you can't really see it well on a T1-weighted MRI. The ventricles have their volumes given individually. 2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume? if they are labeled as hypointensities in the aseg.mgz. Are you manually editing them there or in the wm.mgz? We use to edit the WM lesions (mainly for the ones close to the cortex) by using control points and checking that the ?h.white looks fine (staying at the edge of the lesion and not inside. Should we correct the WM lesions differently? Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it? Could you suggest to us the best way to compute the BPF ? Thanks a lot in advance, (again) Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] WM volume CSF BPF
Dear All, We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5. Images belong to a group of Multiple Sclerosis patients. We would like to ask some questions and we apologize for the fact that we have quite a number of them :-) First, regarding measurements coming from mris_anatomical_stats: 1) What is exactly included in total WM volume? 2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ? 3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately. 4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume? Second, some other questions on the aseg.stat file: 1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF? 2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume? Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it? Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM volume CSF BPF
On Thu, 25 Oct 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Dear All, We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5. Images belong to a group of Multiple Sclerosis patients. We would like to ask some questions and we apologize for the fact that we have quite a number of them :-) First, regarding measurements coming from mris_anatomical_stats: 1) What is exactly included in total WM volume? in mris_anatomical_stats this is the total volume occupied by voxels in the wm.mgz volume that are on. We now use mris_wm_volume to compute the volume using the surfaces, which we believe is more accurate. 2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ? there is no lateralization in this calculation, but you could use the aseg.mgz to get lh and rh volumes (in the aseg.stats file) 3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately. it depends whether they were classified as wm in the wm.mgz. If you use the mris_wm_volume method, then the hypointensities *will* be included in the volume. 4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume? just cortical GM. Second, some other questions on the aseg.stat file: 1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF? CSF is sulcal CSF and we don't label very much of it, as you can't really see it well on a T1-weighted MRI. The ventricles have their volumes given individually. 2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume? if they are labeled as hypointensities in the aseg.mgz. Are you manually editing them there or in the wm.mgz? Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it? Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] wm volume
Hi all, is there a way I can attain the total wm volume for each of the hemispheres? And is it possible to estimate the wm volume of certain gross anatomical areas, like the different lobes? Thanks! Best wishes, Lars Tjelta Westlye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wm volume
you can get an estimate by loading the filled volume into matlab and counting the # of 127 (rh) and 255 (lh). Nothing lobar though - what would it mean? Where would you draw the borders? cheers, Bruce On Thu, 5 May 2005, Lars Tjelta Westlye wrote: Hi all, is there a way I can attain the total wm volume for each of the hemispheres? And is it possible to estimate the wm volume of certain gross anatomical areas, like the different lobes? Thanks! Best wishes, Lars Tjelta Westlye ___ 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] wm volume
sure. There are white matter parcellation schemes around, but we don't have one at the moment. cheers, Bruce On Thu, 5 May 2005, Lars Tjelta Westlye wrote: Thanks for your swift reply, Bruce! I don't know how the lobar drawing would be done, but am curious if there exist any kind of 'predefined regions' that could further refine the estimates of the total wm volume. It could be interesting to estimate where the wm loss is most prominent in aging, for example. I don't know if this is something that is easily done, though. Thanks again! Lars you can get an estimate by loading the filled volume into matlab and counting the # of 127 (rh) and 255 (lh). Nothing lobar though - what would it mean? Where would you draw the borders? cheers, Bruce On Thu, 5 May 2005, Lars Tjelta Westlye wrote: Hi all, is there a way I can attain the total wm volume for each of the hemispheres? And is it possible to estimate the wm volume of certain gross anatomical areas, like the different lobes? Thanks! Best wishes, Lars Tjelta Westlye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
