Re: [Freesurfer] Question

Dear Bruce is there any 3D image file which shows the segmentation regions after this correction ?and if there is not is it right to use aseg.mgz file for reporting Dice or Jaccard Index (I have manual segmentation as gold standard)? Best Regards, Nazanin On Wed, Jan 18, 2017 at 5:18 PM, Bruc

Re: [Freesurfer] mri_vol2surf

Thanks a lot, Bruce. Cheers, Zhivago... On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl wrote: > Hi Zhivago > > tksurfer is deprecated and uses one of the methods available in > mri_vol2surf, so our advice would be to use vol2surf > > cheers > Bruce > On Wed, 18 Jan 2017, Zhivago wrote: > > [clea

[Freesurfer] mri_mcsim OSX last version

Hi list, mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a newer Linux version is available and indicates to ask for other versions. Is it possible to have the last osx version? thanks! Gari ___ Freesurfer mailing list Freesurfer@nm

Re: [Freesurfer] 'nuisance factors adjusted' values

Thanks Douglas. My command lines are 'mri_surfcluster --in /Volumes/My_Book_Thunderbolt_Duo/subjects_DCNTDC/qdec/Untitled/rh-Diff-WT-Hetero-Intercept-thickness/sig.mgh --thmin --subject fsaverage --hemi rh --ocn ocn.mgh' 'mri_segstats --i /Volumes/My_Book_Thunderbolt_Duo/subjects_DCNTDC/qdec/Unt

Re: [Freesurfer] PETSURFER Tutorial Problems

efore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch wrote: > > Dear expert

Re: [Freesurfer] Roi parcellation

can you please include the entire correspondence. We get a lot of emails and it's hard for us to keep track otherwise thanks Bruce On Wed, 18 Jan 2017, Aya Kabbara wrote: > > Thank you.. > > Actually, I realized that using tksurfer I can do a manual parcellation. > However, I need an automati

Re: [Freesurfer] Roi parcellation

Hello, Two options I can think of--develop your own atlas (time consuming), or apply the Lausanne atlas parcellation, and combine the smaller ROIs to get the ones you want. See this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043869.html https://github.com/m

[Freesurfer] Postdoc position and PhD studentships available at Cardiff, UK {Disarmed}

[Apologize for cross-posting] Dear all, We are seeking applicants for 1 postdoc position and 2 fully-funded PhD studentships at Cardiff University Brain Research Imaging Centre (CUBRIC). These posts link to a project funded by the European Research Council (ERC). The successful candidates will wo

[Freesurfer] Roi parcellation

Thank you.. Actually, I realized that using tksurfer I can do a manual parcellation. However, I need an automatic parcellation. Is there a way? Get Outlook for Android ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

[Freesurfer] volume based GLM group analysis(whole brain and ROI).

Hello Freesurfer, I would like to do a GLM volume based analysis using the cortical volumes from desikan atlas (structural not functional). However, I can't find the steps/tutorials on how to do this on the freesurfer website. Does anyone know how to do this using freesurfer? Basically, I want to p

Re: [Freesurfer] Cortical volume from masked region

I would probably map the mask to the surface,eg, mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz The run mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats On 01/17/2017 11:24 A

Re: [Freesurfer] WM lobes and Corpus Callosum

You can use mri_binarize to replace the CC values with WM values, eg mri_binarize --i aseg.mgz --replace 251 2 --replace 252 2 ... --o aseg.nocc.mgz If your version of mri_binarize does suppor the --replace option, you can get this versoin https://gate.nmr.mgh.harvard.edu/safelinks/greve/mr

Re: [Freesurfer] 'nuisance factors adjusted' values

what are your command lines? On 01/18/2017 01:39 AM, hiroki.s...@med.tohoku.ac.jp wrote: > Dear experts, > > I have some questions. > I did Qdec group analysis with three nuisance factors. And one region > remained after FDR correction. > Then I did 'mri_surfcluster' specifying the FDR-determined

Re: [Freesurfer] installation fail :(

There's 2 problems: 1) Do not include the "$>". That is just a symbol representing the beginning of the command line. 2) is meant to be a generic term for the process of defining your FREESURFER_HOME environment variable and sourcing the setup script. On your macOS system this would be the fo

Re: [Freesurfer] Recommended method of using data with variable sizes

yes, the easiest thing to do would be to reslice one like the other then register and average them (-rl in mri_convert) On Wed, 18 Jan 2017, Alex Cohen wrote: yes. If you try to feed them both to recon-all, it errors out due to dimension mismatch (lines 939+) so I presume I'd have to do it fi

Re: [Freesurfer] question about cortical volume group analyses

Sorry about the delay. The jacobian factor accounts for stretching or compression when transferring the data from the individual to the group. This makes sure that the total volume after conversion is the same as before (this is not needed for thickness but it is for surface area). If you are g

Re: [Freesurfer] Recommended method of using data with variable sizes

yes. If you try to feed them both to recon-all, it errors out due to dimension mismatch (lines 939+) so I presume I'd have to do it first, unless there is an expert-pref to do this. -Alex Alexander Li Cohen, M.D., Ph.D. E-mail: ale

Re: [Freesurfer] mris_make_surfaces error with bbr-init-header

I transferred file using ftp transfer. Thanks, Sneha From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Wednesday, January 18, 2017 1:58:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init

Re: [Freesurfer] Recommended method of using data with variable sizes

average what? The different voxel size images? On Wed, 18 Jan 2017, Alex Cohen wrote: I will likely end up running each separately on several subjects to get a handle on how they're behaving; however assuming I did what to average them, have you all found a particular method more useful than a

Re: [Freesurfer] Recommended method of using data with variable sizes

I will likely end up running each separately on several subjects to get a handle on how they're behaving; however assuming I did what to average them, have you all found a particular method more useful than another for this? i.e., mri_robust_register, bbregister, etc... -Alex --

Re: [Freesurfer] Recommended method of using data with variable sizes

Hi Alex you get to decide whether to average your data or not. It's a totally empirical question which one is better - why don't you run them each and visually inspect the results? cheers Bruce On Wed, 18 Jan 2017, Alex Cohen wrote: Hi all, What is the current best practice recommendation f

Re: [Freesurfer] PETSURFER Tutorial Problems

Hello, Thank you for reporting this. This was indeed a bug in the Mac version and will be fixed in the upcoming release. In the meantime, I provided a link to a fixed version of the problematic script. Please overwriting your existing version of FREESURFER_HOME/bin/xcerebralseg with the one pr

Re: [Freesurfer] question about cortical volume group analyses

Dear All, The email below probably fell through the cracks so I am resending it. Appreciate your thoughts and suggestions. Best Ri - Original Message - From: Ritobrato Datta To: Freesurfer support list Sent: Tue, 17 Jan 2017 14:05:10 -0500 (EST) Subject: question about cortical volum

[Freesurfer] Recommended method of using data with variable sizes

Hi all, What is the current best practice recommendation for using multiple T1s and/or T2s for recon-all where the sizes of the images are slightly different. For instance: two T1w images of 0.9x0.9x0.9 and 1x1x1 resolution, however the 1x1x1 image seems to have better grey-white separation, etc.

Re: [Freesurfer] mris_make_surfaces error with bbr-init-header

oh, something else went wrong, it's not a memory issue.If you upload the subject we will take a look Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote: Sure, please find it attached. Thanks, Sneha From: freesurfer-b

Re: [Freesurfer] WM lobes and Corpus Callosum

Hi Prad - That part of the corpus callosum belongs neither to the left nor to the right hemi, it connects the two. So any split would be arbitrary. You could write a script that finds if a voxel is closer to the left or the right hemi for example. Best, a.y Fro

Re: [Freesurfer] WM lobes and Corpus Callosum

Hello Anastasia, Thank you for your reply! I had created the 4 WM lobes for each hemisphere to extract regional volumes for white matter lesions in each lobe. As some of our participants have WML in the corpus callosum very close to the midline, they are not included in the WM lobes create

Re: [Freesurfer] mris_make_surfaces error with bbr-init-header

Hi Bruce, Total is 23108 kB from /proc/meminfo and flair vozel size is 1., 0.9766, 0.9766. I ran quite a few recon-all after this one failed and it did not complain. It just fails when I run recon-all -autorecon3 with -bbr-init-header flag. Thanks, Sneha _

Re: [Freesurfer] mris_make_surfaces error with bbr-init-header

hmmm, can you send us the recon-all.log file? On Wed, 18 Jan 2017, Sneha Pandya wrote: Hi Bruce, Total is 23108 kB from /proc/meminfo and flair vozel size is 1., 0.9766, 0.9766. I ran quite a few recon-all after this one failed and it did not complain. It just fails when I run reco

Re: [Freesurfer] Fwd: QDEC versus Terminal annotation

That vertex (# 130) is just on the border with cuneus, so technically the information is correct On 01/17/2017 11:29 AM, Martin Juneja wrote: > Hi FreeSurfer community, > > I am sorry for reposting the following questions in the discussion forum: > > -- Forwarded message -- > Fro

Re: [Freesurfer] mris_make_surfaces error with bbr-init-header

Hi Sneha how much RAM do you have in your machine? And what is the resolution of your data? cheers Bruce On Wed, 18 Jan 2017, Sneha Pandya wrote: Hi all, I have successfully ran recon-all on my subjects with multiple T1s. We want to use flair to refine pial surfaces as for all the subject

[Freesurfer] mris_make_surfaces error with bbr-init-header

Hi all, I have successfully ran recon-all on my subjects with multiple T1s. We want to use flair to refine pial surfaces as for all the subjects pial surfaces are messy and will demand lots of control point edits. After successfully running entire recon-all stream I am running following com

Re: [Freesurfer] Question

Hi Nazanin the volumes reported in the aseg.stats file have been corrected for partial volume effects. cheers Bruce On Wed, 18 Jan 2017, N Saf wrote: Dear FreeSurfers, I have a question about aseg file. I load the aseg file of bert subject in itk-snap and read the volume for 17 and 53 label

[Freesurfer] Neuroimaging postdoctoral position

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, there is a position available as a postdoctoral student funded by the Research Council of Norway. The research area is psychiatric neuroima

Re: [Freesurfer] mri_vol2surf

Hi Zhivago tksurfer is deprecated and uses one of the methods available in mri_vol2surf, so our advice would be to use vol2surf cheers Bruce On Wed, 18 Jan 2017, Zhivago wrote: [cleardot.gif] Hi, From whatever I read, there seem to be 2 ways for overlaying activation maps on surfaces. 1)

[Freesurfer] Question

Dear FreeSurfers, I have a question about aseg file. I load the aseg file of bert subject in itk-snap and read the volume for 17 and 53 label but it is a bit larger of the volume in bert stats file. I do the same for some of my subjects too and I see the same result .I don't know why it is like th

[Freesurfer] recon-all error (Freesurfer)

 Hello FreeSurfer Developers,   I'm attempting to process running segmentation.But I have a problem. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.02) Platform: Ubuntu 16.04 LTS3) uname -a: Linux gwkim 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_6