[Freesurfer] viewing group analysis results

Hello users, I am doing the group analysis stats results...using FDR correction 0.01 and checking the pial surface with curvature and overlay. I see this line come up whenever i change the FDR..is this some kind of error which I need to be concerned about? surfer: Error sending tcl command

[Freesurfer] QDEC

Hello developers, How can I get access to QDEC? Regards Chacko. Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=listsid=396546091

[Freesurfer] longitudinal analysis error

Hello all, I got an error while running longitudinal analysis using recon-all -long and the process exited with errors. THis is the error message: mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz logging cutting

[Freesurfer] longitudinal analysis - error

Hello all, This is an error I got while running the longitudinal analysis on one of our subjects.It didnt create the filled.mgz volume and so the surfaces weren't created. [EMAIL PROTECTED] Fill Tue Feb 13 20:59:04 MST 2007 /ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri mri_fill -a

Re: [Freesurfer] input registration matrix

Hello all, To rectify the talairach transform, I am editing brainmask.mgz using tkregister2 and aligning the subject and talairach volume. THank you. Chacko. What are you trying to register? Chacko Cherian wrote: Hello All, After making changes using tkregister2 the input

[Freesurfer] tkregister2:views mixed up.

Hello ALL, Has anybody had trouble with tkregister2..I loaded the transform and the coronal and horizontal views are mixed up.Coronal view of the subject is coupled with the horizontal view of the talairach volume. Thanks in advance Regards, Chacko.

Re: [Freesurfer] tkregister2:views mixed up.

No, It has the same problem in tkmedit too. --- Doug Greve [EMAIL PROTECTED] wrote: Does it view correctly in tkmedit? Chacko Cherian wrote: Hello ALL, Has anybody had trouble with tkregister2..I loaded the transform and the coronal and horizontal views are mixed up.Coronal view

Re: [Freesurfer] tkregister2:views mixed up.

. Where did the data come from? Are the dicoms messed up too? Chacko Cherian wrote: No, It has the same problem in tkmedit too. --- Doug Greve [EMAIL PROTECTED] wrote: Does it view correctly in tkmedit? Chacko Cherian wrote: Hello ALL, Has anybody had trouble

Re: [Freesurfer] tkregister2:views mixed up.

orientation should be ok. Chacko Cherian wrote: It has the problem in tkmedit,after I load the transform..i checked brainmask.img and T1.img after loading the transform and they had this problem..The header and geometry info look fine.. --- Doug Greve [EMAIL PROTECTED] wrote

[Freesurfer] transforms

Hello all, Is there some information on the wiki about the srctoDst voxel-to-voxel transform and the rastoRAas transform? THAnks Chacko. Sucker-punch spam with award-winning protection. Try the free Yahoo!

[Freesurfer] my_average and fsaverage

Hello users, I created an average subject(my_average) with 25 subjects.Now when I compare the fsaverage and my_average inflated views,the display shows fsaverage as way bigger than my_average.Is this normal?Is it something to do with how fsaverage is scaled and displayed? Area-wise my_average is

Re: [Freesurfer] surf2surf

order version that does not support the --s option. If so, then you'll need to spec the src and trg subjects explicitly. Chacko Cherian wrote: Hello users, I wanted to use mri_surf2surf for surface smoothing but it gives me an error saying --s is not an option. mri_surf2surf --hemi

[Freesurfer] surf2surf

Hello users, I wanted to use mri_surf2surf for surface smoothing but it gives me an error saying --s is not an option. mri_surf2surf --hemi lh \ --s average \ --sval lh.gender_age.thickness.mgh \ --fwhm 10 \ --tval lh.gender_age.thickness.10.mgh it didnt work with srcsubject either.The

[Freesurfer] recon-all -long errors

Hello users, I was running longitudinal analysis for a couple of scans and recon-all exited with this error. CTABread(/usr/local/freesurfer/ASegStatsLUT.txt): could not open file No such file or directory atlas_icv = 1.74537e+06 Loading mri/aseg.mgz Loading mri/norm.mgz Loading mri/norm.mgz

[Freesurfer] group-analysis error

Hello all, Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer. Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg

[Freesurfer] group-analysis error

/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm --- Chacko Cherian [EMAIL PROTECTED] wrote: Hello all, Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file

[Freesurfer] thickness reproducibility-longitudinal?

Hello all, http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility Is this page on thickness reproducibility intended for longitudinal analysis or is it just a general group analysis procedure? THanks in advance, Chacko.

[Freesurfer] Longitudinal analysis

Hello users, Is there a typo on the longitudinal analysis page on the wiki.. does the command go like this?? recon-all-long -long -subjid tp1 -subjid tp2 Thanks Chacko. Expecting? Get great news

Re: [Freesurfer] Longitudinal analysis

want to use (like -all). Nick On Mon, 2007-01-22 at 10:35 -0800, Chacko Cherian wrote: Hello users, Is there a typo on the longitudinal analysis page on the wiki.. does the command go like this?? recon-all-long -long -subjid tp1 -subjid tp2 Thanks Chacko

[Freesurfer] regarding .plt files

Hello users, I am using the latest stable version of FreeSurfer and there are two files wm.plt and gm.plt which are created after the recon-all process.What do these signify and how do I open them? Thanks in advance Chacko.

[Freesurfer] command for aseg stats to export to spreadsheet(excel)

Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko.

Re: [Freesurfer] command for aseg stats to export to spreadsheet(excel)

Thank you Jenni. How do i use asegstats2table?What is the command?Is it a tcl script file?If so,could you also mention where it is located. Regards Chacko. - Original Message From: Jenni Pacheco [EMAIL PROTECTED] To: Chacko Cherian [EMAIL PROTECTED]; Freesurfer freesurfer

Re: [Freesurfer] is this ok?

[EMAIL PROTECTED] To: Chacko Cherian [EMAIL PROTECTED] Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 6, 2006 4:25:05 PM Subject: Re: [Freesurfer] is this ok? Hi Chako, I wouldn't worry too much about the inflated - it looks okay. Probably a result of the large motion

[Freesurfer] parameters for N3 correction

Hello users, Is there any information available regarding the parameters used for N3 correction in the autorecon process? Thanks, Chacko. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mritotal.log

Hello all, I wanted to know where the mritotal.log file is created.I checked the /scripts directory but couldnt find it there. I'd like to have a look at the Final objective function value for the subjects I'm running. Thanks in advance Chacko Cherian

[Freesurfer] Ubuntu linx

? Thanks in advance Chacko Cherian. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] error message regarding mri_ca_register_

this could possibly mean? THanks in advance. Chacko Cherian. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] subject failed autorecon1

:21:26 MST 2006 Thanks in advance Chacko Cherian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Slackware 10.0.0

Hello all, I have a small query.Just wanted to know which stable Freesurfer version I should install for Linux Slackware 10.0.0 version. Has anybody experienced any issues usig this platform. Thanks in advance. Chacko Cherian. Arizona State University

[Freesurfer] query regarding T2/T1

Hello all, Can we use tkmedit for T2-weighted images or is it restricted to T1 -weighted? Thanks Chacko. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] dicom files

the file names(for each slice) for the recon-all procedure or is there a simpler way. THanks in advance Chacko Cherian. Arizona State University Graduate Research Assistant __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection

[Freesurfer] dicom format

I got this error while running a single subject in DICOM format.the 'recon-all -autorecon1 -subjid subject_name ' stopped at this stage. INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux

[Freesurfer] error at autorecon2

Hello all, Here's an error I got while doing 'recon-all -autorecon2 -s subject_name. Could someone please clarify. Thank you. Chacko Cherian. [EMAIL PROTECTED] EM Registration Wed Aug 2 16:35:22 MST 2006 /home/ttest/freesurfer/subjects/case1/case1/case1/mri mri_em_register -mask

[Freesurfer] GLIBCXX

Hello all, Could someone please clarify why this library cannot provide the correct 'GLIBCXX_3.4'. Thanks in advance. Chacko. mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz mri_watershed: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4' not found

[Freesurfer] recon-all exited with errors

Hello all, I was running recon-all for one of my images and this happened to be the error that i got.Could someone please clarify, Thanks in advance Chacko. mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo

[Freesurfer] error running tkmedit

Hello everyone, I am using a Red Hat Enterprise Linux AS release 3(Taroon update 6) version.While running tkmedit for the bert data..this is what i get.. tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory. I tried the

Re: [Freesurfer] autorecon1

mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Fri Jul 14 16:40:38 MST 2006 --- Chacko Cherian [EMAIL

Re: [Freesurfer] printing out from tksurfer and tkmedit

when i want to print-out the outputs using Save TIFF as it isn't giving me any results.Is there something else that I need to do to save the outputs as TIFF files?? --- Bruce Fischl [EMAIL PROTECTED] wrote: but you could write a tcl script to do it automatically On Fri, 30 Jun 2006, Kevin

[Freesurfer] printing out from tksurfer and tkmedit

Hello everyone, How can I can I print out the display images from tksurfer and tkmedit other than manually saving them into tiff and then printing them.IS there any way to print them directly? THAnx Chacko. __ Do You Yahoo!? Tired of spam?

Re: [Freesurfer] tesselating

answer! Bruce On Thu, 22 Jun 2006, Chacko Cherian wrote: Yes when I load the image in tkmedit I odnt have any problems.Its perfectly clear and coronal,horizonatal and sagittal are all correct. --- Bruce Fischl [EMAIL PROTECTED] wrote: when you load it in tkmedit does

Re: [Freesurfer] tesselating

No, the nofix surfaces are also displaying just a small piece of the surface..similar to the ?h.orig surfaces. --- Bruce Fischl [EMAIL PROTECTED] wrote: hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote: --- Bruce Fischl [EMAIL

Re: [Freesurfer] tesselating

are also displaying just a small piece of the surface..similar to the ?h.orig surfaces. --- Bruce Fischl [EMAIL PROTECTED] wrote: hmmm, looks okay. Can you see the ?h.orig.nofix surfaces okay? On Thu, 22 Jun 2006, Chacko Cherian wrote: --- Bruce Fischl [EMAIL

[Freesurfer] tksurfer:troubleshooting surface problems

Hello everyone, I have used an Analyze format data(.img) on Freesurfer and was running the Morphometry and REconstruction tutorial on the wiki.THey were running fine till i reached the automatic topology defect correction step. I used :recon-all -fix -s subject_name and it started fxing all the

[Freesurfer] converting .img to .mgz

Hi everybody, I ve got a small question on converting .img scans(Analyze) TO .mgz... suppose i have a raw.img(and raw.hdr) file and I want to use recon-all for converting this to .mgz do I just need to do recon-all -i raw.img -s subject_name Or is there any other way I can directly use .img

[Freesurfer] analyze format

Hello, I am having some trouble in running Analyze format images on freesurfer.Could someone please guide me on how to run images on this format.. THanx Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around

[Freesurfer] freesurfer installation problems

Hello all, I am having some trouble in using the freesurfer version I had downloaded.The FREESURFER_HOME file is missing and so I cannot source or setenv anytime I want to use it.Do I need to tar and unzip again or is there any other way? Thanks in advance Chacko.

[Freesurfer] new to Freesurfer

will help me a long way in my work Thanks in advance Take care Chacko Cherian. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing