Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Elijah - I suggest looking at the axial diffusivity (AD) and radial diffusivity (RD) to help you interpret these results. These are the diffusivity parallel and perpendicular to the main budnle going through a voxel, respectively. Essentially, FA tells you how different the AD and RD are

Re: [Freesurfer] Trac-all -path Segmentation error

Hi Katherine - The dlabel/ directory is created during the -prep step, when the structural segmentation gets mapped from T1 to diffusion space. However bedpost may still run fine without the dlabel/ directory. It seems that the problem is fairly early in the -prep step. Any errors there?

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Kirstie, Yes indeed there were 3 subjects at the bottom-left of the plot. To account for PV, I eroded the boundaries using *-seg-erode 1* during the *mri_segstats* stage, and this resulted in a few subjects with no data for the WM entorhinal region (although these were saved as "0" in the

Re: [Freesurfer] Cortical thickness average

Thanks a lot Elijah, I will give a try to this and will surely get back to you if I had any issue. Thanks again for the help. Regards, Sahil On Thu, Mar 24, 2016 at 6:39 PM, Elijah Mak wrote: > Hi Sahil, > > I did something similar recently. I believe you can use

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Elijah, Is there any chance you could attach a scatter plot? My suspicious mind thinks either a) there are outliers who are doing odd things, or b) the FA values are very different to those in other regions and therefore the correlation with MD wouldn't be expected to be the same. Kx

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Alshikho , Yes, I am sure :) Same sequence for everyone. Just to add. FA and MD were significantly negatively correlated for the other regions including the fusiform, precuneus,

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Are you sure that all your DTI images have the same acquisition parameters?!! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Elijah Mak [fk...@medschl.cam.ac.uk] Sent: Thursday, March 24, 2016 7:33 PM To:

Re: [Freesurfer] Cortical thickness average

Hi Sahil, I did something similar recently. I believe you can use mri_concat with the -mean option to create an average map of the group. Another option might be make_average_subject? https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject Best Wishes, Elijah

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

Doug, I see now what your concern was with just adjusting the beta weights. Since FSFAST is using a pseudo-mixed effects model, there is also a need to pass the cesvar statistics up to the second level. How that might accommodate the derivative boost computation is not straightforward to me.

[Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Freesurfer Community, I recently used mri_segstats to extract FA and MD as suggested here: http://freesurfer.net/fswiki/FsTutorial/Diffusion Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at some of the correlations between FA and MD in the same regions, and came

[Freesurfer] Cortical thickness average

Hello FreeSurfer community, I calculated cortical thickness for 100 controls following the instructions described here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was wondering if there is any way to

[Freesurfer] ROI within subject

Dear. Freesurfer experts. Hi. How are you? I have a question about making ROI. This might be a naive question, but any input would be greatly appreciated. I preprocessed scans per run, thus I have register.dof6.dat file inside all run epi directories. Then, I made ROIs per single subject

Re: [Freesurfer] whole hemisphere is yellow

Can you give us more info about the design and the contrast you are testing? What does the uncorrected map look like? On 03/24/2016 09:56 AM, Miracle Ozzoude wrote: > I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus > area in yellow for one of my results however,

Re: [Freesurfer] REPOST: registering longitudinal data to template

Hi Clara, long_mris_slopes is for the 2 stage approach. It computes a linear fit (within each subject) across time (using the base space), then it maps the results to the template (fsaverage) and applies smoothing. It can compute rate (slope of linear fit) or some percent change measures, also

Re: [Freesurfer] REPOST: registering longitudinal data to template

Thank you, Martin! That clears things up a lot! Could you explain what the difference is between the commands long_mris_slopes and mris_preproc? As far as I understand they give you a different output. But what do they do differently in respect to mapping longitudinal data? Cheers, Clara

Re: [Freesurfer] whole hemisphere is yellow

I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus area in yellow for one of my results however, for the other it displayed the entire hemisphere in yellow. Do I need to use the configure-- overlay? ‎Also, when I tried to view the cluster summary for the entire

Re: [Freesurfer] whole hemisphere is yellow

if it's all yellow it means everything is significant. What threshold are you using? On Thu, 24 Mar 2016, Miracle Ozzoude wrote: > Hello Bruce, > No. This was after I ran the correction for multiple comparisons. Do I need > to change the threshold too? My other results were fine. Thanks > Best,

Re: [Freesurfer] whole hemisphere is yellow

Hello Bruce, No. This was after I ran the correction for multiple comparisons. Do I need to change the threshold too? My other results were fine. Thanks Best, Miracle Sent from my BlackBerry 10 smartphone. Original Message From: Bruce Fischl Sent: Thursday, March 24, 2016 8:45 AM To:

Re: [Freesurfer] Regarding: oblique view

HI Sampada wow, something went terribly wrong. Can you post an image of the actual volume and maybe of the wm segmentation? cheers Bruce On Thu, 24 Mar 2016, Dr Sampada Sinha wrote: Hello Bruce, The recon-all -autorecon2 process exited with the error. The lh inflated no fix image is

Re: [Freesurfer] whole hemisphere is yellow

Hi Miracle have you tried changing the thresholds? What kinds of values are you seeing? Bruce On Wed, 23 Mar 2016, Miracle Ozzoude wrote: > hello doug, > i performed a group analysis and after correction for multiple comparisons > when i tried to load the corrected clusters the whole

[Freesurfer] errors message in QAtools

Hi, I'm running QAtools on a set of subjects processed with FS 5.3.0, and consistently get this message when recon_checker is running: Processing each subcortical label ... (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

On 24 March 2016 at 04:15, Francis Tyson Thomas wrote: > The issue I faced was after following all your instructions when I cam to > the step of "make j4" it threw an error saying that it was not able to find > -lcudart. And it looked like it was looking for it

Re: [Freesurfer] Surface based analysis using FA maps

The point is that more than tissue damage will cause changes to FA. Matt. On 3/23/16, 9:17 PM, "Alshikho, Mohamad J." wrote: >This is theoritically correct! >If we do DTI to study the liver. How these measures can

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

Hi Richard, That was really helpful. All the details were very clear and I was able to get it up and running except for some small hiccups which I fixed with a small hack. The issue I faced was after following all your instructions when I cam to the step of "make j4" it threw an error saying