Re: [Freesurfer] Retinotopic mapping of only polar data

Hi everyone, Doug: thanks a lot for the reply, that indeed worked, I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal

[Freesurfer] only color premotor gyrus use annotation file

Dear Freesurfer experts, I wish to draw a selected gyrus on the whole hemisphere. Could I only color display the selected gyrus and use other color on all others gyrus from annotation file ? if yes, how to do it. Thank help Kl chen ___ Freesurfer

Re: [Freesurfer] only color premotor gyrus use annotation file

Hi Kl, once you select it you can save it as it's own label file. Then delete all labels (under tools menu) and load the label that you saved. cheers Bruce On Mon, 11 Jan 2010, tulu wrote: Dear Freesurfer experts, I wish to draw a selected gyrus on the whole hemisphere. Could I only

[Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: bbregister is for 6 or 12 DOF corregistration ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

it's 6 by default. Not sure if 12 is implemented yet, but I know Doug was thinking about it. cheers, Bruce On Mon, 11 Jan 2010, Gonzalo Rojas Costa wrote: Hi: bbregister is for 6 or 12 DOF corregistration ?... Sincerely, Gonzalo Rojas Costa

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: I have a freesurfer processed patient and the PET of the same patient processed with SPM... the PET images are corregistered to MNI152... How can I corregister the PET to the freesurfer images ?... I tried to corregister using bbregister, but I got bad results (I think that I need 12

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: Forgot the e-mail that I sent you recently... I will try using --12... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 11-01-2010 11:55, Douglas N Greve

Re: [Freesurfer] ICV/brain volume

Hi Xiangchuan, the cerebral gray matter volume should be the difference between the mris_volume of the pial and white surfaces. cheers Bruce On Sat, 9 Jan 2010, Xiangchuan Chen wrote: Hi Martin, Bruce and Mike, Thank you for all your suggestions. For Martin's suggestion: I found that it

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

if it's the same subject you shouldn't need --12. On Mon, 11 Jan 2010, Gonzalo Rojas wrote: Hi: Forgot the e-mail that I sent you recently... I will try using --12... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile.

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

p.s. make sure you are registering the original images, not the ones transformed into MNI space On Mon, 11 Jan 2010, Gonzalo Rojas wrote: Hi: I have a freesurfer processed patient and the PET of the same patient processed with SPM... the PET images are corregistered to MNI152... How can I

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: Yes... I think that it is better to use the original images, but the SPMT_0001 is in MNI 152 space... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Is there some feature like the fast fluid registration in the dev pipeline? --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

that's why bbregister is failing though - you've already applied a 12dof transform to your data, so there is no good 6 dof registration On Mon, 11 Jan 2010, Gonzalo Rojas wrote: Hi: Yes... I think that it is better to use the original images, but the SPMT_0001 is in MNI 152 space...

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

yes, but I wouldn't use it for this. Here you really want to use the data before resampling for registration. You can always map that into the MNI space using the SPM transform On Mon, 11 Jan 2010, Pedro Paulo de Magalhães Oliveira Junior wrote: Is there some feature like the fast fluid

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: Yes... The PET image that I want to corregister to freesurfer (SPMT_0001) is the result of a Two-sample t-test between a patient and a PET database... fot that reason, I have the image in MNI 152 space... I thought that I have two possible solutions: i) use 12 DOF to corregister the

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

why not use the original PET data to generate the registration? On Mon, 11 Jan 2010, Gonzalo Rojas wrote: Hi: Yes... The PET image that I want to corregister to freesurfer (SPMT_0001) is the result of a Two-sample t-test between a patient and a PET database... fot that reason, I have the

Re: [Freesurfer] ICV/brain volume

Hi Bruce, The pial volume includes some sub-cortical matter (e.g., amygdala and hippocampus). Can I use mris_anatomical_stats -l ?h.cortex.label to calculate the cerebral gray matter? Is it more accurate than the sum of the volumes from aparc.stats? Thanks, Xiangchuan -Original Message-

[Freesurfer] display the thickness average on a 3d reconstituting

dear group, what is the best way to display the thickness average on a 3d reconstituting brain? thank you, Asaf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] display the thickness average on a 3d reconstituting

do you mean on the surface or in the volume? For surface, use tksurfer. For the volume, you'd have to run mri_surf2vol, then use tkmedit. doug asaf achiron wrote: dear group, what is the best way to display the thickness average on a 3d reconstituting brain? thank you, Asaf

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Hi: I could use the original PET data to generate the registration, but I need to do the second method that I explain in my e-mail... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel:

[Freesurfer] aparcstats2table for std dev associated with av thickness

Hi all Is there a way to create a multi subject table of the std dev associated with av thickness using aparcstats2table or for that matter any way to create a table similar to the outout of aparcstats2table ? Thanks Ri ___ Freesurfer mailing list

Re: [Freesurfer] aparcstats2table for std dev associated with av thickness

I've modified aparc2stats2table to accept a -meas thicknessstd option. This will output the spatial standard deviation of the thickness for each subject. You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table doug Ritobrato Datta wrote: Hi

[Freesurfer] manually labeled subjects used for building the desikan_killiany gcs file

Hello, there, If it possible that I can view or download the manually labeled subjects you used for building the desikan_killiany gcs file from somewhere in the wiki? Thanks! Guang _

Re: [Freesurfer] manually labeled subjects used for building the desikan_killiany gcs file

Hi Guang, unfortunately the answer is no. We tried very hard to get to the point where we could distribute this data, but is was collected under a set of IRBs that is more than 10 years old that didn't include distribution. We tried to modify the IRBs but they were old enough that we couldn't

[Freesurfer] combining multiple labels to a single label

Hi all, Is there a way / program to specify and combine multiple labels to create a single label ? Please let me know. Thanks a lot Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] combining multiple labels to a single label

Try mri_mergelabels Bruce Fischl wrote: Hi Ri, do you mean surface or volume labels? Either way matlab is probably the easiest, unless Doug has something to do this. cheers, Bruce On Mon, 11 Jan 2010, Ritobrato Datta wrote: Hi all, Is there a way / program to specify and