[Freesurfer] recon-all CTABreadASCII error

Dear FS experts, It represents this message in the command window after ran "recon-all -autorecon-pial -s CON_EIU01 -no-isrunning": Reading annotation reading colortable from annotation file... colortable with 36 entries read originally /autofs/space/terrier_001/users/nicks/freesurfer/average/col

Re: [Freesurfer] Variability in bedpostx output

Wow, that's interesting. In both cases it's called with the default settings, without specifying any special options on the command line. You could verify this by running the respective versions of bedpostx independently of tracula and looking at the outputs. Unless of course something has cha

Re: [Freesurfer] Variability in bedpostx output

Thank you Anastasia. Unfortunately, I posted the question to the FSL list first and after a few go-rounds with clarification and more info, they felt like it was potentially a problem of the calls to the bedposts command from within Freesurfer. Their final assessment was that there should be n

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

Celine - You're very welcome! If this particular motion measure is identical for pretty much all your subjects, there is no point in including it. So you can just use the other 3 motion measures. a.y On Wed, 12 Feb 2014, Celine Louapre wrote: > Hi Anastasia > Thanks a lot for your very nice

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is: 1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume t

Re: [Freesurfer] Variability in bedpostx output

Hi Jeff - Questions about bedpostx output files are best addressed to the FSL list, as it's an FSL program that is not developped by us. The appropriate info to provide them is the FSL (rather than freesurfer) version numbers. a.y On Tue, 11 Feb 2014, jwa...@nmr.mgh.harvard.edu wrote: > Hell

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Hi Francesco - The decimal separator should be dot, not comma. Can you send me the bvecs/bvals that you get after you change from row to column format? (Both the ones that you feed into trac-all and the ones that get created under dmri/.) Thanks, a.y On Tue, 11 Feb 2014, Francesco Baldacch

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Ciao Francesco - Just to clarify, to be able to have your bvecs/bvals in rows, you should have, in addition to the latest version of freesurfer, the update that I linked to below: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates a.y On Tue, 11 Feb 2014, Francesco Baldacchini

Re: [Freesurfer] Tracula version and download problem

Dear Anastasia, Thank you very much for the clarification. Best, Clive On Thu, Feb 13, 2014 at 8:52 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Clive - So you are talking about the overall tract stats, averaged over > the whole tract (and not the stats by position on th

Re: [Freesurfer] Tracula version and download problem

Hi Clive - So you are talking about the overall tract stats, averaged over the whole tract (and not the stats by position on the tract that trac-all -stat outputs). That phrase in the tutorial is not very clear - these could be used as a covariate in mri_glmfit, but the main input of mri_glmf

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

Hi Anastasia Thanks a lot for your very nice talk today. I would have another question on top of the one below. I have looked at the formula to calculate the total motion index, and for the third motion parameter (percentage of slice with signal drop-out), all subjects except 2 had a 0 value. So in

[Freesurfer] bbregister and fnirt

Hi all, We're conducting the registration using bbregister that gives us a registration matrix (a .dat file) BUT the original structural file remains intact, i.e. the registered output can be viewed but not stored. Can we store the co-registered structural image as a .nii file? And if so, how? We

Re: [Freesurfer] dt_recon error for Siemens mosaics image

It is looking for information in the Siemens "ascii header". This is a bit of ascii text that gets stored in a private field in the dicom, but because it is ascii we can just parse the file. It uses this information to determine the size of the mosaic. doug On 02/12/2014 12:23 PM, Gennan Che

Re: [Freesurfer] Fwd: How to avoid tumour from being segmented out

Hi Melanie doing it in tkmedit (or freeview) would be doing it manually. But if you do it this way it should allow you to correct the resulting surfaces and such cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: > > > Thanks,Melanie Morrison > > Begin forwarded message: > > Fr

Re: [Freesurfer] local_gi problem

Hi Krista, Try using the following command: tksurfer BV2 lh inflated -overlay $SUBJECTS_DIR/BV2/surf/lh.pial_lgi -fthresh 1 The error you got is because the overlay needs the full path to the pial_lgi file. Then, not all regions are coloured because the default minimum threshold is 2, and you

[Freesurfer] Fwd: How to avoid tumour from being segmented out

Thanks, Melanie Morrison Begin forwarded message: > From: Bruce Fischl > Date: 12 February, 2014 1:21:56 PM EST > To: Melanie Morrison > Subject: RE: [Freesurfer] How to avoid tumour from being segmented out > > Hi Melanie > > can you cc the list so that others can answer? > > thanks > Bru

[Freesurfer] Fwd: Problems dipslaying annotations in freeview

Hi Ruopeng and freesurfer folks, I am still having trouble loading annotations in freeview, similar to what I mentioned before. When I load 'rh.aparc.a2009s.annot' in freeview, the annotation loads onto the LEFT hemisphere and is tye-died in appearance. In contrast, 'lh.aparc.a2009s.annot' loads

Re: [Freesurfer] dt_recon error for Siemens mosaics image

Possible. Can you give me DICOM tag/tags the program looks for?? Gen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 12, 2014 8:24 AM To: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Running a template through recon-all

Dear FreeSurfer experts, I am trying to map volumetric ROIs obtained from VBM to surfaces in 5-6 year old children. I saw in a couple previous posts that it is recommended to run the template brain through recon-all, map the ROIs to the template surface, and then propagate the ROIs to all subje

[Freesurfer] Postdoc - ICM Paris - Morphometry using 7T MRI

Dear colleagues, Our team is looking for a postdoctoral fellow. Please find below the informations about the position. Many thanks Olivier Colliot _*Research topic: Computational anatomy of the hippocampus using very high resolution MRI at 7 Tesla: diffeomorphic registration and shape analys

Re: [Freesurfer] How to avoid tumour from being segmented out

Hi Melanie you should be able to fill it in in the wm.mgz volume in either tkmedit or freeview (using 255 if in freeview - tkmedit will do this by default) cheers Bruce On Wed, 12 Feb 2014, Melanie Morrison wrote: > Hi there, > > I am creating surfaces from my volume T1-weight scans so that I

Re: [Freesurfer] dt_recon error for Siemens mosaics image

has it been anonymized? On 02/11/2014 02:23 PM, Gennan Chen wrote: > HI! All, > > I got an error when I ran dt_recon > > WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not > contain a Siemens ASCII header > > has this file been anonymized? > > ERROR: cannot unpack mosiacs without

[Freesurfer] How to avoid tumour from being segmented out

Hi there, I am creating surfaces from my volume T1-weight scans so that I can run them in AFNI's SUMA program. Problem is that my tumour has been segmented out because its intensity and the intensity of its surround area is much lower that what is being segmented. How can I avoid this? Or edi

[Freesurfer] freesurfer course

Hello, I am interested in attending a freesurfer course at Martinos Center for Biomedical Imaging in Boston But, it says that the following lectures are only during spring and fall. 1)Functional analysi

Re: [Freesurfer] distribute dots on the surface

what do you mean by "dots"? Eg, a mask surface overlay with 1s in some vertices and 0s in others? Or a label? doug On 2/12/14 9:52 AM, peng wrote: Dear Freesurfers, I have run recon-all and got a set of surfaces for the subjects. I wish to distribute N dots about evenly on the surface

[Freesurfer] distribute dots on the surface

Dear Freesurfers, I have run recon-all and got a set of surfaces for the subjects. I wish to distribute N dots about evenly on the surface to cover most gyri and sulci , but I don't how to implement that. One way is to manually put them in the GUI of freeview, but it is not so convenient if N i

Re: [Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?

Hi Erik yes, those numbers are always estimated from the data unless you specify otherwise. And please remember to cc the list so that others can answer/see the answers in case they are interested in the same type of issue. cheers Bruce On Wed, 12 Feb 2014, Erik Lindberg wrote: OK Thanks 

Re: [Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?

Hi Erik is there a reason not to do it for the whole group? I guess if the one subject you uploaded had significant motion (which caused the blurryness) then it might be the case that it needs separate parameters. In general though it's good to hold this kind of thing constant as it will defin

Re: [Freesurfer] Segmentation using Free Surfer.

Hi Saurabh have you run recon-all on your subjects? If so, you should be all set (see my previous email) cheers Bruce On Wed, 12 Feb 2014, Saurabh Thakur wrote: Hello Free surfer Expert, I have started working on Free surfer. Now i m facing two issues such as : 1. I m trying to use con

Re: [Freesurfer] Number of pixel count

Hi Saurabh we don't measure sulcal CSF as it's really not visible on only a T1. The other measures should all be in the files in the stats directory - no need to measure it yourself. cheers Bruce On Wed, 12 Feb 2014, Saurabh Thakur wrote: Hello Free surfer Expert ,   I am kooking for the e

[Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?

Dear Freesufers, I am trying to understand what happens if I go in and edit the numbers for -min_border_white -min_gray_at_white_border in a single subjects in a large group. Generally we aim to set everything identical when running a group of subjects in FS. I went in and had a look at the re

[Freesurfer] Segmentation using Free Surfer.

Hello Free surfer Expert, I have started working on Free surfer. Now i m facing two issues such as : 1. I m trying to use contour ... but it is working as per guidance in website given. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/VoxelEdit Under heading of Cont