Re: [Freesurfer] Fwd: --sum option in mri_segstats

The --etiv-only option only prints it to the screen and does not create a summary file. The ICV is present in the aseg.stats file and should be present when you run asegstats2table. If you want to get the single ICV number in a file, you can run mri_segstats --subject $(filename) --etiv-only |

[Freesurfer] Fwd: --sum option in mri_segstats

Dear Freesurfers, I have a problem using the "mri_segstats" function. I'm trying to get Intra cranial volumes (ICV) from images that I have previously segmented. As I have lots of images, I'm using this script : " foreach filename (*_conv) mri_segstats --subject $(filename) --etiv-only --sum summ

Re: [Freesurfer] Trac Stats

Hi Anastasia: You were right. It was the '/' in the file. I did this for the entire list and it worked. thanks, Alan On Thu, Aug 15, 2013 at 3:37 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Can you please attach the file Forceps_Major_CC.list.txt? > > > On Thu, 15 Aug 201

Re: [Freesurfer] Trac Stats

Can you please attach the file Forceps_Major_CC.list.txt? On Thu, 15 Aug 2013, Alan Francis wrote: Hi Anastasia: Yes the '/' is really there before the autofs. It is puzzling. thanks, Alan On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki wrote: I didn't suggest taking it off, I

Re: [Freesurfer] Trac Stats

Hi Anastasia: Yes the '/' is really there before the autofs. It is puzzling. thanks, Alan On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > I didn't suggest taking it off, I meant make sure that the '/' is there, > because the error message suggeste

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Sorry Doug, I don't understand, I just have the cluster.mgh file with the MonteCarlo simulation results, is an .mgh file with a big significant cluster ( mc-z.abs.sig.cluster.mgh). Is there a way to create a label for each of the significant clusters? thanks again and sorry if the question is too

Re: [Freesurfer] Trac Stats

Is it really autofs without the '/' in front? On Thu, 15 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Sorry to bother you again. I am trying to extract trac stats from the FS > data. When I run the following script, it gives me an error message: > > csh::alanf@cerebro[/autofs/space/dali_0

[Freesurfer] Trac Stats

Hi Anastasia: Sorry to bother you again. I am trying to extract trac stats from the FS data. When I run the following script, it gives me an error message: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : tractstats2table --load-pathstats-from

Re: [Freesurfer] Bus error for tkmedit and tksurfer

Hi Ye when did this start happening? Are you sure you downloaded the version for the correct architecture? Bruce On Wed, 14 Aug 2013, ye tian wrote: > Dear Freesurfers, > > Tkmedit and tksurfer both return "Bus error" for me. I can even have a > glimpse of the surfaces before tksurfer collaps

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Thanks Doug! Could you give me an example please? I cannot get it to work, with this command I get a zero label... mri_annotation2label --subject fsaverage --hemi lh --annotation lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster thanks again! Gari On Thu, Aug 15, 2013 at 4:44 PM, Dougla

Re: [Freesurfer] Bus error for tkmedit and tksurfer

Dear Zeke, Indeed, deleting x11 and xquartz and reinstalling xquartz is what solves the problem! Sincerely, Ye On Wed, Aug 14, 2013 at 6:13 PM, Z K wrote: > Ye, > > Please see the following page which may help diagnose your issue: > > https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_

Re: [Freesurfer] Preproc

Thanks Anastasia. On Wed, Aug 14, 2013 at 10:12 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Alan - This appears to be the same error message as the one for subject > 118 that you sent yesterday. So I'd try here whatever you did to fix that > one. > > a.y > > > On Wed, 14

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Hi Gari, you can use mri_annotation2label doug On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote: Hi list, we have a cluster that survived the Monte Carlo simulation for thickness, and we would like to obtain more data from that exact cluster (volume for example), is it possible to automatic

Re: [Freesurfer] fcseed-sess error

Hi Omar, it is not finding any ventricle voxels. Check the FS segmentation to make sure that the ventricles are labeled and also check the registration to make sure it looks ok. doug On 8/14/13 12:04 PM, O S wrote: > Dear Support, > > I am trying to use fcseed-sess to create a ventricle and C

Re: [Freesurfer] Correction multiple comparisons for parcelated areas

Hi Anna, you can use FDR (ie, Ben-Hoc). You can also use gaussian random fields (GRF) to do voxel-wise or cluster-wise stats. In our implementation, we actually use a monte carlo simulation. Run mri_glmfit and spec the label you want to constrain your results to (--label), then run mri_glmfit-

[Freesurfer] Finding a reference..

Dear experts Just a simple question. Is there a published study that showed a superiority of cortical thickness analysis (i.e., FreeSurfer) over VBM approach in assessing cortical grey matter changes in brain disorders? If so, please let me know. Thanks in advance for your help. Kim

[Freesurfer] Antw: Re: [tracula] error running trac-all -prep

Hi Anastasia I ran the command you sent me and it runs without any errors. I also attached the command line for you. Furthermore i ran data with 12 diffusion directions and i keep getting the same kind of problems. sincerely Florian >>> Anastasia Yendiki 02.08.13 19.59 Uhr >>> Hi Florian -

[Freesurfer] Fwd: FS version

-- Forwarded message -- From: Cristian Paz Date: 2013/8/14 Subject: Re: [Freesurfer] FS version To: Bruce Fischl Thank you for your reply! now - on the third try, I left it for three hours without checking and now it is actually running fiurther. great! what types of problem do