[Freesurfer] Help with surface parcellation

Hello Everyone. I have a subject that throughout all the process "looked pretty good", however, when I reached the final process of checking surfaces and loading the aparc.annot file, I paid attention that all my "unknown area" , covers my -almost fully my "corpus callosum" label. What should I do

Re: [Freesurfer] mris_wm_volume

Hi Bruce, I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps? Cheers, -Morgan Bruce Fischl wrote: that looks like the correct usage. Can you send the entire screen output? On Fri, 20 Jul 2007, Morgan Hough wrote: Hi Nick, Thanks for the tool. I

Re: [Freesurfer] calculation of total cortical gray matter volume

Hi Bruce, Our subjects don't have this label (?h.cortex) in their label directories. Was this introduced with a recent version? What is the best approximation of this cortical gray matter volume measure for people who have older recons? Cheers, -Morgan Hi Mike, you need to exclude non-co

[Freesurfer] Another question

Dear Freesurfers Another problem that I'm facing while checking my surfaces is: when I load the aparc.annot I get a mass with the colors, which I assume can be a result of either loading the wrong lh/rh, on the original surface , or a result of noise. How can I fix it? Thanks again Sharon

[Freesurfer] Combining annots?

I have a question about using labels from different annots. The Desikan annot has a large region labeled unknown including medial wall and lateral insula and operculum. The Destrieux annot has a separate medial wall label. Is there an easy way to use the Destrieux annot label of the medial wall

Re: [Freesurfer] Another question

Hi Sharon, do you get any errors? Usually this means the surface was regenerated but not the parcellation (so it doesn't match anymore). Can you rerun the parcellation step and see if it fixes things? Bruce On Tue, 24 Jul 2007, Sharon Ruso wrote: Dear Freesurfers Another problem that I'm

Re: [Freesurfer] mris_wm_volume

works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps? Cheers, -Morgan Bruce Fischl wrote: that looks like the correct usage. Can you send the

Re: [Freesurfer] Help with surface parcellation

Hi Sharon, can you send us some images? Not quite sure I understand. Bruce On Tue, 24 Jul 2007, Sharon Ruso wrote: Hello Everyone. I have a subject that throughout all the process "looked pretty good", however, when I reached the final process of checking surfaces and loading the aparc.anno

Re: [Freesurfer] mris_wm_volume

Morning Bruce, I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the binary I have. The subject is located at NM

[Freesurfer] corpus callosum

I was wondering if I can use the surface area estimate of the aparc corpus callosum label as a decent subject specific measurement of its cross-sectional area. Thanks in advance. Cheers, -Morgan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] corpus callosum

Hi Morgan, we have explicit labeling of the cc that is more accurate that will be included in the upcoming release. Bruce On Tue, 24 Jul 2007, Morgan Hough wrote: I was wondering if I can use the surface area estimate of the aparc corpus callosum label as a decent subject specific measure

Re: [Freesurfer] corpus callosum

Hi Bruce, Would you believe results based on the current labels or do I need to wait for the new version? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, we have explicit labeling of the cc that is more accurate that will be included in the upcoming release. Bruce On Tue, 24 Jul 2007, M

Re: [Freesurfer] corpus callosum

I would use the voxel labels of the cc. We can give you a beta if you want. On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, Would you believe results based on the current labels or do I need to wait for the new version? Cheers, -Morgan Bruce Fischl wrote: Hi Morgan, we have explici

[Freesurfer] annotations

Hi everybody, when I try to load annotations (xh.aparc.annot) in one of the scans in tksurfer, I always get this error (on both hemispheres): CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Hemispheres match and I already re-ran autorecon-3, which went fine according t

[Freesurfer] Problems with recon-all

Hey everyone, seems that when I run recon-all it almost immediatly tells me I am missing a COR-.info file. I am using Par/Rec data that i converted into Analyze 7.5(.hdr, .img) is this not compatible for use in recon-all? corRead(): can't open file /usr/subjects/athpro/Swimmers_Jun06/060615_26SS

[Freesurfer] Annotations II

Sorry - I forgot to provide the other details machine: tkmeg environment: nmrenv Subjects-Dir: /autofs/space/megraid_083/MEG-MRI/seder/freesurfer current working directory: subjects-dir command line: tksurfer nmr00192 xh pial (+loading the annotations) Thanks again for helping, Claus _

Re: [Freesurfer] Problems with recon-all

can you send us the full recon-all cmd line and the screen output? On Tue, 24 Jul 2007, Andrew Ellison wrote: Hey everyone, seems that when I run recon-all it almost immediatly tells me I am missing a COR-.info file. I am using Par/Rec data that i converted into Analyze 7.5(.hdr, .img) is thi

Re: [Freesurfer] mris_wm_volume

okay, I think I know what's happing. Try this and see if it fixes it: from the subject's mri dir mri_convert --in_center --in_center 0 0 0 aseg.mg aseg_test.mgz then run mris_wm_volume -aseg aseg_test.mgz $subject $hemi On Tue, 24 Jul 2007, Morgan Hough wrote: Morning Bruce, I just chec

Re: [Freesurfer] mris_wm_volume

Hi Bruce, I try this in $subject/mri but I get the following: mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz mri_convert: error converting "--in_center" to a float for --in_center flag type mri_convert -u for usage Do I need to set the output datatype with -odt uchar or some

Re: [Freesurfer] mris_wm_volume

oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, I try this in $subject/mri but I get the following: mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz mri_convert: error converting "--in_center"

Re: [Freesurfer] mris_wm_volume

Hi Bruce, That did it. Great. The output is mm^3? Thanks again. Cheers, -Morgan Bruce Fischl wrote: oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, I try this in $subject/mri but I get the following: mri_c

Re: [Freesurfer] mris_wm_volume

yes On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, That did it. Great. The output is mm^3? Thanks again. Cheers, -Morgan Bruce Fischl wrote: oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, I try this

Re: [Freesurfer] mris_wm_volume

p.s. future versions of mris_wm_volume won't need this On Tue, 24 Jul 2007, Morgan Hough wrote: Hi Bruce, That did it. Great. The output is mm^3? Thanks again. Cheers, -Morgan Bruce Fischl wrote: oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 J

[Freesurfer] Problems still with recon-all

Hey all so when i run recon-all after ive set up all my subjects directories (previous issue) i am told the following [EMAIL PROTECTED] freesurfer]# recon-all -autorecon1 -subjid 060615_26SS INFO: SUBJECTS_DIR is /usr/subjects/athpro/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw

[Freesurfer] Partitioning GM/WM boundary surface

I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this

Re: [Freesurfer] Partitioning GM/WM boundary surface

Hi Morgan, yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall. cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote: I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering

Re: [Freesurfer] Problems still with recon-all

Andrew, When the freesurfer script is run, that is, when you type: source $FREESURFER_HOME/SetUpFreeSurfer.csh does it output any error messages? You should see something like: freesurfer-Linux-centos4-stable-v3.0.5-20070717 Setting up environment for FreeSurfer/FS-FAST (an

[Freesurfer] about mris_make_surfaces

Hi all, I am trying to use mris_make_surfaces to create the final surface. Is aseg.mgz necessary for running this command? If not, how can I let this command skip this file? Thanks. Ning -- When was the last time you had a conversation with the moon or made a wish on a falling star? The time

Re: [Freesurfer] about mris_make_surfaces

don't include -aseg in the cmd line On Tue, 24 Jul 2007, Ning Liu wrote: Hi all, I am trying to use mris_make_surfaces to create the final surface. Is aseg.mgz necessary for running this command? If not, how can I let this command skip this file? Thanks. Ning _