Re: [Freesurfer] Successfull Recon-all

Hi Hassan the only thing you can do is visually inspect the surfaces for accuracy cheers Bruce On Wed, 15 Apr 2015, Hassan bakhshi wrote: Hi, Finally I could run recon-all with nifti files, dicom couldnt run it showed that recon-all done without errors, but how can i be sure about the

Re: [Freesurfer] dimension mismatch

thanks, its working like you suggested! Im wondering if you have any idea how I can minimize this effect within subcortical areas since, youre right, DTI space has bigger voxels. Im thankful for any suggestion !! Tom Gesendet:Mittwoch, 15. April 2015 um 15:14 Uhr Von:Douglas Greve

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

Sorry, I misread your previous email as Indeed BPM does do Clusterwise correction. instead of Indeed BPM doesn't do Clusterwise correction. The FWHM is the full-width-half-max and is a measure of the spatial smoothness. This is always needed for cluster-wise correction. This is usually

Re: [Freesurfer] Installing FreeSurfer on Fedora 21

Ranjan, You may want to try installing it on a local hard disk. Do you have any scratch space you can use on the computer? HTH, D On Tue, Apr 14, 2015 at 5:09 PM, Ranjan Maitra maitra.mbox.igno...@inbox.com wrote: Nick, Thanks! It does match in the gzipped tarball: ~$ md5sum

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

Thank you Douglas for this detailed answer. Matthieu 2015-04-15 15:19 GMT+02:00 Douglas Greve gr...@nmr.mgh.harvard.edu: Sorry, I misread your previous email as Indeed BPM does do Clusterwise correction. instead of Indeed BPM doesn't do Clusterwise correction. The FWHM is the

Re: [Freesurfer] mri_vol2vol

Because resampling from 1.5 to 0.25 will generate a huge data. Xiaomin Date: Wed, 15 Apr 2015 09:11:10 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol But why do you need to have the same resolution as the

Re: [Freesurfer] tkmedit SetBrushShape does not enable 3d

Hi Chris we stopped developing tkmedit some years ago. Can you use freeview for this instead? cheers Bruce On Wed, 15 Apr 2015, Chris Adamson wrote: In tkmedit, if I use a tcl script with   SetBrushShape 3 0 1   The radius and shape are set to 3 and circular, respectively. However, the

Re: [Freesurfer] mri_vol2vol

But why do you need to have the same resolution as the original functional? On 4/14/15 10:30 PM, Xiaomin Yue wrote: yes, that's precisely what I want. the reason is the following. A subject was scanned multiple times across days with slightly different slice position for each time. What I

Re: [Freesurfer] dimension mismatch

I would think that going into the DTI space would make this worse since the voxels are bigger (?). But if that is what you want to do, use mri_label2vol to map the aparc+aseg.mgz into the DTI space, then spec that aparc+aseg in the mri_segstats cmd doug On 4/15/15 2:13 AM, Thomas Potrusil

[Freesurfer] midbrain mask

Dear FS experts, Can you please guide me how to create a binary mask of the left midbrain (VTA, SN)? Thanks for your help Andre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] midbrain mask

oh, if you have no anatomical images then we can't help you Bruce On Wed, 15 Apr 2015, André Schmidt wrote: Thanks Bruce. I'll try this. The problem is I have no anatomical images for my subjects. What can I use as input volume in mri_extract_label? I want use this mask to extract time

Re: [Freesurfer] midbrain mask

Thanks Bruce. I'll try this. The problem is I have no anatomical images for my subjects. What can I use as input volume in mri_extract_label? I want use this mask to extract time series afterwards. Thanks again. Best wishes Andre Von:

Re: [Freesurfer] midbrain mask

Hi Andre you can use mri_extract_label to make a binary mask of anything we label. Note that we don't explicitly label VTA or SN (yet), so you'll probably need to use the brainstem label cheers Bruce On Wed, 15 Apr 2015, André Schmidt wrote: Dear FS experts, Can you please guide me how to

Re: [Freesurfer] midbrain mask

p.s. sorry, maybe not brainstem, maybe ventral diencephalon On Wed, 15 Apr 2015, André Schmidt wrote: Dear FS experts, Can you please guide me how to create a binary mask of the left midbrain (VTA, SN)?  Thanks for your help Andre ___ Freesurfer

Re: [Freesurfer] Installing FreeSurfer on Fedora 21

Ranjan, I installed Fedora21 onto a laptop. I then download and installed freesurfer and, after installing a few basic packages (tcsh libXcrnSaver), I was able to open freeview without any errors. Which means the library not found issue you are encountering has something to do with your local

Re: [Freesurfer] Exporting Qdec Data

Try using --vox instead of --crs On 04/15/2015 01:44 PM, Lindsay Renae Wessel wrote: Hello all, I am running Qdec on a large number of subjects and trying to extract the data from the plots generated by clicking find clusters and go to max. I would like to export the data from the

[Freesurfer] Exporting Qdec Data

Hello all, I am running Qdec on a large number of subjects and trying to extract the data from the plots generated by clicking find clusters and go to max. I would like to export the data from the corresponding vertices. I found the following line of code from an earlier, similar question

[Freesurfer] Appropriate file for vertex by vertex thickness analysis in Matlab

If one wanted to do a vertex by vertex thickness analysis for a group of subjects in Matlab, which file in each freesurfer run would one want to use to import into Matlab? Eric Axelson Department of Psychiatry Iowa Neuroimaging

Re: [Freesurfer] Excluded high intensity gray matter

Hi Bronwyn what is your goal? You won't ever get good surfaces there. Is it messing stuff up elsewhere? cheers Bruce On Wed, 15 Apr 2015, Bronwyn Overs wrote: Dear Freesurfer mailing list, I am currently editing a scan (using fs version 5.3) and have come across a section of the

Re: [Freesurfer] Appropriate file for vertex by vertex thickness analysis in Matlab

?h.thickness in each subject's surf dir cheers Bruce On Wed, 15 Apr 2015, Axelson, Eric D wrote: If one wanted to do a vertex by vertex thickness analysis for a group of subjects in Matlab, which file in each freesurfer run would one want to use to import into Matlab?   Eric Axelson

Re: [Freesurfer] Exporting Qdec Data

Thanks! I now get the following error: ERROR: Option out.dat unknown The exact command I have entered (for vertex 33) is: mri_segstats --i y.mgh --vox vertexno 33 --avgwf out.dat Thanks again. From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Excluded high intensity gray matter

Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au

Re: [Freesurfer] Exporting Qdec Data

try mri_segstats --i y.mgh --vox vertexno 33 0 0 --avgwf out.dat On 4/15/15 6:41 PM, Lindsay Renae Wessel wrote: Thanks! I now get the following error: ERROR: Option out.dat unknown The exact command I have entered (for vertex 33) is: mri_segstats --i y.mgh --vox vertexno 33 --avgwf

Re: [Freesurfer] Excluded high intensity gray matter

Hi Bronwyn I don't think there's anything to be done. The images don't carry enough information to generate reliable estimates in those regions, so all you can do is ignore them. cheers Bruce On Thu, 16 Apr 2015, Bronwyn Overs wrote: HI Bruce, It isn't messing stuff up elsewhere, but I am

[Freesurfer] Amazon EC2 for FreeSurfer 5.3

Dear FreeSurfer users, Has anyone succeeded in running FreeSurfer 5.3 in a cloud processing system, such as Amazon EC2? I have seen prior posts in regard of FreeSurfer 5.1 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021181.html), but not for 5.3. Regards, Pedro Rosa.

Re: [Freesurfer] tkmedit SetBrushShape does not enable 3d

Ok I will try freeview. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, 15 April 2015 10:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] tkmedit SetBrushShape does not

Re: [Freesurfer] Excluded high intensity gray matter

HI Bruce, It isn't messing stuff up elsewhere, but I am just worried about including this participant in GLM analysis if this problem cannot be fixed. What would you recommend? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia

Re: [Freesurfer] dimension mismatch

Hi doug! youre right, its working without --inv flag. But I have problems with partial volume effects within subcortical areas close to the ventricle. ADC values are falsified for some regions when using mri_segstats (especially caudate and putamen). I want to overcome this problem by resampling

[Freesurfer] Successfull Recon-all

Hi, Finally I could run recon-all with nifti files, dicom couldnt run it showed that recon-all done without errors, but how can i be sure about the quality of the resultws. I ran the tkmedit and tksurfer as the website said! I got the stats too, how can i be sure that stats are correct

Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

Hello Douglas, Sorry if I haven't been clear. I'm trying to explain my needs : 1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit would do. However, outputs of this toolbox only give me beta maps and uncorrected Tmaps. 2) With only these uncorrected Tmaps outputs, I'd like to

[Freesurfer] FLAIRpial refinement after manual editing of brainmask

Dear Freesurfer experts, I am reposting this question since I did not get an answer to my post from last week. We are using FLAIR images to refine pial surfaces. It generally performs well, however in some cases there is still need for manual editing of brainmask. After manual