[Freesurfer] Hippocampal subfield segmentation error

Dear Experts I have been experiencing a problem while running the following command *segmentHA_T1.sh subject_name* The program exits with the following error "MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660

[Freesurfer] Repronim Training Workshop on Reproducible Research Nov 10-11 before SFN

*ReproNim Training Workshop: Nov 10 full day - Nov 11 morning - George Washington** University* *Register and information at:* ​https://tinyurl.com/repronim-sfn17 *Purpose:* The issue of lack of reproducibility has been described in several scientific domains for several years, raising concerns

Re: [Freesurfer] control point and aseg edit

Thank you very much Bruce. Best, Paul On Thu, Sep 14, 2017 at 4:02 PM, Bruce Fischl wrote: > I mean there will be no subsequent command that turn of the use of control > points in the aseg > > > cheers > Bruce > > > On Thu, 14 Sep 2017, miracle ozzoude wrote: > >

Re: [Freesurfer] control point and aseg edit

I mean there will be no subsequent command that turn of the use of control points in the aseg cheers Bruce On Thu, 14 Sep 2017, miracle ozzoude wrote: Thanks Bruce. resetting means, all my changes will be incorporated into the final output files?  Best,  Paul On Thu, Sep 14, 2017 at 3:52

Re: [Freesurfer] control point and aseg edit

Thanks Bruce. resetting means, all my changes will be incorporated into the final output files? Best, Paul On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl wrote: > I'm not sure it matters, but if you put it at the end nothing will reset it > > On Thu, 14 Sep 2017,

Re: [Freesurfer] control point and aseg edit

I'm not sure it matters, but if you put it at the end nothing will reset it On Thu, 14 Sep 2017, miracle ozzoude wrote: Hello Bruce, Yes, that is my end goal. I have a patient i edited the aseg to include left-cerebral white matter and also, want to normalize the intensity using expert

Re: [Freesurfer] control point and aseg edit

Hello Bruce, Yes, that is my end goal. I have a patient i edited the aseg to include left-cerebral white matter and also, want to normalize the intensity using expert option. Where should I place the "-canorm-usecps" flag ? After the command like " recon-all -autorecon2 -autorecon3 -expert

[Freesurfer] Using FreeSurfer5.3 via VirtualBox

To whom it may concern, How does one access the files in a shared folder when using FreeSurfer5.3 via VirtualBox on a windows unit? I have not had success with the "sudo mount -t vboxsf /media/" command which I have seen on several forums. Furthermore, I continually receive a warning which

Re: [Freesurfer] control point and aseg edit

do you want the control points to be applied to the aseg? If so, you need to also specify -canorm-usecps cheers Bruce On Thu, 14 Sep 2017, miracle ozzoude wrote: Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert option for control point. That's recon-all -autorecon2

Re: [Freesurfer] hippocampus subfields in longitudinal dataset

Dear Lara, The sh script implements a longitudinal segmentation algorithm that segments both time points simultaneously using a subject specific atlas, improving the reliability of the segmentation. You can read the details here http://www.sciencedirect.com/science/article/pii/S1053811916303275

Re: [Freesurfer] control point and aseg edit

Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert option for control point. That's recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time. Best, Paul On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl wrote: > do you

[Freesurfer] adding volumes of seperated parts of one structure?

dear all, what do you think about adding the volumes of seperated parts of one structure to a complete volume? e.g. the corpus callosum or also cingulate gyrus. is it ok to get the complete volume value by just adding the volumes of the seperated parts? beside that, am i right that wmparc

Re: [Freesurfer] labels used by freesurfer

thx so far! really thank you.. do you know how to find out more about that label? what do you think about how to get any informations about a possible adding of different structure parts to a „complete one“ for example the Corpus callosum thing? greets bl > Am 14.09.2017 um 18:40 schrieb

[Freesurfer] what does the CSF label describe?

dear all, i already tried to find out what the label CSF stands for.. but beside realizing that its not a common/regular part of the ventricle system i couldn’t get any other informations regarding the meaning? of the CSF label. i tried to find out whats it about by using freeview (screenshot

Re: [Freesurfer] control point and aseg edit

do you want it to regenerate the aseg? If not, then a). If so, then you would just run autorecon2 (instead of autorecon2-cp) cheers Bruce On Thu, 14 Sep 2017, miracle ozzoude wrote: I used the expert option for control points and manually edited the aseg.presurf.mgz. Which is the proper

[Freesurfer] control point and aseg edit

I used the expert option for control points and manually edited the aseg.presurf.mgz. Which is the proper flag to use in other to incorporate the respective changes? a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time or b) recon-all

[Freesurfer] hippocampus subfields in longitudinal dataset

Hello Freesurfer experts, I have a longitudinal data set already processed in the longitudinal pipeline of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0. I'm wondering whether I will arrive at the same result using either of the following two approaches: 1. run

Re: [Freesurfer] labels used by freesurfer

On 09/13/2017 05:38 PM, Benjamin Luerweg wrote: > dear mr. greve, > dear fs community, > > > > *REGARDING CSF and CSFVol:* > > i still don’t understand the whole CSF and CSFVol thing. > it seems to be impossible that CSFVol ist the volume of the CSF label > because CSFVol is *bigger* than CSF.

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: By removing --rip-unknown I got the same results... Why ?... Sincerely, Gonzalo Rojas Costa > Date: Tue, 12 Sep 2017 12:33:11 -0400 > From: Douglas N Greve > Subject: Re: [Freesurfer] lobes volume (WM and GM) > To: freesurfer@nmr.mgh.harvard.edu >

Re: [Freesurfer] Cluster-Defining Threshold of p=0.025

Andy, please remember to post to the FS list, thanks. As for your question, this is a bug in mri_glmfit-sim that hard codes the allowable thresholds. I've attached a version that should work with 1.6. On 09/14/2017 10:06 AM, Jahn, Andrew wrote: Thanks again; I was able to create new

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Now that I know what the error and that you are using bash, I can give you instructions on what to try next. Try running unset FS_LOAD_DWI On 09/14/2017 01:13 AM, M Janani wrote: > Hi Douglas, > > As you recommended, I ran unsetenv FS_LOAD_DWI command in the terminal, > but I got Bash

Re: [Freesurfer] correcting defect

Hi Meng we can't diagnose either of these issues without more information and possibly some screen shots. The topology fixer will take a very long time if the initial surfaces have large defects. You can view these by visualizing the ?h.inflated.nofix and ?h.orig.nofix. The -openmp flag

[Freesurfer] correcting defect

Hi all, I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half of the subjects was stuck at the ‘Correcting Defect’ step. However, when I changed to FreeSurfer version 5.3.0, the ‘Correcting defect’ step finished successfully. Is it possibility that the unsuccessful

[Freesurfer] Brain without skull and manual edits

Dear all, I would like an accurate segmentation of the brain without skull in native space. I am running a recon-all with Freesurfer 6 and Ubuntu 16.04. When it finishes, I find mistakes and I erase some skull voxels from brainmask.mgz. I run recon-all again and it finished without errors.

Re: [Freesurfer] license error

Thanks for reply. Even that is not working for me. I using ubuntu machine. Thanks, Ritesh Mahajan From: "Benjamin Luerweg" To: "freesurfer" Sent: Thursday, September 14, 2017 4:54:30 PM Subject: Re: [Freesurfer] license

Re: [Freesurfer] license error

Beside that I recognised that some issues with the license file are based on the following aspect: While running freesurfer on Mac OS it Didn't work for me creating the license file under Mac OS itself. I realised that after creating the file under windows 10 and copying that file back to

[Freesurfer] license error

Hello team, I created the license.txt at location FREESURFER_HOME and pasted the lines sent to me after registration. Still i find the following errors. "ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to