Re: [Freesurfer] Subfields Development Version MATLAB:scriptNotAFunction

External Email - Use Caution Dear Lachian (and everyone), I am SO sorry about this. I’ll be fixed very soon, I promise. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.co

Re: [Freesurfer] LME model and contrast for longitudinal covariate and different scanners

External Email - Use Caution Hi Donatas, please find my thoughts in-line. Best regards, Kersten On So, 2018-05-27 at 11:59 +0200, Donatas Sederevicius wrote: > External Email - Use Caution > > Dear Freesurfer experts, > > I have some doubts while running LME analysis

[Freesurfer] white matter and grey matter

External Email - Use Caution Hello Team, 1) How can i just get the white matter and grey matter together? 2) At what stage of free-surfer i can get this? I tried looking at the brainmask.mgz at the end of recon-all -autorecon1 stage. But, it looks like it has CSF and other parts

Re: [Freesurfer] white matter and grey matter

Hi Ritesh can you clarify what you mean? Do you want a segmentation? You can get that in the aparc+aseg.mgz at the end of the recon-all processing. cheers Bruce On Wed, 30 May 2018, Ritesh Mahajan wrote: >External Email - Use Caution > > Hello Team, > > 1) How can i just get the white

[Freesurfer] Open Position in Neuroimaging: Barcelonaβeta Brain Research Centre – Pasqual Maragall Foundation, Barcelona, Spain

External Email - Use Caution *Doctoral Position in the Neuroimaging Research Group in the Barcelonaβ**eta Brain Research Centre – Pasqual Maragall Foundation, Barcelona, Spain* Barcelonaβeta Brain Research Center (BBRC) invites applications for a full-time graduate student positio

[Freesurfer] Missing register.dof6.lta.file after FAST Preprocessing

Hi Team, I am using FsFastTutorialV6.0 to run FAST Preprocessing. The Functional-Anatomical Cross-modal Registration should have 6 files but I lost the register.dof6.lta. I try to run the command register-sess -s $subj -per-run -fsd

Re: [Freesurfer] QDEC, order of groups for interpretation of results

I'm pretty sure that is uses the order in the .levels file. It will create a y.fsgd file in the output folder. Look at the order in that as that will be definitive. On 5/29/18 2:15 PM, Avi Gharehgazlou wrote: Hello experts, I am using QDEC to compared LGI values between groups (typically

[Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hello, I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link ( https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it

[Freesurfer] manual edits

External Email - Use Caution Dear FS experts, My question is very basic and I appreciate your help. I ran recon-all on a low quality T1 image. I'd like to fix the segmentation error (attached). Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be fixed by sett

Re: [Freesurfer] manual edits

Hi John I'm not sure I understand exactly what you are referring to. We automatically fill in the ventricles so that they are contained within the interior of the ?h.white surfaces. Is that what you thought was incorrect? cheers Bruce On Wed, 30 May 2018, John Anderson wrote: Exte

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hi Miracle, I believe Doug (CCed) ran into a similar problem recently, and I think the problem had to do with mixing versions. What exact version are you using? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Im

Re: [Freesurfer] manual edits

External Email - Use Caution Hi Dr Bruce. I highly appreciate your quick response. kindly see attached is another view. The boundaries of the corpus callosum are not correctly defined on multiple slices. Can this be fixed by setting control points in the CC regions? Thanks ​S

Re: [Freesurfer] manual edits

Hi John is this causing a problem for you? What type of analysis do you want to do that is impacted by this? If you upload the subject we will take a look, but these regions are typically excluded from the surface analysis as they are non-cortical anyway. cheers Bruce On Wed, 30 May 2018,

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hello Eugenio, Thanks for the response. All my processing was done with FreeSurfer v6.0 although, we have version 5.3 installed on the server too. I always set my environment to version 6 ( export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; sourc

Re: [Freesurfer] manual edits

External Email - Use Caution Hi Dr Bruce, I ran surface based analysis between one subject and a group of controls. The problem is that I don't expect any difference in this region at least visually (i.e. by looking at the CC in controls and compare it with the subject's data).

[Freesurfer] slice time correction before motion correction?

Is there any way to do slice time correction prior to motion correction, with SMS/multiband data? Thanks, Stephanie + Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford St. Cambridge, MA 02138 Phone: 617-529-1854 +

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hey so kvlAutoCrop is looking for sources.sh in /opt/freesurfer-6.0.0/ which seems to be FREESURFER_HOME at that point. However, from the rest of your code, it seems that FREESURFER_HOME is /opt/freesurfer-6.0.0/freesurfer/ Please double check. Chee

[Freesurfer] Visualizing Supratentorial volume

External Email - Use Caution All, Is there any way to graphically visualize the segmentations for SupraTentorialVol and SupraTentorialVolNotVent, for example in freeview or tkmedit? Based on the descriptions I have read for the supratentorial values, I want to use them for an anal

Re: [Freesurfer] slice time correction before motion correction?

you mean with fsfast? No, not possible On 05/30/2018 11:50 AM, McMains, Stephanie wrote: > > Is there any way to do slice time correction prior to motion > correction, with SMS/multiband data? > > Thanks, > > Stephanie > > + > > Stephanie McMains > > Neuroimaging Staff Scient

[Freesurfer] EEG and MEG Source Reconstruction with FieldTrip @OHBM2018

External Email - Use Caution Dear all, on 17 June 2018 we will host a workshop at the OHBM2018 conference  . The course is aimed at researchers who want to learn how to do MEG and/or EEG**source reconstruction.

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hello, I checked and my sources.sh is located in /opt/freesurfer-6.0.0/freesurfer/sources.sh not /opt/freesurfer-6.0.0/sources.sh. I opened the kvlAutoCropt file and it found this source $FREESURFER_HOME/sources.sh kvlAutoCrop.bin "$@" Can I edit the

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution No, the contents of kvlAutoCrop are what they should be. What I don’t understand is why the code is looking for /opt/freesurfer-6.0.0/sources.sh (this is what your log says). Are you sure FREESURFER_HOME is properly defined? Cheers, /Eugenio -- Juan

Re: [Freesurfer] Missing register.dof6.lta.file after FAST Preprocessing

What happened when you ran register-sess? You can also run preproc-sess and it will figure out what it needs to re-run On 05/30/2018 10:23 AM, Wang, Zhuonan wrote: > Hi Team, > > I am using_FsFastTutorialV6.0 > _ to run > FAST Prepro

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Yes, because I processed all my subjects with v6.0 without any issue. When i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0". I always insert this lines " export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; source $FREESURFER_HOME/Se

Re: [Freesurfer] Visualizing Supratentorial volume

I'm not sure what you mean. You can just use freeview to load the aseg. Or do you want all the non-STV removed? If that, you can create a mask of STV using mri_binarize and --match run on the aseg.mgz, then use mri_mask aseg.mgz stvmask.mgz aseg-stvonly.mgz On 05/30/2018 11:56 AM, James Gulli

[Freesurfer] midbrain mask in standard-space?

External Email - Use Caution Hi Freesurfer email list, I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline).

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hi again, The two following statements are inconsistent! I believe that’s the root of the problem: a. When i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0". b. I always insert this lines " export FREESURFER_HOME=/opt/freesurfer-6.0.0

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Thanks. So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0; source $FREESURFER_HOME/freesurfer/SetUpFreeSurfer.sh" (based on printenv). However, when i tried to run my script i got another error (/opt/freesurfer-6.0.0/freesurfer/SetUpFre

Re: [Freesurfer] midbrain mask in standard-space?

Hi Dan which brainstem atlas do you mean? cheers Bruce On Wed, 30 May 2018, djpet...@u.washington.edu wrote: >External Email - Use Caution > > Hi Freesurfer email list, > > I'm trying to get the midbrain mask from the brainstem segmentation > pipeline into standard space, for use

Re: [Freesurfer] midbrain mask in standard-space?

External Email - Use Caution The "brainstem pipeline" described here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Thanks! -Dan On Wed, 30 May 2018, Bruce Fischl wrote: > Hi Dan > > which brainstem atlas do you mean? > > cheers > Bruce > > > On Wed, 30 May 2

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hard to tell without seeing the contents of the directories, but I'd put my money on: export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh recon-all ... Juan Eugenio Iglesias Centre for Medical Im

Re: [Freesurfer] midbrain mask in standard-space?

External Email - Use Caution Hi Dan, The mesh can be rasterized in its reference space, but such does not correspond to any volumetric image. Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.co

Re: [Freesurfer] midbrain mask in standard-space?

External Email - Use Caution Thanks for responding, is there some known mapping of this reference space to MNI-space or another standard space? On Wed, 30 May 2018, Iglesias Gonzalez, Eugenio wrote: External Email - Use Caution Hi Dan, The mesh can be rasteri

Re: [Freesurfer] midbrain mask in standard-space?

Hi Dan do you have he voxel segmentations of your data in subject space? If so, you can use mri_vol2vol and the subject's transforms/talairach.lta to map it into MNI space cheers Bruce On Wed, 30 May 2018, djpet...@u.washington.edu wrote: External Email - Use Caution Thanks for resp

Re: [Freesurfer] white matter and grey matter

External Email - Use Caution Hello Bruce, Yes, i do want segmentation. But i am more interested in getting just white matter and grey matter in segmented brain. As the segmentation results also have left ventricles and right ventricles and other parts as well. I am more interes