Re: [Freesurfer] wmparc parcellation for thalamus and brainstem

Hi Vasudev - These regions are part of the subcortical segmentation (aseg) volume: http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI a.y On Thu, 25 Aug 2016, Dev vasu wrote:   Dear all, After running through 

[Freesurfer] wmparc parcellation for thalamus and brainstem

Dear all, After running through recon-all ,I have obtained wmparc parcellation file (see the attached figure ). I would like to obtain parcellation at specific regions of interest for my study i.e Brain stem region and Thalamus region, could you please let me know how i could perform

Re: [Freesurfer] WmParc

you can also use mri_binarize --i wmparc.nii --match 1006 --o lh_entorhinal.nii On 05/13/2016 06:12 PM, Pradeep wrote: > Hi, > > This task will be a bit easy using fslmaths > > - convert mgz file to nii using mri_convert > -then use fslmaths -thr -uthr > > > example: > fslmaths wmparc.nii

Re: [Freesurfer] WmParc

What version of FS are you using? You may need a newer version of mri_aparc2aseg. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg On 05/12/2016 06:53 AM, Caroline Beelen wrote: > > If we changed the command –-ribbon to –- no ribbon, the script ran, >

[Freesurfer] WmParc

Dear FS team, We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran the following command: mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by our subject) We get the following

Re: [Freesurfer] WMPARC fsaverage

I made one and put it here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz Note that this should not be used for anything other than visualization, ie, it has little or no scientific value On 9/24/15 6:25 PM, Mohammed Goryawala wrote: ​ Hello FreeSurfer Experts,

Re: [Freesurfer] WMPARC fsaverage

Thank you Doug. On Mon, Sep 28, 2015 at 11:32 AM, Douglas Greve wrote: > > I made one and put it here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/wmparc.mgz > > Note that this should not be used for anything other than visualization, > ie, it has

[Freesurfer] WMPARC fsaverage

​Hello FreeSurfer Experts, This question has been asked before by someone and I am looking to do something similar. ​*If this isn't possible, could we obtain this from fsaverage? I noticed **that $FREESURFER_HOME/subjects/fsaverage does have an aparc+aseg.mgz * *is there also a way to get

Re: [Freesurfer] wmparc

Hi Sujith, sorry for the delay. The rule is that the voxel has to be within 5mm of the label. The unsegmented is the WM that is not within 5mm of any cortical label. Here is the ref https://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2008.pdf doug On 02/07/2014 04:53 PM, sujith vijayan

[Freesurfer] wmparc

Hi All, I have a few questions about wmparc: What rule is used to determine what grey matter structure corresponds to a white matter point? What exactly has to be the case when UnsegmentedWhiteMatter is reported? Is there a reference you could point me to? Thanks, Sujith

[Freesurfer] wmparc

Hi All, I have a couple of question about wmparc: What rule is used to determine what grey matter structure is reported for a point in the white matter? What exactly has to be the case when UnsegmentedWhiteMatter is reported? Is there a reference you could point me to? Thanks, Sujith

[Freesurfer] wmparc 2 wmsurf

I'm running FSv5.1.0 on RHEL6. 1) My goal is to run a glm-fit on White Matter aparc regions for a between group surf-based analysis and evaluate spatial maps of significant differences. 2) I noticed that fsaverage does not have a wmparc.mgz file, so I'm currently working with bert

[Freesurfer] wmparc

How much is the dilation (perpendicular to the cortical surface) for the creation of the white matter ROIs? Is there a citation for this? Chris Bell ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] wmparc

Hi all, I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in 5.0 there are volumes (segmentations) that do not appear in the wmparc.stats file (and appear in 4.5 version), for instance the subcortical structures, ventricles, cerebellum. In wmparc V 4.5 I have 1189 rows

Re: [Freesurfer] wmparc

Hi Jose, I believe we just got rid of redundant information. The subcortical structures are in the aseg.stats and don't need to be in the wmparc.stats. On Wed, 6 Apr 2011, Jose Soares wrote: Hi all, I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in 5.0 there are

Re: [Freesurfer] Wmparc Destrieux atlas

aparc2aseg using Destrieux atlas now seems to run OK for a different subject anyway - and I managed to get the same image as you did. But there are two problems: 1. when I do tkmedit subjid T1.mgz -segmentation wmparc.a2009s.mgz with color LUT, it still shows Killiany/Desikan conventions for wm

Re: [Freesurfer] Wmparc zero volumes

We don't usually use the Destrieux atlas for this as the wmparc was oritinally intended to measure gyral white matter. However, you can still run the commands, something like cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \ --volmask --annot

Re: [Freesurfer] Wmparc zero volumes

also be sure to add the flag --a2009s to the end of the mri_aparc2aseg command shown below (i forgot to mention this the first time aroun). this will fix the problem where you were not seeing the correct labels (you should now see the Destrieux labels when viewing in tkmedit). per the

Re: [Freesurfer] Wmparc Destrieux atlas

To get the Destrieux atlas parcellations in the wmparc, first have a look at the -wmparc section of the recon-all table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable those last two commands would be modified like this: mri_aparc2aseg --s subjid --labelwm --hypo-as-wm --rip-unknown

[Freesurfer] Wmparc Destrieux atlas

Hi all Could anyone help me with extracting the wmparc volume stats in accordance with Destrieux atlas? As it stands now the segmentations corresponding to whitematter beneath Destrieux 2009 parcellations are returned empty when called for Many thanks Lena \_

[Freesurfer] Wmparc zero volumes

I want to extract wm volumes using wmparc for parcellations contained in Destrieux 2009 atlas ­ but when I inspect my wmparc stats file, most of the volumes that I am interested in are reported as zero. What should I do to read these volumes? Many thanks Lena

[Freesurfer] wmparc creation

Hello- I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz and all was running well until

[Freesurfer] wmparc

I'll try this again as I'm stuck and in need of help. I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg

Re: [Freesurfer] wmparc creation

Does the mri dir exist in the directory that you are running it from? joel bruss wrote: Hello- I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm

Re: [Freesurfer] wmparc/white matter problems?

Hi Doug, The white matter in aseg seems to follow the same pattern as the white matter in wmparc...it goes into the ribbon (through the white matter surface into gray matter). -Ryan On Dec 7 2007, Doug Greve wrote: Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they

Re: [Freesurfer] wmparc/white matter problems?

Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they look in that area? Ryan Muetzel wrote: Hi Doug, The images are attached. Thanks again for your help! -Ryan On Dec 6 2007, Doug Greve wrote: Can you send a pic? Ryan Muetzel wrote: Hello, We are running

Re: [Freesurfer] wmparc/white matter problems?

Can you send a pic? Ryan Muetzel wrote: Hello, We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However,

[Freesurfer] WMparc step command line

could someone send me the command line for the last step in recon3 stream. The new version differs from the wiki table and I need to run just that last WMParc step. Thanks Amy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] WMparc step command line

recon-all -wmparc -s subject Amy DeLuca wrote: could someone send me the command line for the last step in recon3 stream. The new version differs from the wiki table and I need to run just that last WMParc step. Thanks Amy ___ Freesurfer mailing