Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc

Dear Doug, Thanks Doug. In my server, I cannot visualize the file but seeing the time courese window. I want to know whether there is a limit in graphics card for visualing the inflated data. Thanks. All the best. 2013-12-18 Rujing Zha 发件人：Douglas N Greve 发送时间：2013-12-18 00:32 主题：Re: [Fre

Re: [Freesurfer] design matrix and contrast in fsgdf

Dear Doug, Thanks for your precious help. Considering the 2nd example, I just want to know whether some brain surface thickness correlate the score without subjects coming from control or patient group. I think my aim is the same as want you told me "test whether the score is equal to 0 or not".

Re: [Freesurfer] qdec analysis with 2 covariates

Yes, it is insignificant. I had you set the clusterwise p-value threshold (--cwp) to .9 which means keep all the clusters regardless of how significant it is because you wanted the 40 clusters. On 12/17/2013 12:21 PM, Jon Wieser wrote: > I would think that a p-value of 0.8013 is very insig

Re: [Freesurfer] qdec analysis with 2 covariates

I would think that a p-value of 0.8013 is very insignificant. Am I missing somthing? Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Tuesday, December 17, 2013 10:46:36 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Yes, with a

[Freesurfer] mri_glmfit-sim Error

After running a group comparison using qdec I wanted to use mc-z for multiple comparison correction I tried running: mri_glmfit-sim \ --glmdir MTA_ADHD_MJ2 \ --sim mc-z 1000 2.0 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite ERROR: dimension mismatch between X and

Re: [Freesurfer] Tracula error: libnetcdf.so.6

Hi Anastasia, It was solved after reinstalling netCDF and updating the links (and some 64 bit packages missing too), now it is working, many thanks!! Gari On Tuesday, December 17, 2013, Anastasia Yendiki wrote: > > Hi Gari - This is coming from the new code in the update that I posted > recently.

Re: [Freesurfer] trac-all -path Help needed

Hi Francesco - Can you please send us your tracula log file, from scripts/trac-all.log? It's impossible to guess what went wrong without seeing the log file. Thanks, a.y On Tue, 17 Dec 2013, Francesco Baldacchini wrote: Hi everybody, I'm having problems running the trac-all -path command.

Re: [Freesurfer] talairach transformation error and general recon-all error

I looked at the nifti files in freeview. The orientation in freeview is correct, but it appears all of the T1s that resulted in an error are washed out in freeview. I can vaguely see the outline of the head, but there's a gray box covering the image. When I click on regions of bone or brain in t

Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Hi Vincent - TBSS shouldn't care what mask was applied to the FA maps that you feed into it. Of course it's best if the same mask has been applied to both the FA maps and bedpostx outputs. However, the diffusion and structural masks should only differ in voxels around the brain, not deep in th

Re: [Freesurfer] Problems dipslaying annotations in freeview

For the subject that you were not able to load the annot, did you check the recon-all log file? Did recon-all complete properly? doug On 12/17/2013 01:35 PM, Laura Taylor wrote: > Hi again, Douglas and freesurfer experts. > > Unfortunately my problem cannot be explained by having made manual >

Re: [Freesurfer] upgrading to freesurfer 5.3

Hi Laura - Please read the information on the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Tracula in 5.2 and 5.3 is identical. The motion measures are not in 5.3 but in a newer update, that you can download from that wiki page. As an aside, you should not be using reco

Re: [Freesurfer] New features in TRACULA

Hi Ruth - If you download the update and unzip it, you'll see an executable called dmri_motion. You can run it without any arguments to see the help text. Try something like this: dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out output.txt a.y On Fri, 13 Dec 201

Re: [Freesurfer] Tracula error when running bedpostX (2nd step af trac-all)

Hi Matthieu - This error had to do with a change in bedpostx's command line arguments after an FSL upgrade. The problem is fixed in the newer version of tracula. Again, I'd strongly recommend upgrading to the newer tracula. Hope this helps, a.y On Thu, 12 Dec 2013, Matthieu Vanhoutte wrote:

Re: [Freesurfer] Problems dipslaying annotations in freeview

So when you say you cannot load it, what do you mean? doug On 12/17/2013 02:55 PM, Laura Taylor wrote: > Hi Douglas, > > I checked the status of each subject once recon-all was completed (by > looking in the terminal window before I closed it). Each of my > roughly 90 subects had the message

Re: [Freesurfer] Tracula error: libnetcdf.so.6

Hi Gari - This is coming from the new code in the update that I posted recently. Which build of freesurfer 5.3 and which build of the tracula update do you have? Using our Centos 6 build, I was not able to replicate your error. a.y On Wed, 11 Dec 2013, Garikoitz Lerma-Usabiaga wrote: > Hi An

Re: [Freesurfer] talairach transformation error and general recon-all error

It could be that SPM is setting some scaling factor in the nifti header that FS is not reading properly. Which version of FS are you using? doug On 12/17/2013 02:38 PM, JARED NIELSEN wrote: > I looked at the nifti files in freeview. The orientation in freeview is > correct, but it appears all

Re: [Freesurfer] Problems dipslaying annotations in freeview

Hi Douglas, I checked the status of each subject once recon-all was completed (by looking in the terminal window before I closed it). Each of my roughly 90 subects had the message "*recon-all -s* subjectID *finished without error*at date and time". When I look at the recon-all.log file the same

Re: [Freesurfer] trac-all inquiry

Hi David - Based on the error message in your log file, the right angular bundle (rh.cab) is also failing. Looks like a similar problem with the right ILF, probably that tract is also affected by the blank slices in your volume. Nothing on the list after rh.cab gets reconstructed because of t

Re: [Freesurfer] Problems dipslaying annotations in freeview

Hi again, Douglas and freesurfer experts. Unfortunately my problem cannot be explained by having made manual edits and then not finishing recon-all. When I load subjects that I did not manually edit, I am either unable to load an annotation file (specifically r/lh.aparc.a2009s.annot) at all, or I

Re: [Freesurfer] GLM p value display

The cluster p-value is the significance corrected for multiple comparisons. It is possible for a cluster to be large and yet made up of voxels whose individual significances are low. The p-value for such a cluster may be significant, whereas a small cluster made of individual highly significan

Re: [Freesurfer] GLM p value display

Oh so we don't report the significance itself? because for example if we have a small cluster but highly significant, does the cluster-wise correction p value take it into account? (compared to a large cluster but with lower significance). I may not have completely got this. Thanks Doug Celine > H

Re: [Freesurfer] GLM p value display

Hi Celine, you should report the clusterwise p-value (which is neither of those). doug On 12/17/2013 12:11 PM, Celine Louapre wrote: > Hi all > I am wondering what is the best to present GLM results in a table on top > of the visual display. > For the significant clusters after clusterwise correc

[Freesurfer] GLM p value display

Hi all I am wondering what is the best to present GLM results in a table on top of the visual display. For the significant clusters after clusterwise correction, should we display the Max -log10(p) as in the summary file itself, or the p value directly, or a transformed pvalue like a Z score? Thank

Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR

Is that all it says? Can you send the log file? On 12/16/2013 10:00 PM, Rujing Zha wrote: > Hi Doug, > Thanks Doug. > I tried the "-run 15" option, it generate a "015" folder. However > unpacksdcmdir code echo ERROR message: > "ERROR:mri_convert > child killed: segmentation violation ", > and

Re: [Freesurfer] qdec analysis with 2 covariates

Yes, with a 95% confidence range of .7962 to .8065 doug On 12/17/2013 11:04 AM, Jon Wieser wrote: > so in the following cluster, the cluster-wise p-value is 0.80130? > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow > CWPHi NVtxs Annot > 1 3.247

[Freesurfer] trac-all -path Help needed

Hi everybody, I'm having problems running the trac-all -path command. It's giving me this error: *Segmentation fault (core dumped) Linux opbg 3.11.0-15-generic #23-Ubuntu SMP Mon Dec 9 18:17:04 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at mar 17 dic 2013, 16.09.33,

Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc

You can load is as an overlay in tksurfer or freeview and scroll through the frames On 12/17/2013 07:21 AM, Rujing Zha wrote: > Dear all, > I read the tutorial > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > and I want to know how to visualize the lh.gender_age.thicknes

Re: [Freesurfer] design matrix and contrast in fsgdf

That looks correct. The contrasts for the 2nd example will test whether the score is equal to 0 or not (and not an interaction between diagnosis and score). It is not wrong, but I just wanted to make sure you know what you are testing. doug On 12/17/2013 01:50 AM, Rujing Zha wrote: > Dear al

Re: [Freesurfer] qdec analysis with 2 covariates

so in the following cluster, the cluster-wise p-value is 0.80130? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 1 3.247 90900134.66-37.1 -33.2 -24.5 0.80130 0.79620 0.80640 267 fusiform - Original Message -

[Freesurfer] Tracula upgrading to Freesurfer 5.3

Tracula experts, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in

Re: [Freesurfer] data uploaded

Hi Rujing the multi-frame I'm not going to be able to help with - you need to run recon-all on the anatomical not an epi image. I'll try to find time to take a look at the other one though cheers Bruce On Tue, 17 Dec 2013, Rujing Zha wrote: Hi Bruce, I uploaded the data to your server. Al

[Freesurfer] Very strange error in surface reconstruction after a2-cp

Dear FS experts, I have a very strange error after running autorecon2-cp. I never saw this kind of error with previous versions of FS. I run recon-all -all on my subject, and obtained very good surface reconstructions, with the exception of few excluded wm voxels (see attachment called "befo

[Freesurfer] data uploaded

Hi Bruce, I uploaded the data to your server. All files can be divided into 2 subjects. And one subject has incorrect segmentation (subject), the other has a multiframe ERROR(LJH_error). Thanks. All the best. 2013-12-17 Rujing Zha___ Freesurfer maili

Re: [Freesurfer] Optimal registration

unfortunately not. Bruce On Tue, 17 Dec 2013, Dídac Vidal wrote: Hi, I'd like to ask whether there exist any (implemented/objective) measure to identify a correct surface reconstruction beyond the visual inspection in order to identify gross defect or wm/gm boundary. Thanks in advance. --

[Freesurfer] Optimal registration

Hi, I'd like to ask whether there exist any (implemented/objective) measure to identify a correct surface reconstruction beyond the visual inspection in order to identify gross defect or wm/gm boundary. Thanks in advance. -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Fac

[Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc

Dear all, I read the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and I want to know how to visualize the lh.gender_age.thickness.10.mgh. Thanks. All the best. 2013-12-17 Rujing Zha___ Freesurfer mailing list Freesurfer@