Re: [Freesurfer] -qcache in recon-all commnd

It is not. -qcache is a preprocessing step prior to doing group analysis with QDEC. If you use it, you should only do so after you have finished all the individual analysis (eg, manual edits) On 4/11/18 10:02 PM, Alexopoulos, Dimitrios wrote: Is it recommended to use the -qcache flag in the

Re: [Freesurfer] Surface label to volume and then back to surface

Hi Doug, thanks for the explanation! Also --projfrac-max -.1 1 .1 is a big improvement, I think it should be good for my purposes. Feeling good about this now! Cheers, DB ___ On 04/11/2018 12:44 PM, David Beeler wrote: > Hi Doug, thanks for the response! So

[Freesurfer] -qcache in recon-all commnd

Is it recommended to use the -qcache flag in the basic recon-all -all command? What does it do and what are the advantage of using it? Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a

Re: [Freesurfer] newbie trac-all -bedp question

It would answer the question "if I were a voxel of the forceps major, how likely would I be to be in any particular location?" From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Krieger, Donald N.

Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

Are you doing this inside or outside of FSFAST? If outside you would register your fmri to the anatomical with bbregister, then use mri_vol2surf to map it to the surface, then surf2surf to map it to fsaverage, then smooth, then mri_glmfit to test for a differnece between groups, then

Re: [Freesurfer] mri_surf2surf results in large area with zero values

can you send your command line and terminal output? On 04/11/2018 05:41 AM, Frauke Beyer wrote: > Dear experts, > > I have an issue with mri_surf2surf (i suspect). I have resampled > T1-values to the fsaverage template using mri_vol2surf and a --projfrac > of 0.25 with the default white matter

Re: [Freesurfer] Running matlab-based components of freesurfer on windows 10 linux shell

The fsfast commands require matlab or octave. I'm not sure how that will work in the linux shell in windows On 04/11/2018 03:50 PM, Savio Wong wrote: > Hi everyone, > > I have installed freesurfer on windows 10 linux shell following this link: > >

Re: [Freesurfer] Surface label to volume and then back to surface

On 04/11/2018 12:44 PM, David Beeler wrote: > Hi Doug, thanks for the response! So it looks like my initial > transform from surface label to anatomical volume wasn't working > because my template.nii.gz and brainmask were in a different space > than the functional data I was processing. This

Re: [Freesurfer] Canonical HRF shape generated by FSFAST

X.runflac(1).flac.ev(2).tirf is the time samples (eg, 0 to 30 sec) X.runflac(1).flac.ev(2).Xirf is the actual HRF If you are  using the spmhrf, you can look at the matlab function fast_spmhrf On 04/11/2018 10:56 AM, Sarah Cole wrote: > Just one clarification, this is for first level analysis

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

p.s. you probably want to grab a new freeview also, as it lets you jump to the voxel coords of each control point so you can see them On Wed, 11 Apr 2018, Hoopes, Andrew wrote: Hi Anna,   You can download the new mri_normalize from this link -

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Anna, You can download the new mri_normalize from this link - https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize To get it into your FS installation, first set executable permissions and then move it into your $FREESURFER_HOME/bin directory

[Freesurfer] Running matlab-based components of freesurfer on windows 10 linux shell

Hi everyone, I have installed freesurfer on windows 10 linux shell following this link: http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/ Recon-all and freeview run perfectly on the system. However, when I tried to run mkcontrast, I encountered the

Re: [Freesurfer] -make all error

Hello Carissa, There have been some changes to the files related to the “—make all” option. You can try downloading an updated version of the recon-all.makefile from the list of files under, ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/ and replace the

Re: [Freesurfer] newbie trac-all -bedp question

Ok - I have that sum. For the forceps major, it's 111,685. If I normalize by that, i.e. divide each voxel value by that, then I certainly get something that looks like a probability distribution since the sum of the normalized voxel entries over the entire volume is 1.0 as you had said in an

Re: [Freesurfer] newbie trac-all -bedp question

Hi Don - You would normalize these numbers by their sum, not by their maximum (i.e., not by 255). a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Krieger, Donald N. Sent: Wednesday,

Re: [Freesurfer] newbie trac-all -bedp question

Hi, Anastasia. Yes, that makes it simpler. I can see that each of the path.pd.nii.gz has a voxel entry for the same number of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I presume is the volume of this person's brain as delivered by freesurfer. Most of those

Re: [Freesurfer] Subparcellation Problem

Also, I'm using Freesurfer 5.3 On Wed, Apr 11, 2018 at 1:50 PM, Connor Garris wrote: > Hello, > > I'm running into a problem when subparcellating my regions of interest > where after subparcellating there are some sublcusters that are labelled > identically by freesurfer

[Freesurfer] Subparcellation Problem

Hello, I'm running into a problem when subparcellating my regions of interest where after subparcellating there are some sublcusters that are labelled identically by freesurfer even though they are distinct subclusters. More specifically, I ran one iteration of mris_divide_parcellation passing it

Re: [Freesurfer] newbie trac-all -bedp question

Thanks, Anastasia. I'll think about this and get back if I can't figure it out. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, April 11, 2018 12:46 PM To: Freesurfer support list

Re: [Freesurfer] newbie trac-all -bedp question

The probability maps are independent for each tract. Each one just tells you how likely this one tract is to go through any given voxel, but it tells you nothing about other tracts. Does this make sense? On Apr 11, 2018 12:00 PM, "Krieger, Donald N." wrote: Thanks for

Re: [Freesurfer] Surface label to volume and then back to surface

Hi Doug, thanks for the response! So it looks like my initial transform from surface label to anatomical volume wasn't working because my template.nii.gz and brainmask were in a different space than the functional data I was processing. This happened because I was taking the raw f.nii.gz,

Re: [Freesurfer] newbie trac-all -bedp question

Thanks for getting back, Anastasia. I'm not suggesting that it should be done differently than it is. I'm just trying to understand how the voxel values map to probability. That's why I described the wrong headed way I was thinking about it ... so you could tell me where I'm going wrong.

Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the brain. On Apr 11, 2018 11:19 AM, "Krieger, Donald N." wrote: I was thinking that for a single voxel, the total of the values assigned to the voxel over all the tracts would have a maximum of 255 and

[Freesurfer] -make all error

Hello, I am running recon-all for several subjects’ 7T data using Freesurfer version 6.0 and currently trying to ensure appropriate skull stripping and pial/wm surface generation. For a few participants that needed some control points added and for which I reran them through the –autorecon2-cp

Re: [Freesurfer] DICOM input to recon-all

Hi Karin, This tutorial will explain how to find your dicom input file: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice Best, Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Karin Westin

Re: [Freesurfer] newbie trac-all -bedp question

I was thinking that for a single voxel, the total of the values assigned to the voxel over all the tracts would have a maximum of 255 and that 255 would correspond to a probability of 1.0. I can see is likely wrong but for sure it's too simple since each voxel could contain crossing fibers from

Re: [Freesurfer] Canonical HRF shape generated by FSFAST

Just one clarification, this is for first level analysis (individual subjects). Thanks On Wed, Apr 11, 2018 at 9:54 AM, Sarah Cole wrote: > Hi Doug, > > At the end of my FSFAST analysis, I would like to plot the Canonical HRF > shape generated by FSFAST for my events. I

[Freesurfer] Canonical HRF shape generated by FSFAST

Hi Doug, At the end of my FSFAST analysis, I would like to plot the Canonical HRF shape generated by FSFAST for my events. I have found this thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031902.html but I am not sure if I understand this line:

Re: [Freesurfer] newbie trac-all -bedp question

The volume would have to be normalized to a total sum of 1 for the voxel values to represent an actual distribution. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Krieger, Donald N. Sent:

Re: [Freesurfer] newbie trac-all -bedp question

Great - thanks - that's what I need. I can use the probability for each pixel as a weight for the neuroelectric current count for that pixel to quantify the activity for the tract. I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 0.0 - 1.0 Thanks again - best -

Re: [Freesurfer] newbie trac-all -bedp question

Hi Don - No, dlabel/ contains files that are used in the pathway reconstruction, but the output of the reconstruction is saved in dpath/. There's a subdirectory in there for each pathway, and it contains a volume called path.pd.nii.gz. This is the probability that each voxel belongs to this

[Freesurfer] DICOM input to recon-all

Hi everybody! I'm very new to freesurfer and I'm trying to perform a reconstruction using recon-all. My problem is I don't see how I can access a single file to input to recon-all. I've run dcmunpack -src but the only output I get is Found 2 unique series: 4 401 Subject (name of subject) Date

Re: [Freesurfer] newbie trac-all -bedp question

Thanks for the additional information, Anastasia. I will look for those files. What I am after is a list of xyz coordinates for each of the 18 tracts. I see masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm looking for. They have names like _AS_..nii.gz where str1

[Freesurfer] mri_surf2surf results in large area with zero values

Dear experts, I have an issue with mri_surf2surf (i suspect). I have resampled T1-values to the fsaverage template using mri_vol2surf and a --projfrac of 0.25 with the default white matter surface. Then I loaded these values in Matlab using MRIread, inverted them and saved them back into a file