Re: [Freesurfer] Gray matter volume image per group

It will be easier not to use make_average_subject. Just use mris_preproc as if you are doing a group analysis. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 The output of mris_preproc (lh.gender_age.thickness.00.mgh) can be compressed to an average with mri_concat lh

Re: [Freesurfer] Gray matter volume image per group

External Email - Use Caution Dear Doug, Thanks for the fast reply. Well we calculated the measures surface area (SA) , thickness (THK), volume (VOL) in each participant (in surf folder) of our groups and evaluated the differences between them using Monte Carlo. Now we wanted ju

Re: [Freesurfer] Gray matter volume image per group

What do you mean by "gray matter Volume"? Do you just want a map where the value at a voxel is the fraction of GM in that voxel? What space (eg, cvs, fsaverage, mni305) are you planning to make the average in? On 7/27/2020 4:33 AM, Oana Georgiana Rus wrote: > External Email - Use Cautio

[Freesurfer] Gray matter volume image per group

External Email - Use Caution Dear Freesurfer Community, I want to have an image of the average gray matter Volume in each of my 3 groups, and I did not find a good way to do it. I easily obtained an image from the GM thickness and area by using make_average_subject in each of m

Re: [Freesurfer] Gray Matter Intensity at each vertex

Use mri_vol2surf, something like mri_vol2surf --mov norm.mgz --hemi lh --projfrac 0.5 --regheader subject --o lh.norm.mgz On 8/5/2019 11:57 AM, Axelson, Eric D wrote: External Email - Use Caution Is there a way to extract the gray matter intensity value at each vertex of a surface file

[Freesurfer] Gray Matter Intensity at each vertex

External Email - Use Caution Is there a way to extract the gray matter intensity value at each vertex of a surface file (lh/rh.curv/pial/etc)? Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communication

Re: [Freesurfer] Gray matter normalized intensity

The intensity is partially what VBM is picking up, so it is not at all unreasonable to look at. On 3/21/19 9:52 PM, Bruce Fischl wrote: Hi Dorothy yes, we have looked at intensity effects in the gray matter before (David Salat for example has done this). It certainly reflects degree of myelinat

Re: [Freesurfer] Gray matter normalized intensity

of Dorothy > Sincasto > Reply-To: Freesurfer support list > Date: Thursday, March 21, 2019 at 8:44 PM > To: Freesurfer support list > Subject: [Freesurfer] Gray matter normalized intensity > > External Email - Use Caution > > Dear Freesurfers > > Usual

Re: [Freesurfer] Gray matter normalized intensity

Hi Dorothy yes, we have looked at intensity effects in the gray matter before (David Salat for example has done this). It certainly reflects degree of myelination as well as other things. Which volume are you looking at? The norm should be ok for this cheers Bruce On Thu, 21 Mar 2019, Doroth

Re: [Freesurfer] Gray matter normalized intensity

Thursday, March 21, 2019 at 8:44 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Gray matter normalized intensity External Email - Use Caution Dear Freesurfers Usually, the mean normalized intensity in aseg.stats is not considered import

[Freesurfer] Gray matter normalized intensity

External Email - Use Caution Dear Freesurfers Usually, the mean normalized intensity in aseg.stats is not considered important. However, by mistake, I put it in my analysis and found out that the mean intensity of the thalamus explains a lot the variance of my data. What could be

Re: [Freesurfer] Gray matter segmentation

Objet : Re: [Freesurfer] Gray matter segmentation Can you tar up and upload the subjects to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when they are there On 3/4/19 4:59 PM, Maxime Perron wrote: > > External Email - Use Caution > > Hi Freesurfer Experts,

Re: [Freesurfer] Gray matter segmentation

ad time to look at my problem? > > > Cheers, > > Maxime > > > *De :* Maxime Perron > *Envoyé :* 26 février 2019 14:26 > *À :* Freesurfer support list > *Objet :* Re: [Freesurfer] Gray matter segm

Re: [Freesurfer] Gray matter segmentation

Hi Maxime what does the aseg look like in that region? The pial surface gets "frozen" adjacent to the cc (so it is fixed to be in the same location as the white). Maybe the cc if off by a bit? cheers Bruce On Sat, 23 Feb 2019, Maxime Perron wrote: External Email - Use Caution

Re: [Freesurfer] gray matter volume of the entorhinal cortex

External Email - Use Caution Thank you! El lun., 4 feb. 2019 a las 15:29, Bruce Fischl () escribió: > Hi Jose > > the threshold is set so that the EC label has the average surface area of > the labels that went into the average. It is probably more accurate than > the aparc as it

Re: [Freesurfer] gray matter volume of the entorhinal cortex

Hi Jose the threshold is set so that the EC label has the average surface area of the labels that went into the average. It is probably more accurate than the aparc as it is based on actual cytoarchitectural landmarks that are visible in ex vivo mri. cheers Bruce On Mon, 4 Feb 2019, Labor

[Freesurfer] gray matter volume of the entorhinal cortex

External Email - Use Caution Dear Freesurfers, gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to

Re: [Freesurfer] Gray Matter Manual Edit Reverting

glad to hear it worked out Bruce On Mon, 26 Nov 2018, David S Lee wrote: External Email - Use Caution Hello Bruce,  Thank you for the quick response.  I unchecked "do not draw on voxels in the range of" in the "Recon Edit" window, and I was able to get the clone to work nicel

Re: [Freesurfer] Gray Matter Manual Edit Reverting

External Email - Use Caution Hello Bruce, Thank you for the quick response. I unchecked "do not draw on voxels in the range of" in the "Recon Edit" window, and I was able to get the clone to work nicely. Thank you for your time! David On Mon, Nov 19, 2018 at 1:38 PM David S Le

Re: [Freesurfer] Gray Matter Manual Edit Reverting

Hi David does this not work in freeview? Can you describe to Ruopeng (ccd) exactly what you tried? cheers Bruce On Mon, 19 Nov 2018, David S Lee wrote: External Email - Use Caution Hello Experts,  I am currently using FreeSurfer version 6.0 to make manual edits to T1w image

[Freesurfer] Gray Matter Manual Edit Reverting

External Email - Use Caution Hello Experts, I am currently using FreeSurfer version 6.0 to make manual edits to T1w images. In an earlier version 5.3, when GM has been erroneously removed, I used the "clone tool" to bring back voxels based on the original T1w. However, this tool

Re: [Freesurfer] Gray matter mask

You have to run recon-all through to the end. You can then extract a GM mask from that. You will need to register your PET image to the anatomical (mri_coreg), map the PET into the anatomical space, then use mri_segstats to compute the mean PET in the GM mask. Alternatively, you may want to use

[Freesurfer] Gray matter mask

Hello FS team, I am new to FS and using version 5.3 on a Mac. I have minimal programming background and this might be a very easy question, however I was not able to find a similar one in the archive. I have T1 MRI images from multiple subjects and I need to extract the brain gray matter mas

[Freesurfer] Gray matter volume calculation

Dear Freesurfer team, We are analyzing the gray matter volume of some customized labels, using mris_anatomical_stats. We are wondering about some characteristics of the obtained volume. Is the volume of a label (as calculated by mris_anatomical_stats) the sum of the volume elements of each v

Re: [Freesurfer] Gray Matter Errors, Ignored Areas

see: http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Fri, 8 Jan 2016, Julio Alberto González Torre wrote: Where could I upload it? 2016-01-07 14:44 GMT+01:00 Bruce Fischl : Hi Julio it's hard to tell why this is happening, but if you upload the entire subject

Re: [Freesurfer] Gray Matter Errors, Ignored Areas

Where could I upload it? 2016-01-07 14:44 GMT+01:00 Bruce Fischl : > Hi Julio > > it's hard to tell why this is happening, but if you upload the entire > subject directory and give us the coordinates of the inaccuracy we will > take a look > > cheers > Bruce > On Thu, 7 Jan 2016, Julio Alberto Go

[Freesurfer] Gray matter intensity

Hello, I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. And have successfully gotten the wm-gm signal intensity contrast, but

[Freesurfer] Gray Matter: GM mask vs Surface

Dear all, What is calculated in the aseg.stats cortical gray matter? As you see in the file attached, GM mask is integrating some of the skull (bad skull strip). But the surface line is correct. Do I have to adjust the segmentation for a correct value in the aseg.stats cortical grey matter or is

Re: [Freesurfer] Gray matter missed in the pial layer after mri_segment

Hello Erin, Thank you so much for asking. I have been curious to know this, too. Sincerely, Ye On Wed, Jul 17, 2013 at 12:41 PM, Erin Browning wrote: > Hello-- > > We have a set of scans with bad artifact throughout the temporal lobe and > the superior cortex. We've had to do the normalizatio

[Freesurfer] Gray matter missed in the pial layer after mri_segment

Hello-- We have a set of scans with bad artifact throughout the temporal lobe and the superior cortex. We've had to do the normalization steps (n3 correction, normalization) manually on most of these scans to preserve the gm/wm boundary. Now, when we run mri_segment, it leaves out some gray matter

Re: [Freesurfer] Gray matter

Hi Gabriel, I will try it! Thank you! 2013/3/22 Gabriel Gonzalez Escamilla > Hi Jordi, > > I think you are looking for the information contained on the wiki: > http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats > > *TotalGray* - total gray matter volume. This is simply the sum of SubCo

Re: [Freesurfer] Gray matter

Hi Jordi,I think you are looking for the information contained on the wiki:http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStatsTotalGray - total gray matter volume. This is simply the sum of SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes both surface-based volume calcul

[Freesurfer] Gray matter

Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calcula

[Freesurfer] Gray Matter probabilistic Segmentation

Dear FreeSurfer experts, I have some experience with FSL and SPM, but not a lot with FreeSurfer, so please bear with me. When I observe FreeSurfer segmentations, I see that images are binary (either a voxel belongs to a tissue class, or it does not) and not probabilistic. I want to obtain tot

Re: [Freesurfer] gray matter surface

Hi Eric there's a flag in the always-soon-to-be-released 5.2 that will run it cheers Bruce On Tue, 19 Feb 2013, Eric Cunningham wrote: oh interesting! i'm not sure if it will apply to me, but how would one go about the hires T2 / FLAIR based refinement? thanks, -eric On Tue, Feb 19, 2013 at

Re: [Freesurfer] gray matter surface

oh interesting! i'm not sure if it will apply to me, but how would one go about the hires T2 / FLAIR based refinement? thanks, -eric On Tue, Feb 19, 2013 at 11:44 AM, Bruce Fischl wrote: > Hi Eric > > yes, the bits of dura left around (your red circles) will make the > thickness incorrect in thos

Re: [Freesurfer] gray matter surface

Hi Eric yes, the bits of dura left around (your red circles) will make the thickness incorrect in those regions. If you want to fix it you can try the graph cuts skull stripping, or if you have a hires T2 or FLAIR we can typically refine the surfaces to avoid dura. As for the yellow arrow, I

Re: [Freesurfer] Gray matter hyperintensities and subcortical segmentation

if it's consistently in the same part of the pallidum you could manually correct some set of subjects (10 or so) and try building your own atlas and relabeling. cheers Bruce On Mon, 30 Apr 2012, Julius Juurmaa wrote: > Hello! > > This is probably a novice question, but here goes. We are using >

Re: [Freesurfer] gray matter/csf surface reconstruction

Hi Shani we described in in the recon1 NeuroImage paper (1999) and the PNAS paper, I think the next year. We don't impose any constrains on the pial surface as it evolves from the white surface (e.g. "link" terms in the energy functional), but let the vertices move whereever they want to in or

[Freesurfer] gray matter/csf surface reconstruction

Dear freesurfers, In order to generate cortical vector normals connecting homologous vertices of the inner and outer surface, I would like to better understand how the gray matter/csf surface is reconstructed and how correspondence between inner and outer surfaces is achieved. Does anyone can exp

Re: [Freesurfer] gray matter not incuded in pial surface

If you can compress the whole subject dir and load them here, that'd be great. https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -Khoa On Tue, 2 Aug 2011, _andre...@sapo.pt wrote: > Hi, > > I'm not being able to solve the segmentation problem on in this > subject. What files do I ne

Re: [Freesurfer] gray matter not incuded in pial surface

Hi, I'm not being able to solve the segmentation problem on in this subject. What files do I need to upload and were, please? Thank you, Andreia Citando Bruce Fischl : > Hi Andreia > > it's tough to tell from one slice. There appear to be some bright stuff > in the superficial gray matter, w

Re: [Freesurfer] gray matter not incuded in pial surface

Hi Andreia it's tough to tell from one slice. There appear to be some bright stuff in the superficial gray matter, which may be messing stuff up, not sure what it is, or it could be something happening through-plane that we can't see. If you want to upload the dataset I'll take a look cheers B

Re: [Freesurfer] gray matter not incuded in pial surface

There is some white matter there being excluded as well. If you include that, the pial surface will likely grow out and include that gm. On Aug 1, 2011, at 7:37 AM, _andre...@sapo.pt wrote: > Dear FS experts, > > I'm correcting the pial surface when it includes more than it is supposed, > but

Re: [Freesurfer] Gray Matter Mask - twist on previous post

Hi Emily, is it a volume or surface functional map? If volume, I think it should be pretty straightforward to sample it onto the surface with mri_vol2surf then go from there. There is probably a way to do this in SUMA also. cheers, Bruce On Wed, 9 Jan 2008, Emily Trittschuh wrote: Dear Gr

[Freesurfer] Gray Matter Mask - twist on previous post

Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset. Thank

Re: [Freesurfer] Gray matter mask

Do you mean cortical masks? If so, then {lh,rh}.ribbon.mgz are binary masks. You can convert them to nifti with: mri_convert lh.ribbon.mgz lh.ribbon.nii doug Anil Roy wrote: Hello all, Is there a method to generate a gray matter mask in Freesurfer that can be fed into AFNI. Could you pleas

[Freesurfer] Gray matter mask

Hello all, Is there a method to generate a gray matter mask in Freesurfer that can be fed into AFNI. Could you please point me to any existing documentation on the FS wiki that already does this as I was unable to find anything. Thanks a lot, Anil. __

RE: [Freesurfer] gray matter misclassified as csf

:[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

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 vol

[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).

Re: [Freesurfer] Gray matter volumes

Hi Derin, In addition to what Bruce mentioned, I would like to add that though corpus callosum is included as one of the anatomical structures in the cortical parcellation atlas (Desikan-Killiany), I actually would not use the values from it. We really intended for this structure to be used mo

Re: [Freesurfer] Gray matter volumes

1) yes, I would do the surfaces. 2) ignore the WM volume in mris_anatomical_stats. It's old and no longer accurate. It's going to disappear I think in the next release. Use the aseg instead. cheers, Bruce On Wed, 19 Jul 2006, Derin Cobia wrote: Hi again, Two questions: 1). You said earlie

[Freesurfer] Gray matter volumes

Hi again, Two questions: 1). You said earlier that GM volumes from mris_anatomical_stats are more accurate than from the aseg files. Would you recommend using the surface-based GM volumes instead of the ones from the aseg.stats files? I ask because we have ~200 subjects processed for volume, b