Re: [Freesurfer] Longitudinal analysis - contrast

Hi Alex I think that Martin added the flag --qdec to mris_preproc for version 5.2. Martin, could you confirm this please? The code for building the study design matrix X that is in the wiki is just an example of how lme tools can be used for that purpose but the actual instance of your code will

Re: [Freesurfer] mris_ca_train / mris_ca_label problem

sorry, I don't have the original email anymore. How did you create lh.ico3_morph.annot? On Wed, 5 Dec 2012, Roan LaPlante wrote: No, it is empty in tksurfer.  But lh.ico3_morph.annot shows up fine.  Somewhere in mris_ca_train or mris_ca_label something seems to go wrong. thanks, R On Wed,

Re: [Freesurfer] mris_ca_train / mris_ca_label problem

No, it is empty in tksurfer. But lh.ico3_morph.annot shows up fine. Somewhere in mris_ca_train or mris_ca_label something seems to go wrong. thanks, R On Wed, Dec 5, 2012 at 8:20 PM, Bruce Fischl wrote: > Hi Roan > So > > /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.an

Re: [Freesurfer] mris_ca_train / mris_ca_label problem

Hi Roan So /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot Looks ok when loaded in tksurfer? Bruce On Dec 5, 2012, at 4:34 PM, Roan LaPlante wrote: > /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot _

Re: [Freesurfer] aparc stats

Hi Don, the average thickness is not weighted by vertex area. The volume computation is relatively simple: the volume of a vertex is computed as the thickness * the average area of the triangles that are adjacent to the vertex. doug On 12/05/2012 06:35 PM, Donald Hagler wrote: > Is there a de

[Freesurfer] aparc stats

Is there a detailed description somewhere of how the gray matter volume values are calculated for the aparc stats files? Also, is the average thickness weighted by area? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] Longitudinal analysis - contrast

Can you please help with this ? Thanks in advance ! best, Alex. Le 05/12/2012 6:12 PM, Alex Hanganu a écrit : Hi Jorge, On the page presenting the "../fswiki/LinearMixedEffectsModels", I think there is a misunderstanding - You show the command: "mris_preproc --qdec " but "--qdec" is n

Re: [Freesurfer] Longitudinal analysis - contrast

Hi Jorge, On the page presenting the "../fswiki/LinearMixedEffectsModels", I think there is a misunderstanding - You show the command: "mris_preproc --qdec " but "--qdec" is not recognized, and in the help menu of "mris_preproc" I don't see this flag. So I guess you meant the "--fsgd" fl

[Freesurfer] image flip after use of mri_vol2surf/mri_surf2vol

Hello, I'm relatively new to Freesurfer so chances are that this is a pretty basic error on my side but here goes anyhow. I'm trying to use mri_vol2surf for surface-based smoothing of functional MRI data. I would then like to extract time courses from the surface with spm functions by convertin

Re: [Freesurfer] question retinotopic mapping

It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: > Hi Doug, > > I tried now several wa

[Freesurfer] mris_ca_train / mris_ca_label problem

Hello freesurfer experts, I am having difficulties using mris_ca_train and mris_ca_label. I am trying to get third party-software to accept a user-defined parcellation in the form of a .gcs file, which I created from sample data using mris_ca_train. I have reproduced the portion of the workflow

Re: [Freesurfer] recon-all -voxels numbers

Hi Sérgio no, sorry, but you can map everything back to the original space if you want. cheers Bruce On Wed, 5 Dec 2012, Sérgio Pereira wrote: Hello, I want to run recon-all on my subjects, but my images are 256x256x176 and I would like to maintain the same resolution, but in the end I ha

Re: [Freesurfer] Longitudinal analysis - contrast

Hi Alex This error is likely due to the Qdec variable being empty. So, nothing was read into this variable when you applied Qdec = fReadQdec('qdec.table.dat'); Please check that. If you don't find a solution to this then send me your Qdec table data file and I will check it out. Best -Jorge

Re: [Freesurfer] Longitudinal analysis - contrast

Yeah, wrote that wiki page yesterday after all the emails on the list. Glad it helps. Best, Martin On Wed, 2012-12-05 at 13:49 -0500, Alex Hanganu wrote: > Hello Martin, > > Thanks for pointing out about qdec, I missed that part. > > We performed this analysis on qdec. > > Thanks for explani

Re: [Freesurfer] Longitudinal analysis - contrast

Hi Jorge, thanks for such a detailed help !!! Martin explained very well the advantages of this method, so we are working on it now, and we have an Error. we loaded the lh.thickness_sm10.mgh file, read the surface and label. Then we read the qdec.table.dat. During the "sids = Qdec(:,1);" cm

Re: [Freesurfer] Longitudinal analysis - contrast

Hello Martin, Thanks for pointing out about qdec, I missed that part. We performed this analysis on qdec. Thanks for explaning the advantages of each longitudinal statistic method (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics) ! We are working now with the LME Model. Sincer

[Freesurfer] recon-all -voxels numbers

Hello, I want to run recon-all on my subjects, but my images are 256x256x176 and I would like to maintain the same resolution, but in the end I have 256x256x256. There is any way to keep the original resolution? Thank you, Sérgio Pereira ___ Freesurfer

Re: [Freesurfer] question retinotopic mapping

Don't use the -retinotopy flag. Look here http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis for more documentation on how to visualize the results doug On 12/05/2012 12:15 PM, Julia Foecker wrote: > sorry, there was a typo in the command line > > this is the correct ve

Re: [Freesurfer] Mssing Insula and mri_label2vol script

Thanks Doug, The mri_label2vol for linux32 works for the Windows virtual machine version of FreeSurfer. Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, December 05, 2012

Re: [Freesurfer] Extracting resting state time series from surface space using Lausanne 2008 parcellation

Hi Chris, thanks for the heads up on the documentation. I have updated it to read: --avgwf textfile For each segmentation, computes the average waveform across all the voxels in the segmentation (excluding voxels masked out). The results are saved in an ascii t

Re: [Freesurfer] question retinotopic mapping

Hi Julia, what is your command line when you give it the hemisphere? Also, when you run it, put "-debug" as the first argument and send me the terminal output. doug On 12/05/2012 10:55 AM, Julia Foecker wrote: > Hi Doug, > > I tried now several things to use the tksurfer command but it does n

Re: [Freesurfer] Mssing Insula and mri_label2vol script

for mac use ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.mac doug On 12/05/2012 05:11 AM, José Ángel Pineda wrote: > Hi again, > > Sure I did set the permissions for execution, an

[Freesurfer] Mindboggle-101 manually labeled brain data now available! {Disarmed} {Disarmed}

We are happy to announce the release of the Mindboggle-101 dataset, the largest and most complete set of free, publicly accessible, manually labeled human brain images in the world: http://mindboggle.info/data/ This has special relevance to the FreeSurfer community, since we made use of FreeSurfe

[Freesurfer] Error upon trying to load NIFTI image in freeview

Hi everyone, I tried opening a NIFTI (.nii.gz) image in freeview, but it gives me repeated "Failed to load " errors. That same image loads fine in FSLview, but even when trying with other NIFTI images, I get the same error. The default image (/home/virtualuser/freesurfer/subjects/bert/mri/brainm

Re: [Freesurfer] Mssing Insula and mri_label2vol script

Hi again, Sure I did set the permissions for execution, and also for this new one I am still having the same error. "*Exec format error. Binary file not executable*". I tried this on two macs (OSX Snow Leopard). I am still thinking that this is a compilation issue of the script, that is just compi