[Freesurfer] mris_convert gifti

Hi, sorry to bother, I'm re-posting this question just in case it got lost. Thanks. Hi, I have a question about mris_convert. I've created some regions on the surface and now I would like to make them directly readable into SUMA. I ran this command but it ended with an error message.

[Freesurfer] QA-Tools installation problem

Dear experts, we have a problem with installation of QA-Tools. It seems that it is not because of ImageMagick and Gawk not being properly installed, but rather there seems to be some problems with environmental variables. For example, when changing into QA-Tools directory in the terminal and

[Freesurfer] LGI problem

Hi Marie: I am trying to run the LGI post processing step on 60 ASD subjects. I am using FreeSurfer 5.3. The recons went well and the processed brains look great. However when I run the LGI step, I am getting the following error which is as follows: Could you please help me? [alanf@micc

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

Dear professor Bruce! Sorry for bothering again, well I did exatly as you told before in order to process different subject at the same time: recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all there Pat 1 (and the rest) are subjid. thought I got this error message: ARNING: tcsh v6.17.06 has an exit

[Freesurfer] Tksurfer_fminmax flag

Hi Doug, After running FSFAST tool and correcting the results for multiple comparisons. I want t visualize the results using the command line (AS IN WIWKI): tksurfer fsaverage lh inflated -overlay my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz -annot

Re: [Freesurfer] Tksurfer_fminmax flag

Hi Mohamad the minmax flags allows you to set the min and max thresholds for the colorscale in tksurfer. It doesn't change any pvalues - just how they are displayed. Since you are displaying -log10(p), a min of 2 will only show pvalues that are .01 and a max of 3 will saturate the color scale

[Freesurfer] Incomplete Cerebellum Segmentation

Hi Freesurfers, I've just completed recon-all -all and pulled up the brain in Freesurfer V5.0 on my Linux machine, and realized I needed to run the following command recon-all -skullstrip -wsthresh 30 -clean-bm -no-wsgcaatlas -s sub122.fs to pick up cerebellum that was missing. After the

[Freesurfer] mri_glm --wls flag

Hi Doug, I finished recently running FSFAST on fmri data set. I want to run group GLM for the following analysis: OSGM, FSGD( no covariates) For OSGM I ran the following command line like in Wiki: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir

Re: [Freesurfer] mri_glm --wls flag

Can you tar or zip the following files and post them to me on our file drop (see below): ces.nii.gz cesvar.nii.gz fsgd C1.mtx C2.mtx C3.mtx C4.mtx doug On 4/30/15 2:06 PM, Alshikho, Mohamad J. wrote: Hi Doug, I finished recently running FSFAST on fmri data set. I want to run group GLM for

Re: [Freesurfer] mris_convert gifti

Francesca, How was lh.EKppa.annot created? Is it a custom list of annotations? Does it include an embedded colortable appropriate for those annotations? Can you send me the files 'lh.EKppa.annot' and 'lh.white'? I can try to replicate the problem. Also, can you run this: mris_info

Re: [Freesurfer] crossing medial surfaces

Hi, Following up on this thread, has there been any updates regarding the crossing medial surfaces problem? Thanks. Dear Bruce, where could I upload the base of a child participant? Is there a freesurfer specific platform or something? Cheers, Clara - Ursprngliche Mail - Von:

Re: [Freesurfer] mri_glm --wls flag

Hi Doug, To this email address freesurfer@nmr.mgh.harvard.edu or to your email? Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, April

Re: [Freesurfer] -openmp 8 and -use-gpu questions

I'm testing the total processing time of recon-all -all using -openmp 4,6,8,12 . The runs with 4 and 6 threads took almost the same amount of time. The runs with 8 and 12 threads took almost the same amount of time. (1)Is the work divided evenly between the threads (mri_ca_register,

[Freesurfer] -openmp 8 and -use-gpu questions

I'm testing the total processing time of recon-all -all using -openmp 4,6,8,12 . The runs with 4 and 6 threads took almost the same amount of time. The runs with 8 and 12 threads took almost the same amount of time. (1)Is the work divided evenly between the threads (mri_ca_register,

Re: [Freesurfer] FreeSurfer Correction

I don't know what you mean. can you elaborate? On 04/30/2015 06:41 PM, Ghazal Kiani wrote: Hi, We were wondering when viewing group data on the inflated brain using FreeSurfer, if FreeSurfer applies any correction and how we c an control the correction value? Thanks, Ghazal

Re: [Freesurfer] crossing medial surfaces

Hi Clara did you upload the dataset to our ftp site? Bruce On Thu, 30 Apr 2015, silve...@gmx.com wrote: Hi,   Following up on this thread, has there been any updates regarding the crossing medial surfaces problem?   Thanks.     Dear Bruce, where could I upload the base of a child

[Freesurfer] FreeSurfer Correction

Hi, We were wondering when viewing group data on the inflated brain using FreeSurfer, if FreeSurfer applies any correction and how we c an control the correction value? Thanks, Ghazal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

Re: [Freesurfer] mri_mcsim with different threshold

Sadly, no. On 04/30/2015 04:05 AM, Alain Imaging wrote: Hi Douglas, indeed reading more carefully the documentation page of mri_mcsim I figured it out. But thank for confirming it! Is there any rule (or also rule of thumb) for choosing the cluster-forming threshold ? A. Date: Wed, 29

Re: [Freesurfer] Tksurfer_fminmax flag

The minmax options are for thresholding. 1.3 means 10^-1.3 = 0.05 which means that clusters with p.05 will be displayed. The max just sets the maximum color scale. For CWP=.0009, -log10(CWP) = 3.0458, so any min threshold less than that will show that cluster. doug On 04/30/2015 10:26 AM,

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm recon-all -s

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up

Re: [Freesurfer] LGI problem

Hi Alan, Do you have the image processing toolbox installed in matlab? If not, I guess this is the source of the error. Best, Marie On Apr 30, 2015, at 7:51 AM, Alan Francis alandarkene...@gmail.commailto:alandarkene...@gmail.com wrote: Hi Marie: I am trying to run the LGI post processing