Re: [Freesurfer] axial or sagittal?

I¹d add that SNR may also change if you don¹t acquire as much data axially as you did sagittally. Really it¹s better to acquire your 3D T1w/T2w/FLAIR scans sagittally as this is most efficient. Peace, Matt. On 4/8/16, 10:23 AM, "Bruce Fischl"

Re: [Freesurfer] mri_vol2surf after recon-all

not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz You can always just run the following command directly fslregister --mov icbm.nii.gz --s $subject --reg $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12 --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta This will use

Re: [Freesurfer] mri_vol2surf after recon-all

thanks, Doug. I'll get started on running all brains using recon-all. The MNI has several ICBM templates now: ICBM152 linear ICBM152 nonlinear symmetric VI ICBM152 nonlinear 2009 Do you know which one mni152reg is using? Trisanna -- Ph.D. Candidate McGill University Integrated Program in

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

And now you want to do an ROI analysis or a map-based analysis of the subcortical structures? We don't do the latter as that is a VBM analysis. On 04/08/2016 01:07 PM, Jennifer Legault wrote: > Apologies for likely using the wrong term. I meant to say that I've > done the cluster-thresholding

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

Apologies for likely using the wrong term. I meant to say that I've done the cluster-thresholding for the surface data, using the mri_surfcluster command with annot -aparc as an argument. On Fri, Apr 8, 2016 at 1:03 PM, Douglas N Greve wrote: > This is what I don't

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

This is what I don't understand: "done the cluster-thresholding for the aparc data" The aparc data is an ROI and so you should not have (could not have) done clusterwise thresholding (?) On 04/08/2016 12:57 PM, Jennifer Legault wrote: > Hi Doug, > > I'm currently running the LME

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

Hi Doug, I'm currently running the LME mass-univariate analysis (I've previously conducted the LME univariate analyses with ROIs with little to no problems) and, thanks to your help, have run my data through this analysis and done the cluster-thresholding for the aparc data but not the aseg data

Re: [Freesurfer] Left right flip surfaces

Look at http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi if you want to compare all subjects, then you'll need to do this for all subjects not just the ones you want to flip On 03/28/2016 02:30 PM, Ajay Kurani wrote: > Hello Freesurfer Experts, > >I processed all of my brains through

Re: [Freesurfer] mri_vol2surf after recon-all

On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote: > thanks, Doug. I am still extremely confused, however. *Am I meant to > run recon-all first? *I was told in a previous email that I should do > this first, however, I thought that Freesurfer takes the volumes and > does a linear

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

On 04/01/2016 04:44 PM, Jennifer Legault wrote: > Hi Doug, > > Thanks for your quick response! When running the LME mass univariate > analysis, I am assuming this also includes subcortical structures, > correct? Which processing are you doing? It should be obvious if you are doing

Re: [Freesurfer] mri_vol2surf misaligment

can you show a pic? What were your matlab commands to read in and write out the volume? On 04/04/2016 07:36 AM, Francesca Strappini wrote: > Dear Freesurfers, > > I run the preprocessing step of some functional data with > preproc-sess, then the Fourier analysis with matlab. Now, I'm trying >

Re: [Freesurfer] Regarding: Group analysis of WMHs

You can binarize each WMH volume, ie, mri_binarize --i aseg.mgz --match 77 --o wmh.mgz Convert to mni305 space with mri_convert wmh.mgz wmh.mni305.mgz --apply_transform transforms/talairach.xfm -oc 0 0 0 View to check (only need to do for one subject): tkmedit fsaverage orig.mgz -ov

Re: [Freesurfer] Regarding: Group analysis of WMHs

ps, you may want to smooth the wmh volumes, eg, mri_fwhm --smooth-only --i all.wmh.mgh --fwhm 5 --o all.wmh.sm05.mgh then use all.wmh.sm05.mgh as input to glmfit On 04/08/2016 12:27 PM, Douglas N Greve wrote: > You can binarize each WMH volume, ie, > mri_binarize --i aseg.mgz --match 77 --o

Re: [Freesurfer] Qdec DOSS

Yes, if the contrast matrix is correct, then everything should be fine. Also check the design matrix (but I'm pretty sure that will be correct). On 04/05/2016 04:07 AM, tom parker wrote: > Hi Freesurfers, > > I posted this question a few days ago but didn't get any replies. > Would you mind

Re: [Freesurfer] Group level analysis: Specifying contrasts

I don't know what you mean, can you just send the header of the fsgd file and the contrast matrix? On 04/04/2016 11:20 AM, Afzal, Afsana wrote: > Hi, > > I want to perform a linear regression for a task with 3 different risk > conditions (low, medium, high) with the following linear trend: low

Re: [Freesurfer] Preprocessing task data with multiple B0-corrected runs

Unfortunately, I only programmed it assuming that you would have only one B0 map per session. There are a couple of work-arounds. One is to create a different session for each run. This is probably easiest but makes the group analysis a little trickier. On 04/05/2016 04:48 PM, Shea, Conor

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Thank you.I confirm, Annotation works fine. However when trying to load label and select .label file.I get the following message: reading colortable from annotation file... colortable with 76 entries read (originally

Re: [Freesurfer] R-Map

Use this version of mri_glmfit. For t-tests is will automatically compute a partial correlation coefficient (pcc.mgh) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit On 04/04/2016 12:12 PM, Morenikeji Adebayo wrote: > Hello Freesurfers, > > I'm interested in creating a

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Hi Pablo if it has the extension .label then it is a label not an annotation, and you should load it as such cheers Bruce On Fri, 8 Apr 2016, pablo najt wrote: Thank you Bruce for the response.Actually the surface works in freeview just fine. However my second issue about  loading

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Thank you Bruce for the response.Actually the surface works in freeview just fine. However my second issue about loading annotation continues.In freeview I clicked on "Annotations" selected inside "label" folder BA1 and everything Freezes.Terminal shows endless column of the text below. Could

Re: [Freesurfer] axial or sagittal?

Hi Gamaliel many things will change when you change the slice direction - amount of wrap, possibly your FOV, slab-selection profile if your protocol is slab-selective, and some types of distortion. These will all change the image which will change our results. Of course even if you don't

Re: [Freesurfer] axial or sagittal?

2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea : > Hello Freesurfers > > I'm trying to do volumetric reconstruction, i already have done this but. > i wanted to see if for the same subject, with different directions of > slices i have the same result, and obviously i had

[Freesurfer] Monte Carlo correction in QDEC

Dear FreeSurfer experts, for the analysis in QDEC I created my own Monte Carlo correction. My questions relate to the threshold option. 1. Would I use neg if I have mostly blue clusters in the QDEC display and pos if I have mostly red clusters? 2. When do I use abs? 3. I compared the neg

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Can you check and see if they look ok with freeview? It might just be a display problem > On Apr 8, 2016, at 9:26 AM, pablo najt wrote: > > Dear FS expert and users, > We are coming across errors on the WM and Gray inflated surfaces. > When trying to open the surfaces

Re: [Freesurfer] Regarding: oblique view

sure. I wish I had a better answer for you On Fri, 8 Apr 2016, Dr Sampada Sinha wrote: Thanks Bruce. Appreciate all your help. Kind regards, Sampada On Friday, April 8, 2016, Bruce Fischl wrote: Hi Sampada I don't think it is possible to get

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try

Re: [Freesurfer] Regarding: oblique view

Thanks Bruce. Appreciate all your help. Kind regards, Sampada On Friday, April 8, 2016, Bruce Fischl wrote: > Hi Sampada > > I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm > slice data. You might get ok asegs. > > sorry > Bruce > > On

Re: [Freesurfer] REPOST: QDEC analysis

That's what I feared. But ok, I'll try that. Thank you! - Ursprüngliche Mail - Von: "mreuter" An: "Freesurfer support list" Gesendet: Freitag, 8. April 2016 14:55:42 Betreff: Re: [Freesurfer] REPOST: QDEC analysis Hi Clara,

Re: [Freesurfer] REPOST: QDEC analysis

Hi Clara, I think the message is correct and Qdec can only do 2 levels. Qdec is rather limited. You need to use mri_glmfit for that. Best, Martin On 04/08/2016 08:14 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I am trying to analyze some single time points of my longitudinal data in

[Freesurfer] Freesurfer install on Debian 7.x

hi zeke, i’m following your instructions for getting freesurfer 5.3.0 installed on debian, though i’m at 7.x as that is what came from ThinkMate on some recently delivered supermicro machines for our lab. i’m not successful, and have paused at an error. 1) libtool-bin does not exist for

Re: [Freesurfer] Regarding: oblique view

Hi Sampada I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm slice data. You might get ok asegs. sorry Bruce On Fri, 8 Apr 2016, Dr Sampada Sinha wrote: Hello Bruce, Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my

Re: [Freesurfer] Regarding: oblique view

Hello Bruce, Thanks for your reply. Brief history of my problem so far is that: as you noticed before, my images have very low resolution and very less contrast. My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; dimension 512x512x20. I do run mri_convert to conform it to

[Freesurfer] REPOST: QDEC analysis

Dear FreeSurfer experts, I am trying to analyze some single time points of my longitudinal data in QDEC. I have 3 groups and created a file for the discrete factor "group" with three levels (1,2 and 3). I have done the same for gender (with 2 levels). The analysis with gender works just fine

[Freesurfer] Regarding: Group analysis of WMHs

Dear freeesurfer experts, I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR separately after processing T1 with recon-all. Presently, I don't have any dwi data where I can project the WMHs onto the WM tracts. Will you please tell me how do I project the WMHs of 29 MDD