[Freesurfer] tksurfer problems

Hello I'm having problems with tksurfer. It crashes whenever I load overlays using File -> Load Overlays. Am not too sure why. Could someone help? I'm using freesurfer 5.1.0 and fsl 5.0.6 on Mac OSX version 10.7.5 Here's what i did bash-3.2$ tksurfer AMP01 rh inflated subject is AMP01 hemi

[Freesurfer] (no subject)

Dear freesurfers, This is the first time I am posting so hope the following makes sense, I don't use freesurfer but manage the installation of freesurfer on our cluster. We have a user who is trying run a script that submits a recon-all job to our cluster using the -localGI flag: recon-all -su

[Freesurfer] bug in surface-based area and volume, and use of total brain volume as a covariate

>> why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? >The vertex-based measures are computed in individual space, not standard >space >doug Dear Doug, I would like to know at what stage the measures compu

Re: [Freesurfer] tksurfer problems

what overlay are you trying to load? On Wed, 19 Mar 2014, Joo Tan wrote: Hello I'm having problems with tksurfer. It crashes whenever I load overlays using File -> Load Overlays. Am not too sure why. Could someone help? I'm using freesurfer 5.1.0 and fsl 5.0.6 on Mac OSX version 10.7.5 Here's

[Freesurfer] Problem about Surface-based Registration

Dear Burce, I have 20 normal subjects, and I want to do inter-subject surface-based registration to all of them. So each one's surface can align properly to the other subject's surface. After that I can put the functional data onto the surface which has aligned to each other already. And now I

[Freesurfer] Fwd: FW: bug in surface-based area and volume, and use of total brain volume as a covariate

Hi all, just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures? Thanks, Andreia Quoting Douglas N Greve : >>> why would one control for total brain volume in doing vertex-based > analyses when the vertex-b

Re: [Freesurfer] what is inflating to sphere rms error?

those are all fine - they are just measures of various energy functionals. cheers Bruce On Wed, 19 Mar 2014, chenchunhuichina wrote: Dear Freesurfers,   I am new to freesurfer and I am afraid of doing something wrong, so I am writing to ask is this error indicating something wrong with my data

Re: [Freesurfer] Problem about Surface-based Registration

Hi Yufeng if all you want to do is map all the individual activation maps into a common surface-based coordinate system,then there is no need to create your own atlas and rerun the registration - just use the ?h.sphere.reg files. If there is some other reason you want to create your own tem

Re: [Freesurfer] Segmentation fault:11 with mris_anatomical_stats {Disarmed}

It looks like this label was created on fsaverage. Is that the case? If so, then you need to run mri_label2label to map it into the space of an individual, then run mris_anatomical_stats doug On 03/18/2014 12:59 PM, Rupa Sabbineni wrote: > Hi Doug > Attached is a label file. > The FS version i

Re: [Freesurfer] bug in surface-based area and volume, and use of total brain volume as a covariate

The normalization is the mapping of values from the individual subject to a standard space so as to align different structures. This does not happen until you run mris_preproc or recon-all -qcache. When you normalized a thickness map, the thickness values themselves are not changed in any way,

Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate

Sorry, the thread of the email that explains the problem and the fix are not included below. Can you re-explain? We get a lot of emails here and it is not possible to remember the context of each one. doug On 03/18/2014 11:32 AM, _andre...@sapo.pt wrote: > Hi all, > > just two quick questi

Re: [Freesurfer] (no subject)

Hi, I have not idea what is going wrong. I would try goggling that error msg to see what it means and how it might be fixed doug On 03/19/2014 06:32 AM, Charnjit Sidhu wrote: > Dear freesurfers, > > This is the first time I am posting so hope the following makes sense, I > don't use freesurfe

[Freesurfer] Fwd: Problem about Surface-based Registration

Hi Bruce, I want to do is map all the individual activation maps into a common surface-based coordinate system. So I do not need to follow the process of creating a registration template from scratch(GW)( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to do the surface-based regi

Re: [Freesurfer] selxavg3-sess error]

Original Message Subject: Re: selxavg3-sess error From:sha...@nmr.mgh.harvard.edu Date:Wed, March 19, 2014 11:15 am To: "Douglas N Greve" -- But this is a

Re: [Freesurfer] selxavg3-sess error

There is not an mcextreg file there. There is mcprextreg file. I think you need to run preproc with -per-session to get the mcextreg file doug On 03/18/2014 02:34 PM, SHAHIN NASR wrote: > Hi, >When I run selxavg3-sess, I face this error: > > ERROR: cannot find volume matching > /autofs/clus

Re: [Freesurfer] selxavg3-sess error

-nuisreg On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote: > Does not accept "-nuis" flag. I changed my mkanalysis-sess to this: > > mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 -paradigm > Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis > mcprextre

Re: [Freesurfer] Problem about Surface-based Registration

Hi Yufeng can you remember to cc the list? And yes, if all you want is a common surface-based coordinate system for your subjects then there is no need for you to run mris_register yourself - it is done by recon-all. All you need to do is run mri_vol2surf for each individual, then map the resu

Re: [Freesurfer] selxavg3-sess error

Does not accept "-nuis" flag. I changed my mkanalysis-sess to this: mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 -paradigm Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -nuis mcprextreg -TR 4 -nconditions 8 -refeventdur 14 -force -fsd bold_Color -per-run and g

Re: [Freesurfer] Recon process

On 03/18/2014 05:05 PM, Lin, Amy (NIH/NIMH) [F] wrote: > Hello all, > > I think this is a fairly simple question, but I could not find an existing > answer online. If I close out the terminal window while recon is running, > will the process end? I've had the issue in the past where my computer

Re: [Freesurfer] selxavg3-sess error

use -nuisreg mcprextreg 3 On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote: > I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error: > > Error: -nuisreg requires two arguments" > > > >> -nuisreg >> >> On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote: >>> Does not accept "

Re: [Freesurfer] Problem about Surface-based Registration

yes, fsaverage On Wed, 19 Mar 2014, yufeng huang wrote: I want to do is map all the individual activation maps into a common surface-based coordinate system. So I do not need to follow the process of creating a registration template fromscratch(GW)(https://surfer.nmr.mgh.harvard.edu/fswiki/Surf

Re: [Freesurfer] selxavg3-sess error

YES! Started to work. Thanks Doug! > use > -nuisreg mcprextreg 3 > > On 03/19/2014 11:34 AM, sha...@nmr.mgh.harvard.edu wrote: >> I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error: >> >> Error: -nuisreg requires two arguments" >> >> >> >>> -nuisreg >>> >>> On 03/19/2014 11:24 AM, sh

Re: [Freesurfer] selxavg3-sess error

I think it is just confused because it expects native to be per-session. One way around this is to just specify -nuis mcprextreg instead of -mcprextreg doug On 03/19/2014 11:15 AM, sha...@nmr.mgh.harvard.edu wrote: > But this is a per-run analysis and preproc-sess is -per-run (in native > spac

Re: [Freesurfer] Problem about Surface-based Registration

it maps your functional data from the volume onto the surface model for each individual subject (using the registration between the surface and the functional data, usually computed with bbregister) On Wed, 19 Mar 2014, yufeng huang wrote: Dear Bruce, My last question:  As I use the  common

Re: [Freesurfer] adding time points to longitudinal base template {Disarmed}

Hi Koushik, What version are you using? Not sure when we added this, maybe in 5.2. So you would need 5.3 for it. If you use 5.3 already, can you send me the exact command and output. Thanks, Martin On 03/19/2014 11:50 AM, Govindarajan, Koushik Athreya wrote: Hi Martin, I tried this

Re: [Freesurfer] Problem about Surface-based Registration

Dear Bruce, My last question: As I use the common surface-based coordinate system, what the purpose of using mri_vol2surf for each individual at this time? Did it register the functional data to the anatomical? Thanks you very much for your attention!

Re: [Freesurfer] adding time points to longitudinal base template {Disarmed}

Hi Martin, I tried this method of -addtp to add a new time point but recon-all failed with the message saying my new timepoint was not in the 'base-tps' file of the base template. Should I be doing something else before I run this step? Thanks Koushik From: Martin Reuter [mailto:mreu...

Re: [Freesurfer] adding time points to longitudinal base template {Disarmed} {Disarmed}

Hi Martin, I use version 5.1. I did try this with version 5.3 also but I end up with the same error: recon-all -long 23061_ip cr096_base -addtp -all ERROR: 23061_ip is not in /home/koushikg/data/longitudinal/cr096_base/base-tps Thanks Koushik From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] selxavg3-sess error

I used "-nuisreg mcprextreg" in mkanalysis-sess. Got this error: Error: -nuisreg requires two arguments" > -nuisreg > > On 03/19/2014 11:24 AM, sha...@nmr.mgh.harvard.edu wrote: >> Does not accept "-nuis" flag. I changed my mkanalysis-sess to this: >> >> mkanalysis-sess -analysis ColorPrj_TR4_1

Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate

My apologies Doug... I thought that this email had all the history... Narly, sorry for "invading" your discussion... My questions came from the first email of Narly which referred to the bug in mris_preproc: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html This bug

Re: [Freesurfer] reconstruction problem with pediatric images

Hi Francesco, How old are your subjects? Lilla On Wed, 19 Mar 2014, Francesco Baldacchini wrote: I have some quality problems with my scans. I'm trying to run recon-all on pediatric brain images but, given the low contrast between cortical regions and the white matter, I do consistently ge

Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate

Have you checked the release notes? http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 03/19/2014 01:57 PM, _andre...@sapo.pt wrote: > My apologies Doug... I thought that this email had all the history... > > Narly, sorry for "invading" your discussion... > > My questions came from the fi

[Freesurfer] reconstruction problem with pediatric images

I have some quality problems with my scans. I'm trying to run recon-all on pediatric brain images but, given the low contrast between cortical regions and the white matter, I do consistently get some problem in the reconstruction of the cortical surface as well as of the segmentation. I was wonderi

Re: [Freesurfer] selxavg3-sess error

yes, or you can just register-sess -per-session ... that should create just the register.dof6.dat you need doug On 03/19/2014 03:10 PM, SHAHIN NASR wrote: > Hopefully this is the last problem with per-run analysis (in native > space) but as far as I see, preproc-sess and selxavg3-sess do not

Re: [Freesurfer] selxavg3-sess error

Hopefully this is the last problem with per-run analysis (in native space) but as far as I see, preproc-sess and selxavg3-sess do not generate /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat Because of that, when I use tksurfer-sess it faces an error:

[Freesurfer] Calculating Total White Matter

Hello, I need assistance calculating Total White Matter. Can I simply add Cortical White Matter + Unsegmented White Matter (given in the aseg wmparc output)? Thanks Elizabeth Adeyemi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

[Freesurfer] Display only desired brain sites in Qdec

Hi Free-Surfer experts, I ran the cortical thickness analysis between two groups (patients and control) using Qdec and find out few brain sites with significant difference. Is it possible to display only desired brain site in Qdec (I would like to display only one brain site in one image example:

Re: [Freesurfer] Display only desired brain sites in Qdec

Do you mean just insula in one image or just the cluster that is in insula? Neither can you do in QDEC. If the latter, then you can do it easily enough by going into the output folder for the contrast, finding the annotation file, creating labels from the annotation ( mri_annotation2label), th

Re: [Freesurfer] Calculating Total White Matter

If you want total cerebral WM, then use the values in aseg.stats # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 182991.109375, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume,

[Freesurfer] Viewing corrected results

Hello Freesurfers, We are doing functional connectivity analyses (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough). We are on the group analysis step of step 8. On our data set, we ran the following glmfit command: mri_glmfit --y ./mgh/v.amy.mgh --fsgd ./FSGD/st

Re: [Freesurfer] tkmedit contrast

Was there any solution for this? Thanks, Mia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Friday, March 14, 2014 1:17 PM To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject:

Re: [Freesurfer] tkmedit contrast

does it work in freeview? On Wed, 19 Mar 2014, Borzello, Mia wrote: > Was there any solution for this? > > Thanks, > Mia > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia > Sent: Friday,

Re: [Freesurfer] Viewing corrected results

When you say they don't match, what do you mean? You have set the cwpvalthresh to .99, so when you run tkmedit, you should set the -fminmax to something like .01 3 otherwise you will not see all the clusters you see in the summary table doug On 3/19/14 6:28 PM, Omar Singleton wrote: > Hello

Re: [Freesurfer] Viewing corrected results

I mean that when we look at the .summary file there are 4 clusters, only one being significant, but when we look at the mc-z.absolute.sig.cluster.mgh file there are additional clusters. The same is true for the mc-z.absolute.sig.ocn.mgh file. Shouldn't these only show the corrected clusters at the

Re: [Freesurfer] Viewing corrected results

The ocn will have all clusters found in the summary file. Are you seeing more than that? What you see in the sig.cluster file depends on what threshold you set when you run tkmedit. Below, you have 1.3 = p < .05, so it should only shows clusters in the summary file that have p < .05 doug On

[Freesurfer] what is inflating to sphere rms error?

Dear Freesurfers, I am new to freesurfer and I am afraid of doing something wrong, so I am writing to ask is this error indicating something wrong with my data? Any help is appreciated. below are detials of my question. Thank you! I used freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 with th

[Freesurfer] expert options command

I've been calling up an expert options file which contains the text "mri_normalize -gentle" but I'm having trouble executing it with this command: "recon-all -s 002 -expert 002/scripts/expert.opts" It results in the following err