Re: [Freesurfer] where to start recon-all after edits

Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -

[Freesurfer] Mask T1 Image Cortex

Hello FreeSurfer Experts, I want to zero out all those voxels from my T1 MRI which are not part of the cortex preferably in the native space. I have run the recon-all on the subject. Any help will be great. Thanks Mohammed Goryawala, PhD University of Miami Miller School of Medicine. __

Re: [Freesurfer] frontal lobe problem on reconstruction

Awesome thank you! Just found out this patient had a previous resection. Thanks again! > On May 18, 2015, at 4:23 PM, "Nick Schmansky, MGH" > wrote: > > Mia, > > Hi, what sort of error? I looked at the image in freeview, and it looks > like the patient is missing their left frontal lobe.

Re: [Freesurfer] kill tksurfer auto

Hi Greg put "exit" at the end of your tcl script and it will quit tksurfer cheers Bruce On Mon, 18 May 2015, Gregory Kirk wrote: > Hi Bruce directed me to the tcl scripting stuff for tksurfer and so with a > combi of tcl and bash I have > almost got my machinery working to make my movies. Jus

[Freesurfer] kill tksurfer auto

Hi Bruce directed me to the tcl scripting stuff for tksurfer and so with a combi of tcl and bash I have almost got my machinery working to make my movies. Just one little fly in the ointment, it keeps putting up one after another tksurfer invocation piled on top the last. I have tried killing la

Re: [Freesurfer] frontal lobe problem on reconstruction

Mia, Hi, what sort of error? I looked at the image in freeview, and it looks like the patient is missing their left frontal lobe. The surfaces look ok in that region given that. btw, to make viewing in freeview easy, add this to your .cshrc, all one line: alias fv "freeview -v mri/T1.mgz mri/b

[Freesurfer] frontal lobe problem on reconstruction

Hi Freesurfers, I ran recon-all and didn't initially get an error. I am not plotting the surface in matlab and am getting an error but am not sure why. Any help would be great! Thanks! 1) BW30 2) recon-all -autorecon1 -autorecon2 -autorecon3 -subject BW30_SurferOutput -i /autofs/space/huygens_

[Freesurfer] QDEC error- Couldn't open file

Hello, I am getting an error when I try to use the "Analyze" feature in the Design tab of Qdec. The error is: Error in Analyze: Couldn't open file //FREESUFER_SUBJECTS/106966-100/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file However, when I go into the 106966-100 subject directory, the fi

[Freesurfer] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas

Dear Freesurfer experts, I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs based on white matter regions as derived in the wmparc.mgz file. I thought of using the "fsaverage" subject, but it does not have the wmparc.mgz file; thus I plan to use the CVS atlas (cvs_avg35_i

Re: [Freesurfer] beta value

Thanks Xiaomin On Mon, May 18, 2015 at 9:15 AM -0700, "Douglas Greve" wrote: yes On 5/18/15 10:38 AM, Xiaomin Yue wrote: > Do you mean by contrasting a condition vs fixation? > > Xiaomin > > > > > On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Greve" > mailto:gr...@nmr.mgh.harvard.edu>> wr

Re: [Freesurfer] Manual labels in terms of anatomical regions

Dear Douglas Greve,   thank you for your answer.  read_annotation gives me the correspondence between anatomical labels and vertices. To match the vertices to an anatomical region, all i need now (I guess) is a routine to load the  vertices in label files as created in tksurfer into matlab. Is

Re: [Freesurfer] beta value

yes On 5/18/15 10:38 AM, Xiaomin Yue wrote: Do you mean by contrasting a condition vs fixation? Xiaomin On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: Yes, but you have to set up the contrasts, it won't do it automatically On 5/16/15 10:

Re: [Freesurfer] beta value

Do you mean by contrasting a condition vs fixation? Xiaomin On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Greve" wrote: Yes, but you have to set up the contrasts, it won't do it automatically On 5/16/15 10:48 PM, Xiaomin Yue wrote: > Hi, > > During the processing of functional data, can f

Re: [Freesurfer] Manual labels in terms of anatomical regions

We don't have anything to do this. You could do it in matlab with read_annotation.m On 5/15/15 6:44 PM, Andreas Werner wrote: Dear Experts, in my analysis i have created a set of surface labels based on significant clusters using tksurfer. For a given label I would like to know which atlas-bas

Re: [Freesurfer] beta value

Yes, but you have to set up the contrasts, it won't do it automatically On 5/16/15 10:48 PM, Xiaomin Yue wrote: Hi, During the processing of functional data, can fsfast generate outputs of the significants for each beta values modeled in the design matrix? Thanks, XIaomin _

Re: [Freesurfer] Preproc-sess failed

that means that the version of 3dvolreg.afni does not match your operating system. What is your OS and what version of FS are you running? On 5/18/15 4:11 AM, Thục Trinh wrote: Hi freesurfer experts, I am practicing on the fsfast tutorial data that were given at Freesurfer website. I run the

Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 23

hmmm, we distribute strlen.m, not sure why you don't have it. I'll attach it so you can put it in $FREESURFER_HOME/matlab cheers Bruce On Mon, 18 May 2015, LiuKai wrote: Ok, I ve figured it out: the "strlen" in the code is not a matlab function. Thus I deleted the lines 38-46, then it w

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Annie, Can you share with us how you resolved the issue, so that other people who might search the email list for similar issues might benefit? Thanks, Thomas On Mon, May 18, 2015 at 3:39 PM, 陳昱潔 wrote: > Hi Dr. Yeo: > > Thank you very much we already solved the problem! > > Very appreciate

Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 23

Ok, I ve figured it out: the "strlen" in the code is not a matlab function. Thus I deleted the lines 38-46, then it works well by just define the fname. Thank you very much!! kai From: li...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: RE: Freesurfer Digest, Vol 135, Issue 23 Date: Sun

[Freesurfer] Preproc-sess failed

Hi freesurfer experts, I am practicing on the fsfast tutorial data that were given at Freesurfer website. I run the command to do the pre-processing on the sess01 <*noproc*>. *preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -fwhm 5 -per-run* it was unfinished and failed with the E