[Freesurfer] hippocampal subfields

Hi all, I'm trying to perform the longitudinal hippocampal subfields processing on a cluster. When I simply access a core on the cluster directly and use it to run the hippocampal subfields it will run, but if I try to submit the process to the cluster, it will either throw errors as I have

[Freesurfer] Editing annot files

Hi, I was wondering if there is any way to edit annot file e.g. I would like to edit *lh.Yeo2011_7Networks_N1000.annot* file in such a way when I overlay this file in freeview, I just display limbic network from Yeo 7 network atlas and hide other 6 networks. I would prefer to use MATLAB for this

Re: [Freesurfer] reposition surface for pial surface

Dear Paul, I cannot see your attachment since I am only getting mail digest (without attachments) and the mail archive does not store attachments. I do not know for which option of surface reposition your question refers to. But, I hope when you play with the tool, you will figure out, as I

Re: [Freesurfer] Interaction effects in QDEC

This is done automatically when you have two categorical variables and two continuous variables. This is equivalent to asking whether the two slopes differ across the two categorical variables. On 01/07/2017 09:30 AM, Heidi Foo wrote: > Hi all, > > I was wondering how I could test for

Re: [Freesurfer] Is the average surface in MNI space?

On 01/07/2017 06:19 AM, Ling Zhao wrote: > > *Dear experts,* > > 1.From the FreeSufer wiki we all knows all of the processing and the > generated files are in the Talairach (MNI305) coordinate. The > FreeSurfer operates > in a conformed space,

Re: [Freesurfer] reposition surface for pial surface

Thank you very much Antonin. I do appreciate it. Do I need to insert a vertex number or just the coordinates? Because when i clicked on the surface outside the pial (see screenshot) the vertex = N/A ( see screenshot). ALso, what step of recon-all should i start? (autorecon-2 or autorecon3)? Best,

Re: [Freesurfer] Help - Error: cannot unpack mosaics without ASCII header

Not sure. Can you upload the set to https://gate.nmr.mgh.harvard.edu/filedrop2 and I'll take a look On 01/10/2017 03:31 PM, Caleb Comoglio wrote: > Hello, > > I am having trouble with the MRI_convert portion of recon-all. I get > the error below when I run recon-all and when I run

Re: [Freesurfer] Multiple comparison correction on subcortical volume

I would say yes, but I've seen plenty of pubs that do not correct. The bonferroni correction is fine. You could also try FDR (though on 4 points it might not make much sense). On 01/10/2017 01:47 PM, neuroimage analyst wrote: > Hi, > > I extracted thalamic, caudate, and putamen volume (left

Re: [Freesurfer] autorecon1 crash (with nu_correct).

Is this happening on all your subjects or just this one? If just this one, have you looked at the image to see if it looks ok? On 01/10/2017 01:09 PM, Jamie Hanson wrote: > Hello Freesurfer List, > > I was running into issues processing subjects, with errors just > getting through the

[Freesurfer] reposition surface for pial surface

Dear Paul, I could chime in with my current limited experiences with this tool (using V6beta version of freeview). Maybe they could be helpful for you. Most straigthforward is using "edit coordinate": Select the surface you want to edit. Select tools-reposition surface - edit coordinate. With

[Freesurfer] Help - Error: cannot unpack mosaics without ASCII header

Hello, I am having trouble with the MRI_convert portion of recon-all. I get the error below when I run recon-all and when I run MRI_convert independently of recon-all. WARNING: file Desktop/3T_20161201_131733544/MR04 does not contain a Siemens ASCII header has this file been anonymized?

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Tamara, mvoing in and popping out sounds like a scaling problem. We do only rigid transforms, so the scaling would already be in your original inputs. If that is the case, it could mean that there was a scanner calibration or something that caused scaled images and that would not be good.

[Freesurfer] Multiple comparison correction on subcortical volume

Hi, I extracted thalamic, caudate, and putamen volume (left hemisphere), and cingulate thickness (right hemisphere) from freesurfer's parcellation. Then I compare these volumes and thickness across two groups using R and found significant differences in these measurements. Do I have to correct

[Freesurfer] autorecon1 crash (with nu_correct).

Hello Freesurfer List, I was running into issues processing subjects, with errors just getting through the autorecon1 step of the pipeline. My terminal outputs the following: /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri

Re: [Freesurfer] reposition surface for pial surface

Thanks bruce for your response. Since there is no documentation, how can i use it because I seen trends on the forum where it was suggested to use reposition surface ( e.g. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html). Use = directions and parameters to input.

Re: [Freesurfer] reposition surface for pial surface

Hi Paul sorry, this is something that Ruopeng put together for me to mess around with - there isn't any documentation cheers Bruce On Tue, 10 Jan 2017, miracle ozzoude wrote: Hello Freesurfer, I would like to learn how to use the reposition surface tool in freeview. Specifically, what

[Freesurfer] reposition surface for pial surface

Hello Freesurfer, I would like to learn how to use the reposition surface tool in freeview. Specifically, what parameters to enter in the gui (see screenshots). Is there any documentation on how to use it if not, can someone with experience work me through it. Thank you. best, Paul

Re: [Freesurfer] ERROR: fast_selxavg3() failed\n

It looks like your FS_OCTAVE_BIN env variable is set to that bin folder. This variable should be set to the octave executable On 1/10/17 7:34 AM, Michael Schirner wrote: > Dear experts, > > I'm attempting to perform step 6 in the FsFastTutorialV5.1 >

Re: [Freesurfer] surface based analysis (projfrac)

When you say in the corpus callosum, do you mean in WM? The surface-based analysis is only for cortical GM. If you mean in GM near the CC, then the analysis is appropriate. The projfrac parameter sets the sampling location between the white and pial surfaces where 0.5 means half way. On

[Freesurfer] surface based analysis (projfrac)

Dear FS experts, I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc"   I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get

[Freesurfer] ERROR: fast_selxavg3() failed\n

Dear experts, I'm attempting to perform step 6 in the FsFastTutorialV5.1 (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel; "First-level Analysis using selxavg3-sess"), but get the following error when I run the selxavg3-sess command: --- octave output

Re: [Freesurfer] automatic segmentation of hippocampal subregions in young children

Dear Tracy, It is true that we haven’t validated our software on such a young population, but I believe that, at age four, the appearance of the brain is close enough to that of adults for automated techniques do a good job (e.g., FreeSurfer has been used on children scans in many studies).

Re: [Freesurfer] dice coefficient computing

Dear Bruce, Thank you very much,you are a life saver.. Best, Nazanin On Mon, Jan 9, 2017 at 11:05 PM, Bruce Fischl wrote: > yes, you can use mri_convert as follows: > > mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz > > assuming the rawavg.mgz