Re: [Freesurfer] registration for AD, MD and RD images

Hi, Bruce, Thank you so much for your help. We tried to use the 'register.dat' file generated from FA registration for the other diffusion maps (AD, MD, RD) and now it works well. Thank you! Best, Shiran From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] TRACULA and priors problem

Hi Jürgen - If your subjects' freesurfer directories have the standard structure as it comes out of recon-all, then you probably have a different problem than the one in that older thread. Have you changed the recon-all output directories in some way? Best, a.y

Re: [Freesurfer] Tracula: anatomical priors

Hi Heidi - TRACULA does not use deterministic constraints like pre-defined ROIs to reconstruct the tracts. For each point along a tract (and not just the end points), it has a prior probability (that it has computed from the atlas subjects) that a tract goes through each of the aparc+aseg

Re: [Freesurfer] Repost: tracula stats including NAs?

Hi Heidi - It's up to you. As long as the N of subjects at each point is included in the statistical test, this will adjust the corresponding p-value accordingly. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] TRACULA tract reconstruction

One potential difference is that TRACULA does not need the gradient vectors to be flipped. It needs to get them the way they are stored in the DICOM header, and that's what mri_convert outputs. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle - I highly recommend using the TRACULA version in 6.0, because it tries to detect the cases that need to be reinitialized and reruns them automatically. (It's ok if the anatomical segmentations come from the 5.3 version of recon-all.) Of course, like with any automatic method for

Re: [Freesurfer] registration for AD, MD and RD images

Hi Shiran if you have the FA registered why do you need to recompute the transform for the other volumes? They are all derived from the same underlying data so should all be in perfect register with each other and hence should share a registration transform. cheers Bruce On Thu, 16 Mar

Re: [Freesurfer] need help clean up pial and wm surfaces

Hi Padma wow, lots of things making this one hard! Low gray/white contrast, low bandwidth/high distortion, noisy, pathology and I'm guessing this was a contrast-enhanced scan (Gad?) as the vasculature and dura are very bright. This latter issue is making things hard as the partial volume of

[Freesurfer] need help clean up pial and wm surfaces

Hi, I’m trying to get pial and wm surfaces for a subject (who has some clinical wm related problems). They were imaged (T1-MPRAGE at 3T) at their imaging center not here at Martinos Center. The gray-white contrast doesn’t look as good as the healthy volunteers that I imaged in the 3T at the

Re: [Freesurfer] Intensity normalization in longitudinal processing

Martin, Thank you for your response. I ran the subject completely (cross and long) in v6.0 and the white matter intensity distribution in the long brain looks similar to the one run with the mixed versions (v5.1 cross and v6.0 long). Since the surfaces also look fine, I understand that this is

Re: [Freesurfer] T1 error

what is the error exactly? Please provide the recon-all.log file and a description of the problem On 03/16/2017 06:28 AM, Manuel Delgado wrote: > Dear list, > After recon-all the T1 seems to have an error. Has anybody had this > problem before? Please find attached the image. I guess I have to

[Freesurfer] Postdoc position at Bangor University (Wales, UK)

Applications are invited for a 3.5-year, full time postdoctoral position with Dr. Kami Koldewyn in the Developmental Social Vision lab in the School of Psychology at Bangor University (Wales, UK). The post is

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

You have commas (ie, ",") instead of decimal points (ie, ".") in your fsgd file. Try replacing them and see if that works On 03/16/2017 08:59 AM, teodora petrova wrote: > Hello, > > I am trying to use the glm_fit to correlate a continuous variable > (index) with cortical thickness, when

Re: [Freesurfer] Extract the cortical thickness

If you run aparcstats2table with the -h option, it will give you documentation and examples. You can also find examples on the tutorial. aparcstats2table will extract all ROIs, but you can choose which one you want after that. Sorry, I'm not sure this has answered your question, but I'm not

Re: [Freesurfer] Recon-all : mri_watershed Error: indices out of bounds

Hi Matthieu typically this means something is wrong witheither the input image (T1.mgz) or the talairach_with_skull.lta transform. You can try running it without the atlas and see if that fixes it. cheers Bruce On Thu, 16 Mar 2017, Matthieu Vanhoutte wrote: Dear Freesurfer's experts, I

[Freesurfer] Recon-all : mri_watershed Error: indices out of bounds

Dear Freesurfer's experts, I ran a classic recon-all and got stucked on a problem I couldn't find in the mailing list: "*mri_watershed Error: indices out of bounds*" *mri_watershed -T1 -brain_atlas /home/global//freesurfer5.3//average/RB_all_withskull_2008-03-26.gca

[Freesurfer] Parahippocampal subfields huge memory demands

Hi all, I believe the website warns for high demands of memory, claiming it may take up to 10G for this processing step. However, when I run this on cluster the memory demands go up to 30G. This is still for one subject using one scan. Is this to be expected, has something changed in the

[Freesurfer] Hippocampal subfields huge memory demands

Hi all, sorry for the double post, but I noticed an error in the chosen title. I believe the website warns for high demands of memory, claiming it may take up to 10G for this processing step. However, when I run this on cluster the memory demands go up to 30G. This is still for one subject using

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, I am trying to use the glm_fit to correlate a continuous variable (index) with cortical thickness, when controlling for age, education, and cognition (MMSE) (all continuous variables). However, I get the following error: ERROR: matrix is ill-conditioned

Re: [Freesurfer] Extract the cortical thickness

Dear Doughlas Thank you for your quick response. I am studying the group analysis from the tutorial. I would like to ask if I could change to the cortical thickness data from the specific ROI I am interested in to analyze. If it can, please show me how. Thank you again and Best regards Duy

[Freesurfer] T1 error

Dear list, After recon-all the T1 seems to have an error. Has anybody had this problem before? Please find attached the image. I guess I have to recon-all again. I am using v 6.0 with Ubuntu 16.04. Thank you. -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla