[Freesurfer] Help -- asegstats2table error, Please Help

Hello, I am trying to make a table of cortical volumes, however when I run the command: asegstats2table -subjects Sub1 Sub2 Sub3 --segno 17 53 --tablefile=aseg.vol.table I receive the following error message: ERROR: The stats file Sub1/stats/aseg.stats is not found or is too small to be a valid

Re: [Freesurfer] extracting hand drawn ROIs to Afni space

Not sure if you've done this, but if you run AFNI's @SUMA_Make_Spec_FS command it will convert all .mgz files to .nii. These can then be loaded as an overlay in AFNI. If you open the @SUMA_Make_Spec_FS command in a text editor, there is a line (387 in my editor) to edit which files to convert,

Re: [Freesurfer] extracting hand drawn ROIs to Afni space

You can load the segmentation as both a segmentation and an input volume in tkmedit, eg tkmedit subject orig.mgz -aux gmroi_volume.nii.gz -seg gmroi_volume.nii.gz You can then see the number of each of your segmentations in the Aux field when you click on your segmentation. There's probably an

Re: [Freesurfer] LGI Path Question

Hi Adam, The place to define matlab is not set in freesurfer, but directly in your environment variables. You have to add the path to your matlab installation directory to the variable $PATH. However, what I am not able to figure out, is why it doesn't work with Matlab 2010. I tested it with

Re: [Freesurfer] Qdec

Hi Chikku, the -qcache command is for cross sectional processing. It is not done in the base and does not need to be done there. The base is like an additional time point so it does run from the start and even contains some extra steps. 12hrs are not unlikely. You will need to also run the rec

[Freesurfer] Question on stats analysis in Qdec

Hello, I am running qdec group analysis on my patient data. I am studying the differences between two Epilepsy onset types and have a few questions. 1) I select "subtype" as my discrete variable and "duration" as my continuous variable. In the display tab two questions appear. 1. Does the avera

Re: [Freesurfer] surface based analyses using PET

Hi Leorah, all those commands are correct. doug On 02/27/2013 02:03 PM, Léorah Freeman wrote: > > Dear FreeSurfers, > > I would like to perform surface based analyses using PET but I am not > sure I am doing things correctly. For each subject, I have > reconstructed the 3DT1 MRI using recon-all

[Freesurfer] surface based analyses using PET

Dear FreeSurfers, I would like to perform surface based analyses using PET but I am not sure I am doing things correctly. For each subject, I have reconstructed the 3DT1 MRI using recon-all –all. Then I have coregistered the PETs with the anatomical using: Bbregister --s name --mov pet.nii

[Freesurfer] LGI Path Question

Hello, I'm trying to run LGI. We have the 2012 version of matlab and the image processing toolbox. I've looked at several threads dealing with path issues, but have been unable to fix my problem. I think our problem is that when I run "recon-all -s ucr001_4-11 -localGI" it seems to start up pro

[Freesurfer] Postdoctoral Position Boston Children's Hospital/Harvard Medical School

The Gaab Lab http://www.childrenshospital.org/research/gaablab and (www.babymri.org)) at the Laboratories of Cognitive Neuroscience at Children's Hospital Boston (Developmental Medicine Center) invites applications for a NIH funded post-doctoral associate in the area of

Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned

Hi Ed, permuting the matrix will not help. The problem is that some weighted combination of columns is equal to some other column. It means thatsome of your covariates are highly correlated. Sometimesthis is obvious (eg, two columns are the same), other times it is very subtle. You will need t

Re: [Freesurfer] FreeSurfer recon-all two sets of error

1. It is not contrast enhanced. 2. I am rerunning recon-all after giving it a manually skull stripped image. Hopefully this will work. So basically did this: recon-all -subjid . -autorecon1 -noskullstrip -notal-check cp T1.mgz brainmask.auto.mgz ln -s brainmask.auto.mgz brainmask.mgz recon-all -

Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned

Hi Doug, Can I do this by just permuting the contrast matrix and the corresponding columns in the fsgd file? Ed On 26 Feb 2013, at 17:43, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Hi Ed, I think it is just the way you have the matrix set up. You'll need to alter the matrix in some w

[Freesurfer] Qdec

Dear all, I am bit confused with the Qdec process. I finished recon all for 2 time points and want to create longitudinal data.From FS tutorial I learned to create within-subject templates for processing,which is running now with recon-all -base -tp -tp ... -all. Now,in an other link

Re: [Freesurfer] Export wmparc to table

Use asegstats2table with --states=wmparc.stats doug On 02/26/2013 08:05 PM, Mohammed Goryawala wrote: > Hello FreeSurfer experts, > > I want to export the white matter volumes from the wmparc stats file > to a table. I cannot find the information on the wiki page. > > Thanks for your help. > >

Re: [Freesurfer] default lateral extent corpus callosum

yes, exactly Bruce On Wed, 27 Feb 2013, Gonzalo Rojas Costa wrote: Hi: What is the default thickness of the corpus callosum?... 5 mm ?... 2 mm for each side from midline ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínic

Re: [Freesurfer] aseg.mgz display only left hemisphere

sure, you can do it easily enough in matlab: [v,M,mr] = load_mgh('aseg.mgz') ; gm = find(v == 3 | v == 42 | (v >9 & v <=13) | v == 17 | v==18 | (v >48 & v <= 54) | v == 47 | v== 8|v==26|v==58|v==80|v==30|v==62); wm = find(v == 2 | v == 41 | v == 7 | v == 46 | v == 16 | v == 60 | v== 77|v==85

Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

Hi Nicola the T2 might in 5.2, but it is pretty thick slices so might hurt more than it helps. Not sure, but you can try it out cheers Bruce On Wed, 27 Feb 2013, Nicola Toschi wrote: > Hello List, > > on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually > acquire T2 and PD imag

[Freesurfer] default lateral extent corpus callosum

Hi: What is the default thickness of the corpus callosum?... 5 mm ?... 2 mm for each side from midline ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56

Re: [Freesurfer] aseg.mgz display only left hemisphere

Hi Bruce, Thank for your response. I am trying to separate white matter, gray matter and csf from aseg.mgz base on the intensity values of subcortical tissues. My aim is to have GM, WM and CSF of both hemispheres not only left hemisphere, is it possible? Azeez .Hi Azeez no, both hemisp

[Freesurfer] (no subject)

Hi, I would like to "sculpt" a label according to Talairach coordinates, precisely to cut the anterior part of the rostral middle frontal gyrus after +50mm AP; how would you procede ? Thank you for your software and thank you in advance for your help ! Yours sincerely, Pj Le Reste __

[Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

Hello List, on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution. Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or wou