[Freesurfer] Subcortical Segmentation Atlas Question

External Email - Use Caution Good Morning FreeSurfer Developers and Experts, I hope all is well. I am relatively new to the use of FreeSurfer and neuroimaging research in general. I have been looking for any documentation or details regarding the probabilistic atlas used for s

Re: [Freesurfer] Subcortical Segmentation Atlas Question

] Subcortical Segmentation Atlas Question External Email - Use Caution Good Morning FreeSurfer Developers and Experts, I hope all is well. I am relatively new to the use of FreeSurfer and neuroimaging research in general. I have been looking for any documentation or details regarding

Re: [Freesurfer] freesurfer subcortical segmentation

No, not yet On 5/19/2020 10:17 AM, ZhangBo wrote: External Email - Use Caution Hi teams, Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas? Thanks ___

[Freesurfer] freesurfer subcortical segmentation

External Email - Use Caution Hi teams, Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas? Thanks___ Free

[Freesurfer] subcortical segmentation

External Email - Use Caution Dear Freesurfer community, Our group is using the new FreeSurfer 6.0 (dev) subcortical segmentation scripts on HCP data (Freesurfer 5.3) segmentHA_T2.sh segmentThalamicNuclei.sh We have successfully segmented the three structures 1. lh.hippo

Re: [Freesurfer] Subcortical Segmentation

yes, you can use freeview to do this. cheers Bruce On Wed, 14 Jun 2017, AKUDJEDU, THEOPHILUS wrote: > > Hi FreeSurfers, > > > Are we able to correct the anatomical boundaries of subcortical structures > delineated with FreeSurfer? On which output file do we do this if it's > possible? > > >

[Freesurfer] Subcortical Segmentation

Hi FreeSurfers, Are we able to correct the anatomical boundaries of subcortical structures delineated with FreeSurfer? On which output file do we do this if it's possible? Thank you Theo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

Re: [Freesurfer] Subcortical segmentation

No, not yet, although they are high on our list Bruce > On Oct 10, 2016, at 2:57 PM, Ankita Sharma wrote: > > Hi, > Does anyone know if subthalamic nuclei and substantial nigra are part of the > automated sub-cortical segmentation (aseg) in Freesufer? > Thanks, > Ankita! > > __

Re: [Freesurfer] Subcortical Segmentation

Hi Raghav you should be able to use the -rl flag in mri_convert. Something like mri_convert -rl rawavg.mgz orig.mgz orig.268slices.mgz or, if you want nifti directly mri_convert -rl rawavg.mgz orig.mgz orig.268slices.nii.gz cheers Bruce On Mon, 10 Oct 2016, Raghav Mehta wrote: Hi Bru

[Freesurfer] Subcortical segmentation

Hi, Does anyone know if subthalamic nuclei and substantial nigra are part of the automated sub-cortical segmentation (aseg) in Freesufer? Thanks, Ankita! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/l

Re: [Freesurfer] Subcortical Segmentation

Hi Bruce, It looks like I was using wrong command to view output in tkmedit. I changed it following: tkmedit bert /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8/mri/normgz -segmentation /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8/mri/aseg.mgz And no

Re: [Freesurfer] Subcortical Segmentation

Hi Bruce, I used following command: recon-all -subject 8 -i /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer /testing-images/8/8.nii.gz -sd /home/raghav/Desktop/MRI_DATASETS/SATA/ freesurfer/testing-images/8 -all -cw256 I had to use -cw256 option due to the fact that in third dimension my volume

Re: [Freesurfer] Subcortical Segmentation

Hi Raghav We don't resample into MNI (or any other space). Was your input already resampled? In general you should send us your full command line and screen output Cheers Bruce > On Oct 9, 2016, at 1:39 PM, Raghav Mehta wrote: > > Raghav ___ Fre

Re: [Freesurfer] Subcortical Segmentation

Hi Bruce, I ran recon-all -all pipeline, but I am getting output in MNI space and not in native space, so question is, is there in way in which I can get output directly in native space or I have to transform them back into native space using inverse transform?? Thanks for your help. Raghav Meht

Re: [Freesurfer] Subcortical Segmentation

Hi Raghav there are individual steps that can be run, but part of the strength of FreeSurfer is that the comprehensive nature of our modeling gives us greater accuracy. For example, the cortical surface models are used to automatically correct the subcortical segmentation and such. In general

[Freesurfer] Subcortical Segmentation

Hi, I am new to freesurfer. I would like to know the command for subcortical segmentation of brain MRI volume. I read on freesurfer wiki page the recon-all -autorecon2 stage is useful for this. *My question is what exact command should I use for this purpose.* I am familiar with FSL. In FSL 'FIRST

Re: [Freesurfer] Subcortical segmentation voxel error

n process or during the actual brain scan. > > - Selina > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Thursday, March 10, 2016 11:26 AM > To: Freesurfer support list > Subject: R

Re: [Freesurfer] Subcortical segmentation voxel error

Hi Selina can you post a picture showing the problem? cheers Bruce On Thu, 10 Mar 2016, Selina Wilson wrote:   Hello all,  I am new to Freesurfer and learning as I go/encounter problems. This might be an obvious question, but has anyone had issues with black holes in their subcortical

[Freesurfer] Subcortical segmentation voxel error

Hello all, I am new to Freesurfer and learning as I go/encounter problems. This might be an obvious question, but has anyone had issues with black holes in their subcortical segmentation runs? The wiki page it suggests contacting the freesurfer mailing list before attempting to manually fix

Re: [Freesurfer] subcortical segmentation of thalamic nuclei

Hi Emma not yet, sorry Bruce On Wed, 26 Aug 2015, Emma Thompson wrote: > Dear Freesurfers, > Is it possible to segment using freesurfer specific thalamic nuclei, for > example, the VPL? > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

[Freesurfer] subcortical segmentation of thalamic nuclei

Dear Freesurfers, Is it possible to segment using freesurfer specific thalamic nuclei, for example, the VPL? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

Re: [Freesurfer] Subcortical segmentation necessary steps

Hi Tony if you run recon-all it will do everything needed. You could stop after mri_ca_label I suppose, but then you won't be able to use the surfaces to correct white matter and cortex. cheers Bruec On Wed, 22 Jul 2015, Tony Koroulakis wrote: > Dear Freesurfer Team, > > I am inquiring as t

[Freesurfer] Subcortical segmentation necessary steps

Dear Freesurfer Team, I am inquiring as to what are the necessary steps to run in recon all if one only wants to perform subcortical segmentation and relevant statistics. I just want to run the necessary steps for these to run properly. Thanks so much for your help. TK __

Re: [Freesurfer] Subcortical Segmentation Information

Hi Jen look at the references in that paper to Kennedy/Caviness and such. The auto labeling is based on the manual protocol developed by the Center for Morphometric Analysis at MGH and is published in a number of papers. cheers Bruce On Thu, 4 Jun 2015, Jennifer Eastman wrote: > Hello, > > I

[Freesurfer] Subcortical Segmentation Information

Hello, I am writing to see if there is more detailed information available about the protocols for identifying the caudate, putamen, and thalamus in the automated subcortical segmentations. I have read the Fischl et al. (2002) paper and I understand the general methodology described there; but

[Freesurfer] Subcortical segmentation edits to aseg.mgz and cortical thickness

Hello, I've made edits to aseg.mgz using FreeView, mostly deleting voxels that were incorrectly labeled as hippocampus. Based on the FreeSurfer tutorial found here: *http://freesurfer.net/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations

Re: [Freesurfer] subcortical segmentation only

Dear Bruce! Thanks a lot for the response. I try to get an idea about the minimal time needed to get the subcortical volumes. Best wishes, Luke > Re: [Freesurfer] subcortical segmentation only > Bruce Fischl Wed, 10 Dec 2014 05:22:18 -0800 > > Hi Luke > > you can r

Re: [Freesurfer] subcortical segmentation only

Hi Luke you can run -autorecon1 and -autorecon2 if all you care about is the aseg (although we have tools for editing the cortical aseg labels with the surfaces that you will not be able to use in this case) cheers Bruce On Wed, 10 Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote: > > Hi FS-folk

[Freesurfer] subcortical segmentation only

Hi FS-folks! I would like to perform a subcortical segmentation only and I am not sure which preprocessing steps I would have to perform to achieve this goal. So far I did always the full monty using reconall -all. Which reconall stages are needed if only the subcortical segmentation is of intere

Re: [Freesurfer] running freesurfer subcortical segmentation on a T2 weighted image only ?

Hi Vincent you mean to create it from a T2? Not really in our distributed version, although Koen Van Leemput (ccd) has some tools that can do this I believe. cheers Bruce On Wed, 23 Jul 2014, Vincent Noblet wrote: > Dear all, > > I was wondering if there is a way to use the segmentation of fr

[Freesurfer] running freesurfer subcortical segmentation on a T2 weighted image only ?

Dear all, I was wondering if there is a way to use the segmentation of freesurfer on a T2 weighted image only (without a T1 weighted image). Sincerely Vincent Noblet ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harva

Re: [Freesurfer] Subcortical segmentation for PAG

no, not yet. Sorry. We have been talking about it Bruce On Thu, 3 Apr 2014, Jeni Chen wrote: > Hi, > > Just wondering if the periaqueductal gray is part of the automatic > segmentation process and if we can obtain the volume. I checked the aseg > table but didn't see it, however, I somehow

[Freesurfer] Subcortical segmentation for PAG

Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni __

Re: [Freesurfer] subcortical segmentation VS surface

Hi Elisa, the fact that the surface does not follow the segmentation is not a problem by itself. The cortical segmentation created by the volumetric segmentation is never used. It just needs to be done as part of the subcortical segmentation. However, tou should make sure that the surfaces fol

Re: [Freesurfer] subcortical segmentation

Hi Liane the brainmask is not for subcortical segmentation - use the norm.mgz if you want to visualize subcortical structures cheers Bruce On Tue, 16 Jul 2013, Liane Hunter wrote: Hello,  I noticed that when I am checking the subcortical segmentation the brainmask does not accurately disp

[Freesurfer] subcortical segmentation

Hello, I noticed that when I am checking the subcortical segmentation the brainmaskdoes not accurately display the subcortical structures ( ie. the putamen is too small). The segmentation appears to be correct when I compare it to the original file. Does anyone know why this is the case? Also, if I

Re: [Freesurfer] subcortical segmentation

Hi Josh it might if the white matter is very dim, as it appears in your images. You might also try 5.2, which I think is better about this kind of thing. If you try control points, make sure that they get applied in the mri_ca_normalize step and not just to cortical normalizaation in mri_norml

[Freesurfer] subcortical segmentation

A subcortical segmentation error sometimes get Freesurfer (v 5.1) is cortical areas coming over into the hippocampus, ignoring the wm inferior and lateral to the hippocmapus (coronal). See attached png. Will adding wm control points help, or do they not inform the aseg segmentation. What is the bes

Re: [Freesurfer] subcortical segmentation

Hi Julia you can just cite that paper and the 2004 sequence-independent segmentation ones. cheers Bruce On Wed, 30 May 2012, Richter, Julia wrote: > Dear FreeSurfer experts, > > I have a question regarding the subcortical segmentation. In the paper by > Fischl et al (2002), I've read that the

[Freesurfer] subcortical segmentation

Dear FreeSurfer experts, I have a question regarding the subcortical segmentation. In the paper by Fischl et al (2002), I've read that the neuroanatomical labels are assigned to the voxels based on probabilistic information automatically estimated from a manually labeled training set. I don't u

Re: [Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

Hi Joshua if you can upload one dataset where the new version is poor and the old one is good I'll look into it. Thanks for helping to track this down Bruce On Tue, 17 Apr 2012, Joshua Lee wrote: Hi All, I thought I'd share my recent experiences with the newest Freesurfer v. 5.10 and subc

Re: [Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

It was version 4.50. I had to walk over to the other room to find out. ;) In any case, I achieved good results by including the use-mritotal flag on the current version. Josh On Tue, Apr 17, 2012 at 12:00 PM, Alan Francis wrote: > Hi Joshua: > > What version of FS 4 did you use? > > best, >

Re: [Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

Hi Joshua: What version of FS 4 did you use? best, Alan On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee wrote: > Hi All, > > I thought I'd share my recent experiences with the newest Freesurfer v. > 5.10 and subcortical segmentation. > > I ran a large sample of brains using the default stream of

[Freesurfer] Subcortical Segmentation Failures with Freesurfer v. 5.10

Hi All, I thought I'd share my recent experiences with the newest Freesurfer v. 5.10 and subcortical segmentation. I ran a large sample of brains using the default stream of Freesurfer v. 5.10. The resulting hippocampal segmentations were extremely poor, yet on the same sample of brains Freesurfe

Re: [Freesurfer] Subcortical segmentation atlas

no, we created our own atlas by manually labeling 39 subjects according to the CMA conventions, then iteratively going back over them to correct for consistent inaccuracies in the manual labelings. It's still an ongoing process as we are currently working on improving the manual putamen labels.

[Freesurfer] Subcortical segmentation atlas

Hello, I am working on comparing hand-drawn subcortical volumes to those output automatically by FreeSurfer. While reading about the segmentation process on the wiki, I came across this line: "The final segmentation is based on both a subject-independent probabilistic atlas and subject-speci

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

I've played around with byteswaping, but alas it doesn't seem to be the issue. The original ANALYZE file is 16-bit little endian (or at least says it is), but when I swap just the .img to big endian and use the original header, or give the original .img a 16-bit big-endian header, the resul

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

not an easy way. You'd have to find out what the byte swapping is in each file (or verify that the byteswapping is different). The other programs may check that the voxel values are "reasonable" and byteswap them if they are not. andrewkra...@ucla.edu wrote: > There's actually quite a large cha

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

There's actually quite a large chance for that, as we convert the DICOMs to ANALYZE on iMacs; skull-strip mostly on PCs; register and do other processing on remote machines running OpenBSD, IRIX, and Linux (some of which are little-endian and some of which are big-endian); and then check ev

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

It looks the same to me in fslview. I'm guessing that there is a byte-swapping problem. Any chance the .img file was created under linux and the .hdr created under windows (or vice versa)? andrewkra...@ucla.edu wrote: > Sure. Since it's probably a bit big for email, I uploaded it to > http://dl

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

Sure. Since it's probably a bit big for email, I uploaded it to http://dl.dropbox.com/u/432093/ANALYZE.zip -- Andrew Quoting Bruce Fischl : > Can you send us the analyze files? > > > > On Feb 24, 2011, at 12:37 PM, andrewkra...@ucla.edu wrote: > >> I actually didn't know you could load analyze

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

Can you send us the analyze files? On Feb 24, 2011, at 12:37 PM, andrewkra...@ucla.edu wrote: > I actually didn't know you could load analyze into tkmedit, but now that I > have, it does look like that too (just without the direction arrows). It > doesn't look like that when I look at it in o

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

I actually didn't know you could load analyze into tkmedit, but now that I have, it does look like that too (just without the direction arrows). It doesn't look like that when I look at it in other viewing programs, though (it looks like you'd expect). -- Andrew Quoting Douglas N Greve : >

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

Does it look like that when you load the original analyze into tkmedit? andrewkra...@ucla.edu wrote: > Sure. Here's a screenshot of the orig.mgz. > > Quoting Bruce Fischl : > >> Can you send us an image? The 16 bit shouldn't be a problem >> Bruce >> >> >> >> On Feb 23, 2011, at 7:28 PM, andrewkra.

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

Can you send us an image? The 16 bit shouldn't be a problem Bruce On Feb 23, 2011, at 7:28 PM, andrewkra...@ucla.edu wrote: > The orig.mgz shows up with weird colors (the grey matter is black, the > background is light gray, and there's a white halo around the brain and in > the ventricles/CS

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF). Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_c

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote: > add the flag -notal-check to the end of recon-all command to skip the > check. > > if you can make your average using nifti format you're better off as > analyze doesnt retain orientation (l/r) info. > > y

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

mri_convert --help has info on specifying orientation, with suitable warnings about the need for you to make sure you know which way is correct. n. On Wed, 2011-02-23 at 14:55 -0800, andrewkra...@ucla.edu wrote: > Thanks for the reply. For the orientation, I know from working with > the sourc

Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

add the flag -notal-check to the end of recon-all command to skip the check. if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info. you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/

[Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image

Hello, I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started. When I run "recon-all -autorecon1 -noskullstrip

Re: [Freesurfer] Freesurfer subcortical segmentation and FSL FIRST

On Mon, 26 Jul 2010, caoaize wrote: Hello Freesurfer Experts, I have a very basic question about the difference between Freesurfer subcortical segmentation tool and FSL FIRSTsub-cortical segmentation tool. May someone give me a point? Thanks.

[Freesurfer] Freesurfer subcortical segmentation and FSL FIRST

Hello Freesurfer Experts, I have a very basic question about the difference between Freesurfer subcortical segmentation tool and FSL FIRSTsub-cortical segmentation tool. May someone give me a point? Thanks. Aize

Re: [Freesurfer] subcortical segmentation

I have used: recon-all -s -subcortseg which runs through step 11 (-calabel), with the understanding re: accuracy that Bruce pointed out. -Julie On 7/7/10 8:07 AM, "Bruce Fischl" wrote: > Hi Salem, > > yes, you can run any individual options in recon-all. See the -help output > and run it th

Re: [Freesurfer] subcortical segmentation

Hi Salem, yes, you can run any individual options in recon-all. See the -help output and run it through step 11 if you want. Note that we do use the surfaces to improve the aseg accuracy at the very end, so you'll be giving that up. cheers Bruce On Wed, 7 Jul 2010, Hannoun wrote: > > > Hi,

[Freesurfer] subcortical segmentation

Hi, I am a new user of freesurfer. Is it possible to do just the volumetric processing stages without the surface processing stages? In fact what I want is to segment the subcortical structures. Is there a command line for this purpose only or should we run all the recon-all steps? Thank you

Re: [Freesurfer] Subcortical segmentation

Martin, In my experience I never found any problem in aseg.mgz cheers PPJ -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Thu, May 13, 2010 at

Re: [Freesurfer] Subcortical segmentation

If you want to use the subcortical volume measures, you defnitely want to make sure they are accurately following the intensity boundaries of the structures. That wiki page is a little misleading in that sense (I'll work on updating it). When I'm checking a recon for the other potential problem

Re: [Freesurfer] Subcortical segmentation

Maybe I've misunderstood. In http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction , after autorecon2 it says to check white and pial surfaces before running autorecon3. The linked tutorials on how to do WM, Pial and Final surfaces edits, does not mention checking the aseg as far as I

Re: [Freesurfer] Subcortical segmentation

It should be part of the workflow. Can you show me where it was not listed? On May 13, 2010, at 7:58 AM, Martin Ystad wrote: > Hi, I noticed that routinely checking the subcortical segmentation > (aseg.mgz) is not part of the Recommended Reconstruction Work Flow. Is > this because the subcorti

[Freesurfer] Subcortical segmentation

Hi, I noticed that routinely checking the subcortical segmentation (aseg.mgz) is not part of the Recommended Reconstruction Work Flow. Is this because the subcortical segmentation is highly accurate, or because manual intervention in the aseg is not recommended anyway? Thanks, Martin Ystad PhD-

Re: [Freesurfer] Subcortical Segmentation

What is your tkmedit command line? Alexa Nardelli wrote: Hi, I am new to freesurfer and to automated segmentation in general and I am having a problem using tkmedit's segmentation. I am able to open my images with freesurfer but I am having problems with the segmenation function. I am not

[Freesurfer] Subcortical Segmentation

Hi, I am new to freesurfer and to automated segmentation in general and I am having a problem using tkmedit's segmentation. I am able to open my images with freesurfer but I am having problems with the segmenation function. I am not sure I am even properly using it? I have gone through the

Re: [Freesurfer] subcortical segmentation

mostly changing gray matter structures won't except in places like lateral putamen which can be so close to insula. The white matter in the aseg is used as the basis of the cortical intensity normalization, so if you change that substantially it will change the cortical estimates as well. Bruc

[Freesurfer] subcortical segmentation

Hi I have done the three recon-all steps of cortical segmentation in my data and I corrected manually the segmentation errors. Now, I will check the subcortical structures. The correction of this subcortical segmentation will afect the previous cortical segmentation? Thanks Abel _

Re: [Freesurfer] subcortical segmentation

Hi Abel, yes, they will change the volume. You can manually correct them in the aseg.mgz if you want. cheers, Bruce On Fri, 18 Apr 2008, abel cruz vadell wrote: Hello I’m doing a thalamus volumetric analysis between two populations and checking the thalamus segmentation I found some pixels

Re: [Freesurfer] subcortical segmentation

Very embarrassing. I thought the column headings were 1. Col 2.Headers 3.Index 4.SegId as that is how they lined up in my text editor. Now I realize that the fourth column is indeed my volume. sorry for all the confusion. mishkin On 6/5/07, Doug Greve <[EMAIL PROTECTED]> wrote: what do you me

Re: [Freesurfer] subcortical segmentation

what do you mean? The 3rd and 4th columns have that info: # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 1 00.0 Left-Cerebral-Exterior 0. 0. 0. 0. 0. 2 2263489

Re: [Freesurfer] subcortical segmentation

Hi Mishkin, Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error m

Re: [Freesurfer] subcortical segmentation

Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields a

Re: [Freesurfer] subcortical segmentation

unfortunately, you have to go thru the segmentation as that is part of the surface-based stream. doug David Perlman wrote: On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems lik

Re: [Freesurfer] subcortical segmentation

you can do that, but the aseg is used to automate generation of surfaces (e.g. ventricle filling), so you would be trading computer time for human time. Bruce On Fri, 1 Jun 2007, David Perlman wrote: On this topic, if I *don't* want subcortical segmentation, but rather only surface generation

Re: [Freesurfer] subcortical segmentation

On this topic, if I *don't* want subcortical segmentation, but rather only surface generation and thickness maps, what's the best option to use for that? It seems like it might be -noaseg, but I couldn't find any references to this flag being used with human data, only with non- human prima

Re: [Freesurfer] subcortical segmentation

yes, sorry. The subcortical segmentation is early in the processing stream, and pretty much the slowest step. Bruce On Fri, 1 Jun 2007, Mishkin Derakhshan wrote: Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in

[Freesurfer] subcortical segmentation

Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in as little time as possible and since I am only looking for label volumes (ie. hippocampal volumes) i figured that there must be some steps I can leave out of -autorecon

Re: [Freesurfer] subcortical segmentation

Hi Eli, no, I wouldn't. After that paper we developed a nonlinear registration procedure, which is the long one, that helps things considerably. cheers, Bruce On Wed, 2 Nov 2005, Eliezer Kahn wrote: Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 ho

[Freesurfer] subcortical segmentation

Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 hours, primarily because of the Cannonical Registration (mri_ca_register) step. However, one the freesurfer papers (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Br

RE: [Freesurfer] subcortical segmentation

- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 6:59 AM To: Fornito, Alexander Cc: Bosky Ravindranath; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] subcortical segmentation Hi Alex, that was a prerelease version. The subcortical stuff seems fine

RE: [Freesurfer] subcortical segmentation

: Fornito, Alexander Cc: Bosky Ravindranath; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] subcortical segmentation Hi Alex, that was a prerelease version. The subcortical stuff seems fine, but we have fixed a couple of small bugs in other things, so we are going to recommend that

RE: [Freesurfer] subcortical segmentation

From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version with m

RE: [Freesurfer] subcortical segmentation

t; > -Original Message- > > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > > Sent: Tue 9/13/2005 5:45 AM > > To: Bosky Ravindranath > > Cc: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] subcortical segmentation > >

RE: [Freesurfer] subcortical segmentation

bugs with it? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite,

RE: [Freesurfer] subcortical segmentation

ailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version

Re: [Freesurfer] subcortical segmentation

not quite, sorry. We *really* don't want to release a version with major problems, so we've been going through everything repeatedly trying to catch everything. We're getting there. Bruce On Mon, 12 Sep 2005, Bosky Ravindranath wrote: To Bruce Fischl and List, I just wanted to know if the s

[Freesurfer] subcortical segmentation

To Bruce Fischl and List, I just wanted to know if the subcortical segmentation feature has been released. Thanks, Bosky ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer