Re: [Freesurfer] Rat template creation: MRIstripskull failed

Hi, Ok, I will look into inverting the image as Martin suggested. Is there some background info available on how to put the segmentation input into the surface-based analysis. In case the inversion doesn't work. I'm particularly wondering if I need to have the images in *.mgz file format or

Re: [Freesurfer] mesh size question

Thank you Martin, I only wanted know if there is a way to do this without using an external program. I will try using a standard tool. Tommaso Martin Reuter wrote: Hi Tommaso, I am not sure about freesurfer, but why don't you simply use a standard tool for mesh simplification e.g. qslim

Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz

Hey Krish, Thanks for your input. Good idea too, never thought about doing that. Tried this in command line and worked without a hitch. Then i realized if you just use command line what I did before works as well. The error must somehow be resulting from issues with tcsh or something. But I

Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz

Also, in case anyone is interested -- if you have a brik volume in the subject folder, specifying mri/orig/001.mgz gives the same error as specifying orig/001.mgz, at least for me. So that wasn't the cause of the problem. John On Thu, Oct 23, 2008 at 7:44 AM, John Sheppard [EMAIL PROTECTED]

Re: [Freesurfer] questions about longitudinal analysis

Hi Wang, 1. An affine transform from tp1 to tp2 would only remove global atrophy, but not the region effects we are interested in. 2. For intra-subject registration the surface-based is not needed as we expect the changes to be small. cheers, Bruce On Thu, 23 Oct 2008, Wang, Xin wrote:

Re: [Freesurfer] mri_convert

mri_convert file.mgz file.img should do the trick (or file.nii for nifti) On Thu, 23 Oct 2008, sameer kumar wrote: Hi Nick, After I run recon-all, the files I get are not in mgz format and I would like to convert them into img format to view them in FSL view. How can I do that? Thanks,

RE: [Freesurfer] FreeSurferColorLUT aparc

and how do you get it into FSL? On Wed, 22 Oct 2008, Juranek, Jenifer wrote: yes, the correct Sgmtn label is displayed in the TkMedit Tools -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:30 PM To: Juranek, Jenifer Cc:

Re: [Freesurfer] mri_convert

Hi all, It says .mgz file not found. I am new to FS so please help me out with this. Thanks, Regards, Sameer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_convert

what file are you trying to convert? On Thu, 23 Oct 2008, sameer kumar wrote: Hi all, It says .mgz file not found. I am new to FS so please help me out with this. Thanks, Regards, Sameer ___ Freesurfer mailing list

Re: [Freesurfer] mri_convert

The output files of recon-all ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_convert

which ones? There are many, some of them are surfaces, which I don't think FSL can show, and some are volume that you could import into FSL (e.g. $SUBJECTS_DIR/$subject/mri/aseg.mgz, which is the whole-brain segmentation) cheers, Bruce On Thu, 23 Oct 2008, sameer kumar wrote: The output

[Freesurfer] creating intermediate surfaces

Hi all - Is there a way to create intermediate surfaces in FreeSurfer? By intermediate I mean some fraction between gray/white and pial. Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th

Re: [Freesurfer] creating intermediate surfaces

yes, mris_expand will do it. cheers Bruce On Thu, 23 Oct 2008, Rudolph Pienaar wrote: Hi all - Is there a way to create intermediate surfaces in FreeSurfer? By intermediate I mean some fraction between gray/white and pial. Cheers -=R ___

[Freesurfer] Bug with aparcstats2table on aparc.a2005s parcellation

Hello, Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s parcellation map. If some of the subjects in the group have missing values of a certain type, aparcstats2table fails to designate a 0 for them. So for instance, it's often

[Freesurfer] optseq psdwin

Hi, I have 2 questions. 1) How do I calculate psd min, max, and dpsd. Is there a formula for calculating these values? I have 4 kinds of stimuli, stim duration = 3s, stim repetition = 25, TR =2 so: optseq2 --ntp 180 --tr 2 --psdwin [?] --ev A 3 25 --ev B 3 25 --ev C 3 25 --ev D 3 25 --o

[Freesurfer] convert multiple Analyze to single 4D nifti

Does anybody know how to convert a series of Analyze files into a single nii file? Each analyze file is a single 3D volume at a time point; the nii file would be 4d. Thanks, Xu -- Xu Cui Department of Psychiatry and Behavioral

[Freesurfer] Bug with aparcstats2table on aparc.a2005s parcellation - addendum

The body of my email was lost because of the attachments: here it is again for those who are curious. Sorry about that, I didn't know a text file attachment would do that. Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s

Re: [Freesurfer] Bug with aparcstats2table on aparc.a2005s parcellation - addendum

Victor, We are aware of this bug. Unfortunately, there is no 'quick fix', which is why it has not been repaired yet. But yes, I agree its an ugly one which creates havoc with automated scripts. Hopefully a fix will appear in the next release. Nick On Thu, 2008-10-23 at 13:19 -0700, Laluz,