[Freesurfer] Cerebellar segmentation

Hello, how is it the best line command to visualize in Tkmedit the cerebellar segmentation? Thanks a lot for your help Massimiliano _ Fanne di tutti i colori, personalizza la tua Hotmail! http://imagine-windowslive.com/Hotmail/

Re: [Freesurfer] Some questions about my analysis

yes, that should be the most accurate. It computes the interior of the white surface, excluding voxels that are not white (ventricle, thalamus, etc) cheers Bruce On Mon, 15 Dec 2008, Christian Scheel wrote: Thanks Doug, Nick and Marie for your great support! With regards to what you wrot

Re: [Freesurfer] Cerebellar segmentation

the only cerebellar segmentation we have currently is just gray/white, and you can visualize it with: tkmedit $subject norm.mgz -seg aseg.mgz cheers, Bruce On Mon, 15 Dec 2008, Massimiliano Calabrese wrote: Hello, how is it the best line command to visualize in Tkmedit the cerebellar s

Re: [Freesurfer] Command Not Found

Christian, I think the paths are still not correct. Try using /home/user/Desktop instead of home/user/Desktop... Also in 3) the variable of the subject directory is called SUBJECTS_DIR instead of SUBJECTS so the command should be: setenv SUBJECTS_DIR /home/user/Desktop/freesurfer/subjec

Re: [Freesurfer] cortical parcellation and local maximum

Maartje, I think you can make use of aparcstats2table when you first run mris_anatomical_stats -l ?h.cortex.label -b -f path_to_homedirectory/subject/stats/?h.cortex.stats subject ?h for every subject and every hemisphere (preferably using a batch file where you can list up all the commands)

Re: [Freesurfer] Command Not Found

Ongoing Problems: Bit of a delay having been away. Here is what I'm doing step by step and then the error message at the bottom. Again I am using CentOS5 Linux shell on a windows machine using Freesurfer V4.1.0 with the monitor settings on 32bit, and license file has been set up. Decided to try au

[Freesurfer] Water threshold for skull strip : 1% is still too high

Hi all I can't get freesurfer to strip the skull properly, even with a water threshold of 1%. There is still so much skull (csf) remaining that a manual edit is not doable. Is there a way to preprocess the anatomical scan to correct this? ( I tried a water threshold of 0% although I'm not sure tha

Re: [Freesurfer] Aparc and aseg description table

Hello Julia, Besides the definitions above the tables, there are some articles mentioned on the wiki site- main page, scroll down- giving information about the definitions of the areas. F.e. Desikan, 2006, about cortical parcellation. Kind regards, Maartje Katzenbauer - Original Message

Re: [Freesurfer] Some questions about my analysis

Thanks Doug, Nick and Marie for your great support! With regards to what you wrote to Maartje about the total gray matter volume I understand that the best way to measure it is using mris_anatomical_stats -l ?h.cortex.label subject ?h for every subject and every hemisphere. Maybe we should in

[Freesurfer] Aparc and aseg description table

Hi all, It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from

Re: [Freesurfer] .mat/.hdr and orientation

I would have thought that that mri_convert cmd (with .img) would have worked. what went wrong? Susie Heo wrote: Hello, I am hoping that someone can help me to solve my orientation/angle acquisition problem: 1) I have an EPI oblique slice in Analyze format with incorrect orientation/angle a

Re: [Freesurfer] make_average

Hi Petr, when you list your subjects, just use the subject's name. It looks like you put path specifiers in there, ie, "./1013" shoudl be simply "1013" doug p.s.bjer...@studmed.uio.no wrote: Hi, Trying to make an average of about 60 subjects. The problem is that the proper files are not pro

Re: [Freesurfer] Water threshold for skull strip : 1% is still too high

Hi Julien, if you put the nu.mgz on our filedrop we'll take a look. cheers, Bruce On Mon, 15 Dec 2008, Julien Dubois wrote: Hi all I can't get freesurfer to strip the skull properly, even with a water threshold of 1%. There is still so much skull (csf) remaining that a manual edit is not do

[Freesurfer] nature of bug in mris_wm_volume

Hello, The ReleaseNotes for v4.1.0 and v4.0.5 indicate refer to a bug in 'mris_wm_volume' related to the white matter parcellation. Was there actually a bug in mris_wm_volume itself? Or, is the issue that the aseg.mgz had some incorrect labeling of "non-white" structures relevant to the mris_wm_

Re: [Freesurfer] reg-feat2anat failed

Hi Xin, the problem is that neither the sform nor the qform are valid. Did the message below not appear when you ran tkmedit? WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented Fix that, and everything will work fine. doug Wang, Xin w

RE: [Freesurfer] reg-feat2anat failed

Thank you very much for your quick reply, Dr. Greve. I asked our institutional MRI center for correct information on qform and sform since the header of nifti files are created by their scripts. But I do not know what they can do to fix this problem. I will appreciate if you have any further sug

Re: [Freesurfer] reg-feat2anat failed

There is a flag in the nifti header saying whether the qform or sform are valid, and it looks like your scripts do not set this flag. You can use mri_convert (the freesurfer program). This will create valid files that can be read into any program. doug Wang, Xin wrote: Thank you very much fo

[Freesurfer] mri_convert 3D set to a single 4D ?

hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid. ___ Freesurfer

Re: [Freesurfer] mri_convert 3D set to a single 4D ?

There are two things you can do, mri_concat spm_*.img --o 4d.img you can also do it with mri_convert, but I don't think it buys you anything over using mri_concat. doug Siddharth Srivastava wrote: hi everyone, is it possible to combine, using mri_convert, a set of 3D s

[Freesurfer] func2roi-sess command issue

Hello, In the stable 3 environment, I ran the func2roi-sess command. This is what was included: func2roi-sess -roidef dACC99_rh -analysis EMerror -anatlabel dACC-rh -maskcontrast ASevfix -maskframe 5 -maskthresh 0.0043648054 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_

Re: [Freesurfer] mri_convert 3D set to a single 4D ?

Hi Doug, Thanks for the reply. I tried mri_concat as you suggested, and got the following: WARNING: analyzeRead(): matfile spmfile1-0003.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it.

Re: [Freesurfer] mri_convert 3D set to a single 4D ?

mri_convert will fail in the same way. But it should have worked. Can you point me to the dir and give me read perms? Siddharth Srivastava wrote: Hi Doug, Thanks for the reply. I tried mri_concat as you suggested, and got the following: WARNING: analyzeRead(): matfile spmfile

Re: [Freesurfer] func2roi-sess command issue

it's only positive for the contrast that you have specified. the roi summary reports the HRF amplitudes for each condition. When you compute the contrast of those, you should get the right sign. doug Dave Brohawn wrote: Hello, In the stable 3 environment, I ran the func2roi-sess command. Th