[Freesurfer] RoI,Space

Experts, I have some snapshots of ROIs made in BrainVoyager (in non-TAL space on inflated brain, as well as ones projected onto TAL space). I need to take the above as reference and make near-exact ones (ROIs) using Freesurfer on inflated brains. Which one of the above do I use as my reference

[Freesurfer] How to remove defects from inflated surface

Hello, I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for.

Re: [Freesurfer] How to remove defects from inflated surface

Some bumps are normal. I think you should post a screenshot. 2009/7/8, pcrai...@cc.hut.fi pcrai...@cc.hut.fi: Hello, I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried

Re: [Freesurfer] RoI,Space

sorry, can you give us more details? I don't understand what you are trying to do Bruce On Tue, 7 Jul 2009, Barnali Basu wrote: Experts, I have some snapshots of ROIs made in BrainVoyager (in non-TAL space on inflated brain, as well as ones projected onto TAL space). I need to take the above

Re: [Freesurfer] How to remove defects from inflated surface

Hi Paula, can you send us a snapshot? The inflated surface can have bumps in it, which usually are not a problem. You can also inflate more using the -n switch. From the surf dir: mris_inflate -n 10 lh.smoothwm lh.inflated where 10 is the default and you can increase it to get smoother

Re: [Freesurfer] How to remove defects from inflated surface

Hi Paula, these aren't defects, they are just small scale bumps that aren't quite smoothed out. They only need manual intervention if the ?h.white and/or ?h.pial surfaces do not appear accurate in tkmedit. I think the ones you are showing are fine, but double check the surfaces to make sure.

[Freesurfer] mri_label2vol

Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?) Thank you -- Natalia Sanchez ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_label2vol

any of the conformed volumes should be fine, since they all have the same geometry (orig.mgz, brain.mgz, ...) On Wed, 8 Jul 2009, Natalia Sanchez wrote: Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?) Thank you

Re: [Freesurfer] make_average_subject error about limit

Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir

Re: [Freesurfer] mri_label2vol

Have you looked at the --help? There's quite a bit of documentation there. Take a look and write back if you still have questions. doug Natalia Sanchez wrote: Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?)

Re: [Freesurfer] make_average_subject error about limit

You probably have an older version that does not recoginze --cortex. Try --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead Feng-Xian wrote: Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the

Re: [Freesurfer] BUG in multiple comparisons correction for ABS

Sorry, looks like a copied old versions to the ftp site. I've put the new ones there, let me know if it fixes it. thanks doug Douglas N Greve wrote: Nasim and Judith (and everyone else), I've found and fixed a bug that was causing the surfcluster results for the mc and perm simulations of

[Freesurfer] reconstructing .mnc file with freesurfer

Hi Everyone, What is the process for reconstructing a .mnc file with freesurfer? Do I just run the recon-all -s *.mncfile* -autorecon-all ? Thanks in advance, jesse __ Note: Information contained in this electronic message and any attachments to this

[Freesurfer] contrast matrix

Hi, I want to analysis three independence groups. And, I want to display a result of A group B group C group with positive(red) and A group B group C group with negative(blue). To show that, how do I write the number of columns in the contrast matrix? Thank you in advance! Feng-Xian

[Freesurfer] recon-all qcache

Hello, I was hoping to get some more information about the qcache option. Would running all my subjects with qcache save me any time if I plan on using mri_glmfit instead of qdec? The GLMs I am running have to be sent through mris_preproc and mri_surf2surf each time since some inputs are #'d

Re: [Freesurfer] reconstructing .mnc file with freesurfer

it would be -i mincfile -s subject name -autorecon-all cheers, Bruce On Wed, 8 Jul 2009, Jesse Bledsoe wrote: Hi Everyone, What is the process for reconstructing a .mnc file with freesurfer? Do I just run the recon-all -s *.mncfile* -autorecon-all ? Thanks in advance, jesse

Re: [Freesurfer] reconstructing .mnc file with freesurfer

not quite, just recon-all -s subjectname -i file.mnc doug Jesse Bledsoe wrote: Hi Everyone, What is the process for reconstructing a .mnc file with freesurfer? Do I just run the recon-all -s /.mncfile/ -autorecon-all ? Thanks in advance, jesse __

Re: [Freesurfer] recon-all qcache

Use mris_preproc with the --cache-in option. This will generate the y file used by mri_glmfit. doug Victoria Williams wrote: Hello, I was hoping to get some more information about the qcache option. Would running all my subjects with qcache save me any time if I plan on using mri_glmfit

[Freesurfer] dimension mismatch error

Hi all, after running a group comparison using qdec I wanted to use mc-z instead of FDR for multiple comparison correction I tried to run mri_glmfit-sim-mc-z.abs.2 and got an error... ERROR: dimension mismatch between X and contrast /Users//subjects/

Re: [Freesurfer] contrast matrix

You can't do that with a contrast matrix. In general, you can't test ANDs with a contrast, you have to test ORs. For AND, you have to use a conjunction in which you make two contrasts A B and B C, threshold both (mri_binarize), then do a logical AND. doug Feng-Xian wrote: Hi, I want to

Re: Fwd: [Freesurfer] mri_label2vol

Hi Natalia, does the label line up in the volume when viewed with tkmedit? How are you mapping it into standard coords? Are you using mri_label2label? cheers, Bruce On Wed, 8 Jul 2009, Natalia Sanchez wrote: Hi FreeSurfer experts! I am kind of new to FreeSurfer and this is my first time

Re: [Freesurfer] image matrix

what is noise0.5_0? It isn't a surface file given the output of mris_euler_number. Try running mris_euler_number rh.orig On Thu, 9 Jul 2009, Feng-Xian wrote: Hi, Thank you for your response! But, I canÿÿt find vertices number of a surface through typing the following command:

Re: [Freesurfer] RoI,Space

Hi Barnali, it won't matter. If you run the subject through recon-all you can either draw the label on the inflated surface, in which case we will automatically figure out where it should be in the volume (based on the ?h.white surface), or you can draw it directly in the volume. The surface

Re: [Freesurfer] RoI,Space

Thanks Bruce. How do I figure out where it should be in the volume based on ?h.white.surface ? On Wed, Jul 8, 2009 at 3:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Barnali, it won't matter. If you run the subject through recon-all you can either draw the label on the inflated

Re: [Freesurfer] RoI,Space

you don't have to - we will. You just draw it on the surface and tksurfer will figure out the volume coords and store them in the label file when you save it. You can then load it in tkmedit to see it in the volume if you want. cheers, Bruce On Wed, 8 Jul 2009, Barnali Basu wrote: Thanks

Re: [Freesurfer] RoI,Space

Thanks again. You have been very helpful On Wed, Jul 8, 2009 at 4:11 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: you don't have to - we will. You just draw it on the surface and tksurfer will figure out the volume coords and store them in the label file when you save it. You can then

[Freesurfer] POSTDOC POSITION OPEN

Subject: POSTDOCTORAL POSITION - structure function of fronto-cerebellar circuits in neurodevelopmental disorders Applications are invited for an immediate postdoctoral opening in the Department of Psychology at the University of Houston, Houston TX. The position is full-time for 1 year,

[Freesurfer] qdec question

Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to