Re: [Freesurfer] Labels for comparison

Hi Bruce, I apologize for my detailist nature. I found the csv files on the ADNI web site containing the numerical values of volume in mm^3 numbers. Do you mean that there should also be the corresponding label maps on the ADNI web site, particularly of the third and lateral ventricles? I kno

Re: [Freesurfer] Hc segmentation: crosssectional stream with v4.5, longitudinal with v5.1

Hi Elisabeth, don't mix versions. There is lots of stuff that can go wrong (files that don't exist in 4.5 cross that the longitudinal stream expects etc.). Since the longitudinal stream has been improved significantly since 4.5 (more reliability, several bug fixes etc) I'd recommend to re-run ever

Re: [Freesurfer] I had a Computer Failure, how can I resume recon-all for base (longitudinal processing)

Hi Natacha, make-all does not work for base and long. The easiest is to delete the base (unless you made edits of course), and rerun the base from scratch. You can also look at scripts/recon-all.log and see where it stopped, then use flags like -autorecon2 -autorecon3 (or more fine steps) to star

Re: [Freesurfer] mni152.register.dat

Thanks Doug, I've done it with the one in SPM: tkmedit -f $SPM8_DIR/canonical/avg152T1.nii -overlay ROI45.nii -fthresh 0.5 is this ok or should I test it with the one from FSL as well? My partner is working with SPM and MarsBar. Both in FS and in SPM the ROI is the same, troubles start when I

Re: [Freesurfer] Labels for comparison

Hi John have you checked with the ADNI folks? I think they have FreeSurfer segmentation on many if not most of their subjects. We place no connectivity constraints on the ventricular segmentations because they get so thin that indeed sometimes 1mm data cannot resolve the connections. So sometim

[Freesurfer] Labels for comparison

Hello, I have successfully developed an automated algorithm combining pixel intensity-based and shape based approaches to segment the lateral ventricles. I have applied my algorithm to a small data set of 1.5 T1 ADNI images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI (subjects

Re: [Freesurfer] Memory allocation problem trac-all -prior

Hi Rui - Just keep in mind that when you're removing lines from trainlist.txt, you're removing subjects from the atlas. So instead of using a tract atlas that's based on 33 subjects, you are now using a tract atlas based on as many subjects as the lines that remain in trainlist.txt. a.y On Tu

Re: [Freesurfer] Question on longitudinal statistics

Hi Anson, 'conversion' means to extract the values from that file (for the specific structure(s)) and put them into a format that can be read by your program (SPSS). For the stats you would not use qdec anyway (you could use mri_glmfit). You may want to check out asegstats2table and aparcstats2ta

Re: [Freesurfer] mni152.register.dat

Hi Gari, Does it appear in the right place if you run tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -overlay ROI45.nii doug On 07/17/2012 01:20 PM, Garikoitz Lerma Usabiaga wrote: > Hi freesurfer experts, > I want to use a volume based MNI152 ROI in Freesurfer, when I check it > over fs

[Freesurfer] mni152.register.dat

Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...: tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat And I have th

Re: [Freesurfer] multiple comparisons correction

On 07/16/2012 09:30 PM, Meng Li wrote: > Dear professor, > Thanks for your reply. > You said that when drawing conclusions from both hemispheres then I > need to use .025, but I found that in qdec interface, the default > value of -cwpvalue is 0.05. So are they inconsistent? This would be consi

[Freesurfer] Question on longitudinal statistics

Hi, In the longitudinal tutorial it states that: "In order to analyze your longitudinal data, you have different options. You could, e.g., open the stats text files in each tpN.long.templateID/stats/ dir, containing statistics such as volume of subcortical structures or thickness averages for c

[Freesurfer] hippocampus subfilelds mask

Dear Freesurfer experts, I successfully run a hippocampal subfield segmentation on anatomical data of one subject (resolution 1 mm^3). Now I am building hippocampal subfields masks. I used the FreeView interface to load the mgz volume files of hippocampal subfields. I saved each subfield separa

Re: [Freesurfer] white-gray contrast algorithm

Try the pctsurfcon program doug On 07/17/2012 11:44 AM, Fred Lado wrote: > I found a thread (with same subject line) in the archive that referred > to Freesurfer tools to measure white-gray contrast, but I could not > find anything further on where the information resides. Is there a > way to

Re: [Freesurfer] white-gray contrast algorithm

I found a thread (with same subject line) in the archive that referred to Freesurfer tools to measure white-gray contrast, but I could not find anything further on where the information resides. Is there a way to measure white-gray contrast in the manner described in several papers (difference in

Re: [Freesurfer] Measuring total cortical volume

This is computed by computing the volume inside the pial surface and subtracting the volume inside the white surface (and accounting for small amounts in the "unknown" region). doug On 07/17/2012 04:47 AM, Emelie Andersson wrote: > Thank You Douglas, > > May I ask if You know how the numbers wer

Re: [Freesurfer] How to register FLAIR to T1?

Does fslregister work by itself? On 7/17/12 10:39 AM, Ed Gronenschild wrote: Hi Doug, I've found a solution to the problem: I converted T1.mgz and FLAIR.mgz to nii.gz and then applied flirt directly with the same options as in flsregister called by bbregister, so flirt -cost corratio -dof 6 -s

Re: [Freesurfer] How to register FLAIR to T1?

Hi Doug, I've found a solution to the problem: I converted T1.mgz and FLAIR.mgz to nii.gz and then applied flirt directly with the same options as in flsregister called by bbregister, so flirt -cost corratio -dof 6 -searchx -90 90 -searchy -90 90 \ -searchz -90 90 -in FLAIR.nii.gz -ref T1.nii.gz

Re: [Freesurfer] How to register FLAIR to T1?

Hi Ed, can you upload the FS analysis of the subject and the FLAIR so I can take a look? doug On 7/17/12 5:21 AM, Ed Gronenschild wrote: Hi Doug, Thanks for your suggestion, but it didn't work out either. Ed On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Hi Sue you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I believe we already distribute the updated template but it's not used. Nick: do you want to send around a patch to recon-all that people can use before 5.2 comes out? thanks Bruce On Tue, 17 Jul 2012, Susan Ruiz wrot

Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

Hi all, Using previous versions of FreeSurfer, we have used the eTIV as a covariate for our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new studies. What would you recommend using for subjects who have been run with 5.1.0? Can you make the template available publicly

Re: [Freesurfer] Memory allocation problem trac-all -prior

Hi all, I think I found the problem. I reduced the number of train files in the trainlist.txt file and it ran without errors. Maybe I will need more memory to run with all train files. thanks 2012/7/16 Rui Lavrador > > > -- Forwarded message -- > From: Rui Lavrador > Date: 2

Re: [Freesurfer] Resend: error in compiling Freesurfer with GPU support

On Tue, Jul 17, 2012 at 4:54 AM, Akio Yamamoto wrote: > Compiling FreeSurfer with GPU support failed with the error message > which is added to the end of this email. > > The current build environment is as follows: > GeForce GTX 690 > CUDA Toolkit 4.2 > CentOS 6.3 > > I wonder if there are any s

Re: [Freesurfer] trac all - cant allocate memory

Hi Michael and Jürgen - This issue has been resolved, see "Updates": http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula It had to do with the original mac executables having been compiled on an older version of MacOS, which was not smart about utilizing all the memory on your computer. I

Re: [Freesurfer] How to register FLAIR to T1?

Hi Doug, Thanks for your suggestion, but it didn't work out either. Ed On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 18 Date: Mon, 16 Jul 2012 11:32:06 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] How to register FLAIR to T1? To: freesurfer@nmr.mgh

[Freesurfer] Resend: error in compiling Freesurfer with GPU support

Hi Freesurfer experts, Compiling FreeSurfer with GPU support failed with the error message which is added to the end of this email. The current build environment is as follows: GeForce GTX 690 CUDA Toolkit 4.2 CentOS 6.3 I wonder if there are any specific requirements for building CUDA-enabled F

Re: [Freesurfer] trac all - cant allocate memory

Hi Michael This is a Mac specific problem. You can reduce the number of a priori tracts used by reducing the entries in the list found in freesurfer/trctrain/trainlist.txt. On my Mac it works with 26 a priori tracts. Cheers Jürgen On [DATE], "Michael Scheel" <[ADDRESS]> wrote: > Dear FS expert