Re: [Freesurfer] TRACULA mask error

th all the directories created by trac-all (dmri, dlabel, etc) for one of these subjects, here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Best, a.y On Thu, 27 Nov 2014, Worker, Amanda wrote: > > Dear All, > > > I have run all of the pre-processing steps on my DTI data

Re: [Freesurfer] Meninges labelled as cortex

have a highres FLAIR or >T2 >or a multi-echo mprage we have tools for automatically avoiding it. > >cheers >Bruce > > >On Wed, 7 Jan 2015, Worker, Amanda wrote: > >> >> Hi All, >> >> >> I have noticed that almost all of my data has some voxe

Re: [Freesurfer] TRACULA mask error

cessing, i.e., do trac-all -prep -nocorr -noqa. Hope this helps, a.y PS: Yes, when you send something with filedrop that I should look at, give my email address as the recipient. On Wed, 7 Jan 2015, Worker, Amanda wrote: > Hi Anastasia, > > Thanks for your response. I have sent over a

Re: [Freesurfer] TRACULA mask error

stasia Yendiki Sent: 12 January 2015 19:58 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error Have you checked that the registration has been fixed? It looks like it might not. On Mon, 12 Jan 2015, Worker, Amanda wrote: > Yes of course. Please find atta

[Freesurfer] Viewing QDEC results in tksurfer

Hi, Is it possible to view the results of a qdec analysis (correlation with a single continuous group) in tksurfer? I am currently unable to open it and I'm getting an error saying "could not open file */mri/transforms/talairach.xfm ..no such file or directory" . Is this a file that is not cr

Re: [Freesurfer] TRACULA mask error

urfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: 12 January 2015 19:58 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Have you checked that the registration has been fixed? It looks like it > might not. > > On

Re: [Freesurfer] Viewing QDEC results in tksurfer

3/2015 07:12 AM, Worker, Amanda wrote: > > Hi, > > > Is it possible to view the results of a qdec analysis (correlation > with a single continuous group) in tksurfer? I am currently unable to > open it and I'm getting an error saying "could not open > file */mri/tra

Re: [Freesurfer] Viewing QDEC results in tksurfer

ts in tksurfer QDEC will not produce mean maps for each group. If this is something you want to do, you will need to do it in the command-line group analysis stream. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 01/15/2015 05:25 AM, Worker, Amanda wrote: > Hi, > >

Re: [Freesurfer] Viewing QDEC results in tksurfer

are for the group) Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: 16 January 2015 19:52 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer what is your command line?

Re: [Freesurfer] Viewing QDEC results in tksurfer

. cheers Bruce On Tue, 20 Jan 2015, Worker, Amanda wrote: > My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" > d- which is when I got the error. > > I have now tried loading fsaverage first with "tksurfer fsaverage lh > inflated" and

Re: [Freesurfer] bbregister error [Was: TRACULA mask error]

e and the trac-all command lines that you ran after running bbregister? Thanks, a.y On Wed, 11 Feb 2015, Worker, Amanda wrote: > Hi, > > Thanks for this. --init-spm does appear to work and when checking the > registration using the instructions bbregister gives it all looks good to me

Re: [Freesurfer] bbregister error [Was: TRACULA mask error]

nitialized, and then rerunning the -prior and -path steps in that order. Hope this helps, a.y On Thu, 12 Feb 2015, Worker, Amanda wrote: > Hi Anastasia, > > Apologies this looks like an error on my part. I had edited the script to > specify --init-spm instead of --init-fsl but forgot to

[Freesurfer] Overlaying .nii

Hi, I am trying to find a way to overlay a .nii file for a single blob of activation - simply to visualise the region of the blob with the cortical surface. Is there a way to do this in either freeview or tksurfer? The blob is in nifti format and the surface is in the usual .mgh format. T

[Freesurfer] extracting subcortical volumes from longitudinal processed data

Hi all, I am trying to extract subcortical volumes from data that has been processed longitudinally, but I am getting the following error. [k1204763@nanlnx9 SAGA]0% asegstats2table --qdec-long long.qdec.table.dat --stats aseg.stats --tablefile aseg.table.txt SUBJECTS_DIR : /home/k1204763/imag

Re: [Freesurfer] qdec error

Hi Lena, Have you changed your Group.levels file to include the two groups you are currently looking at? If this doesn't match your qdec table it will not work. Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lim, Lena

[Freesurfer] Group Analysis with fsgd

Dear all, I am trying to run a group analysis through the terminal using an .fsgd file, with no additional covariates. GroupDescriptorFile 1 Title PDPLUS2 Class PD Class MSA Class PSP Input PDPLUS007/ PD Input PDPLUS005/ MSA Input PDPLUS004/ PSP etc... When I try to run a command similar to the

[Freesurfer] DESPOT T1 map

Hi All, I have a T1 map which has been synthesised from a DESPOT imaging sequence and I am hoping to use this as input to recon-all. Do you know if this will be possible at all, or if there is anything I can do to prepare the T1 map to run through recon-all? Thanks in advance, Amanda _

[Freesurfer] Viewing nifti file in freeview

Hi All, I was hoping someone could help with an issue that I'm having that I'm sure has a simple explanation. I have a proton density map in nifti format that I am trying to convert to mgz using mri_convert. However, when I load the original nifti file into freeview, I get a blank screen an

Re: [Freesurfer] Viewing nifti file in freeview

4 February 2016 12:17 To: Freesurfer support list Subject: Re: [Freesurfer] Viewing nifti file in freeview Amanda, Is there a progress bar still running? Have you tried changing the window min max fields? hth d Sent from my Phone On Feb 4, 2016, at 06:46, Worker, Amanda mailto:amanda.wor...

[Freesurfer] mri_annotation2label

Hi All, I am trying to run a vertex-wise analysis on a pre-defined ROI - the caudal anterior cingulate label as defined by the Desikan atlas. I have used mri_annotation2label to get these labels for each subjects ./label directory. I assumed that as these labels were created in fsaverage space

[Freesurfer] Group thickness means

Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by QDE

[Freesurfer] Group thickness means

Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by QDE

[Freesurfer] deformation fields

Hi All, I am trying to use the subcortical segmentation of regions from the longitudinal template to propogate to each time point using deformation fields. Does anyone know how if this is possible and if so, how can I do it? Thanks in advance, Amanda ___

[Freesurfer] Longitudinal hippocampal subfield registered to base

Hi All, I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been longitudinally processed. I am now trying to register these back into base space using: mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt nearest --out_ty

Re: [Freesurfer] Longitudinal hippocampal subfield registered to base

behalf of Worker, Amanda Sent: Wednesday, March 1, 2017 12:14:50 PM To: Freesurfer support list Subject: [Freesurfer] Longitudinal hippocampal subfield registered to base Hi All, I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been long

[Freesurfer] Cortical thickness repeated measures

Hi all, I have a repeated measures design with two groups (drug and placebo) and two time points (baseline and follow-up). The groups are not very well matched so I'd like to control for age and gender. The data was also acquired across three sites which I'll need to control for. I do not have

[Freesurfer] Univariate Linear Mixed Effects

Hi there, I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could yo

Re: [Freesurfer] Univariate Linear Mixed Effects {Disarmed}

CIs and MCIc and finally slope difference between MCIc and AD. Your test 0 0 0 1 similarly tests slope difference between your two groups. And yes, the remaining columns would be control variables . Best, Martin On 31. Jul 2017, at 13:38, Worker, Amanda mailto:amanda.wor...@kcl.ac.uk>&g

[Freesurfer] Test-retest reliability in longitudinal data

Hi all, I have a longitudinal dataset that I'd like to calculate test-retest reliability for. However, I am not sure whether to calculate this for the cross-sectionally processed data or longitudinal data? It would seem to make sense to use the cross-sectional data, as the time points are inde

Re: [Freesurfer] Test-retest reliability in longitudinal data

d segmentation which could potentially give a false impression of poor reliability and increased risk of false positive results. " Any thoughts appreciated. Thanks, Amanda From: Jovicich, Jorge Sent: 20 September 2017 15:51:40 To: Worker, Amanda Cc: Freesu

[Freesurfer] TRACULA bedpost error

Hello, I am trying to run the second step of the TRACULA processing which is: trac-all -bedp -c /home/... I am currently using freesurfer v5.3.0 and I get the following error: WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bed

[Freesurfer] QDEC cluster stats

Hi All, I am using QDEC to run a correlation analysis and I have a lot of large significant clusters that encompass various different cortical regions. I am hoping to extract mean thickness' from the significant clusters in order to create a plot to display the correlations. Can anyone tell me

[Freesurfer] Visualise QDEC results

Hi, I have run a correlation in QDEC and I have quite a lot of results, some of which pass monte simulation correction at p=0.05 and some of which remain at p=0.0001. Ideally, I'd like a single figure that will display all significant results regardless of their p-value. However, I would need

[Freesurfer] Using a .asc file as overlay in freeview/tksurfer

External Email - Use Caution Hello, I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck. As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command: % mris_

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

urfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Not sure. Can you use mris_convert to convert the asc back to a curv file? On 10/15/2018 11:20 AM, Worker, Amanda wrote: > > External Email - Use Caution > > Hello, > > > I am try

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

lh.thickness.asc lh.white lh.thickness.mgz should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote: > > External Email - Use Caution > > How would I do that? mris_convert doesn't seem to take

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

s Bruce On Tue, 16 Oct 2018, Worker, Amanda wrote: > > External Email - Use Caution > > Thank you! > > > So the answer to the first question is that yes I can convert it back to a > curvature file and that curvature file can be loaded as an overlay. So this &g

[Freesurfer] Multivariable linear regression with binary variables

External Email - Use Caution Hi, I am trying to run a multivariable GLM with mri_glmfit and I am currently setting up my fsgd file. I have 9 binary variables and 1 continuous variable. My understanding is that in the fsgd file, my "class" would be every possible combination of

Re: [Freesurfer] Multivariable linear regression with binary variables

nt to model all those variables since modeling all possible interactions is not going to be possible. On 11/08/2018 12:45 PM, Worker, Amanda wrote: > > External Email - Use Caution > > Hi, > > > I am trying to run a multivariable GLM with mri_glmfit and I am > current

[Freesurfer] statistical map in matlab

External Email - Use Caution Hi, I am working with cortical thickness data in matlab and I have a t-statistic map that I'd like to firstly write to .mgh/mgz format so that I can overlay it in freeview. And secondly, convert it to MNI space and write it out as a volume (preferab

[Freesurfer] Customising overlay

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to create some figures which display regional (Destrieux atlas) values which are typically in the range of 0-10. I would like to have an inflated brain with those regional values overlaid, for both patients

Re: [Freesurfer] Customising overlay

and had no problem inserting colors at arbitrary value for customized color option. Best, Ruopeng On Sep 23, 2021, at 9:00 AM, Worker, Amanda mailto:amanda.wor...@kcl.ac.uk>> wrote: External Email - Use Caution External Email - Use Caution Dear FreeSurfer Developers, I