Re: [Freesurfer] Volumetric Analysis Inquiry

Hi Dan the aseg volumes are native, *not* ICV-corrected. And yes, the standard way to account for ICV is to include it as a covariate cheers Bruce On Thu, 18 Jul 2013, Daniel LaFreniere wrote: Dear FS Experts,  I had a question concerning volumetric analysis. I will soon be starting this a

[Freesurfer] Circular label of pre-defined radius on fsaverage

Hello FreeSurfer Experts, We would like to automatically create circular labels of a pre-defined radius (e.g. 14mm) on the fsaverage surface in freesurfer. For each label, a target vertex with pre-defined RAS/Talairach coordinates should be in the center. Would this be possible? Thank you, Sara

[Freesurfer] Volumetric Analysis Inquiry

Dear FS Experts, I had a question concerning volumetric analysis. I will soon be starting this analysis and have exported my data into a text file using the flag: asegstats2table --subjects [list_of_subjects_for_analysis] --meas volume --tablefile asegstats.txt All of my subjects have the en

[Freesurfer] qdec -- confused by glm output for custom ROIs

Hello, I have a question regarding the interpretation qdec's output for the custom ROI's thickness estimates. I ran an analysis comparing cortical thickness in children with and without ADHD (categorical variable), controlling for age and demeaned ICV, using 5.0. After controlling for multiple

Re: [Freesurfer] recon-all steps specified into volume and surface based stream?

everything upto the tesselation is the volume-based stream. You can also look in recon-all-status.log for which commands are run when doug On 07/17/2013 04:58 PM, Martina Papmeyer wrote: > Dear FreeSurfer experts, > > I was wondering if there is anywhere a table or hint, suggesting which > particu

Re: [Freesurfer] Q) how to overlay two different maps in one template using different colors?

you can overlay them as two different overlays or you can use mri_concat to merge them into a multiframe file then scroll through the frames in freeview On 07/18/2013 03:42 PM, Yune Lee wrote: > Hello Freesurfer experts, > > I'd hope to overlay two different results onto the same fsaverage >

Re: [Freesurfer] pial surface midline fix

Hi Jason does the aseg get the hemispheres right? Is the cc properly labeled? cheers Bruce On Thu, 18 Jul 2013, Louis Nicholas Vinke wrote: > Hi Jason, > If the hemi masks look peculiar in the filled.mgz then you can try seed > points for the corpus callosum. See this page for details, go to s

Re: [Freesurfer] freeview surface vertex point save?

Hi Jason yes, there should be a similar button on the interface, or you can just copy the vertex # and paste it into the freeview interface. cheers Bruce On Thu, 18 Jul 2013, Jason Tourville wrote: Hi there,The tksurfer/tkmedit combo allowed one to select and save a point on the inflated s

[Freesurfer] Q) how to overlay two different maps in one template using different colors?

Hello Freesurfer experts, I'd hope to overlay two different results onto the same fsaverage template, but I'm not quite sure how to do it (I'm using free view). If anybody knows the trick, please give me help. thanks, ysl ___ Freesurfer mailing list Fr

Re: [Freesurfer] Terminated Recon-all jobs

you should be able to run recon-all -s -sd -make all On Thu, 18 Jul 2013, Jonathan Holt wrote: > hey all, > > I've had a few jobs that were recently terminated due to a broken ssh pipe, > is there anything i should do to before re-running those same jobs in order > to avoid any issues? > > j

Re: [Freesurfer] mri_ca_normalize using -seg flag

I think 2, but it ignores the GCA if you give it a segmentation. cheers Bruce On Thu, 18 Jul 2013, Mark Plantz wrote: Hello freesurfers,     I am currently trying to create a normalized .mgz file using the mri_ca_normalize command. Instead of using a .gca atlas, I am using a manually segmente

Re: [Freesurfer] pial surface midline fix

Hi Jason, If the hemi masks look peculiar in the filled.mgz then you can try seed points for the corpus callosum. See this page for details, go to section titled "seed points, fill and cut". https://surfer.nmr.mgh.harvard.edu/fswiki/Edits -Louis On Thu, 18 Jul 2013, Jason Tourville wrote: >

Re: [Freesurfer] Advice on using your LME software

Hi Hussain, our LME is specifically targeted at the mass-univariate setting where we have thousands of measurements on the cortical surface of the brain. From what you describe below, I think it will be sufficient to use any linear mixed model implementation (e.g. Matlab statistic toolbox, R,

Re: [Freesurfer] Motion Correction Options

Hi Panos, also I think 'motion correction' is misunderstood here. This step in the freesurfer pipeline has not been designed to correct the motion artifacts in an image. It was originally designed to allow the averaging of several within session scans to increase signal to noise ratio. This is

[Freesurfer] Advice on using your LME software

Hi, I am a Ph.D student at UC Davis in Laura Marcu's Lab. We are imaging ex-vivo human coronary arteries using two simultaneous imaging techniques (fluorescence and ultrasound). For each image we extract 58 parameters from regions of interest that have been identified with a known disease conditi

Re: [Freesurfer] Terminated Recon-all jobs

Hi Jon, Also, delete the IsRunning.lh+rh file in the scripts recon dir, or add the '-no-isrunning' flag to the recon-all command when re-running. -Louis On Thu, 18 Jul 2013, Z K wrote: > Jon, > > The way to solve this problem is to use the "nohup" command, for example: > > $nohup recon-all -s te

[Freesurfer] freeview surface vertex point save?

Hi there, The tksurfer/tkmedit combo allowed one to select and save a point on the inflated surface and then go to that point in the volume. Does freeview have a similar capability? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearin

Re: [Freesurfer] freeview surface vertex point save?

Hi Jason, Yes, although I think it's only an option in freeview from the 5.2/5.3 Freesurfer releases. -Louis On Thu, 18 Jul 2013, Jason Tourville wrote: Hi there,The tksurfer/tkmedit combo allowed one to select and save a point on the inflated surface and then go to that point in the volume.

[Freesurfer] pial surface midline fix

Hi, I've encountered a recon-all'ed scan in which the pial surface along the posterior midline "jumps" on cortex in the opposite hemisphere. Is there a simple fix for this, perhaps using a hemisphere mask? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Spee

Re: [Freesurfer] Terminated Recon-all jobs

Jon, The way to solve this problem is to use the "nohup" command, for example: $nohup recon-all -s testsubject1 -all -Zeke On 07/18/2013 12:41 PM, Jonathan Holt wrote: > hey all, > > I've had a few jobs that were recently terminated due to a broken ssh pipe, > is there anything i should do to

[Freesurfer] Terminated Recon-all jobs

hey all, I've had a few jobs that were recently terminated due to a broken ssh pipe, is there anything i should do to before re-running those same jobs in order to avoid any issues? jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] Motion Correction Options

Great, thanks Doug! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, July 18, 2013 10:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re:

[Freesurfer] mri_ca_normalize using -seg flag

Hello freesurfers, I am currently trying to create a normalized .mgz file using the mri_ca_normalize command. Instead of using a .gca atlas, I am using a manually segmented image. I have tried using the -seg flag. However, I keep getting an error that I am not inputting the correct argumen

Re: [Freesurfer] reg.dat for ICBM152 to MNI305 (fsaverage)

On 07/18/2013 10:43 AM, Adam Martersteck wrote: > Hi Freesurfer experts, > > Question related to transforming volumes/masks in ICBM-152 space to > MNI-305 space for use with fsaverage. > > 1. What is the proper registration file while utilizing mri_vol2vol? > A. The registration file > {$FREESUR

Re: [Freesurfer] Motion Correction Options

On 07/18/2013 10:13 AM, Fotiadis, Panagiotis wrote: > Hi, > > I had two questions concerning motion correction: > > 1) Besides the motion correction pipeline followed in the recon-all process, > is there any other motion correction pipeline that is available for use? We only have one pipeline, bu

[Freesurfer] reg.dat for ICBM152 to MNI305 (fsaverage)

Hi Freesurfer experts, Question related to transforming volumes/masks in ICBM-152 space to MNI-305 space for use with fsaverage. 1. What is the proper registration file while utilizing mri_vol2vol? A. The registration file {$FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.mni152.2mm.dat >>

[Freesurfer] Motion Correction Options

Hi, I had two questions concerning motion correction: 1) Besides the motion correction pipeline followed in the recon-all process, is there any other motion correction pipeline that is available for use? 2) If I have only one scan is there a way to apply motion correction on it? Because from wh

Re: [Freesurfer] WM and pial surfaces problem

Hi Laouchedi what are the intensities in the white matter in that region in the brain.mgz? If significantly below 110, try sprinkling a few control points there cheers BruceOn Thu, 18 Jul 2013, LAOUCHEDI MAKHLOUF wrote: Hi     i run recon-all on a subject and when checking the surfaces, i no

[Freesurfer] WM and pial surfaces problem

Hi     i run recon-all on a subject and when checking the surfaces, i noticed that a big part of the temporal part is badly segmented; this concerned WM as well as the grey matter. on the RecommendedReconstruction page, it is explained how to remove parts of non-pial structures considered as s