[Freesurfer] Error Talairach registration

Hi All, When I ran recon-all -autorecon1 in one of my subject I encountered the following error ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check

[Freesurfer] Displaying cortical thickness changes in volume images

Dear All, I would like to display my cortical thickness chnages from longitudinal runs on my original T1-w volume images. I am wondering whether this is possible if so can anyone tell how I can do this. Thanks in advance Venkat === Please consider the envir

[Freesurfer] Longitudinal cortical thickness analysis

Dear All, I ran the following steps in a patient of mine at two time points nonhyper_24_06 and nonhyper_24_07 recon-all -autorecon1 -subjid nonhyper_24_06 recon-all -autorecon1 -subjid nonhyper_24_07 recon-all -autorecon2 -subjid nonhyper_24_06 recon-all -autorecon3 -subjid nonhyper_24_06 recon

[Freesurfer] Statistics on longitudinal data

Hi All, I am trying to do cortical thickness analysis on a single subject's longitudinal data. I am attaching the design and group.diff.mtx could any one tell me whether they are correct. Any web link (tutorial) on how to do stats on longitudinal data available. Thanks venkat

[Freesurfer] longitudinal stats

Hi All, I am trying to do cortical thickness analysis on a single subject's longitudinal data. I am attaching the design and group.diff.mtx could any one tell me whether they are correct. Thanks venkat === Please consider the environment before printing this

[Freesurfer] missing lh.thickness.fwhm10.fsaverage.mgh in some subjects

Dear All, I was trying to run "mris_preproc" after completing all autorecon steps in some of my subjects folder under "surf" I see "lh.thickness.fwhm10.fsaverage.mgh" whereas in others it is missing. I ran autorecon 1, 2 and 3 the same way in all the subjects so I am wondering what might be th

[Freesurfer] Error -FSGD file for clinical correlations please help

Dear All, I am trying to correlate clinical disability measure ALSFRS score with cortical thickness in ALS patients. Attached is the fsgd file. I am not able to run mris_preproc with this fsgd file "ERROR message: is no subjects specified" what am I doing wrong here , also my design matrix con

[Freesurfer] thickness_clinical_correlations

Dear All, I am trying to correlate clinical disability measure ALSFRS score with cortical thickness in ALS patients. Attached is the fsgd file. I am not able to run mris_preproc with this fsgd file what am I doing wrong here, also my design matrix contrast is 1 0 am I right. I am interested i

Re: [Freesurfer] Reporting coordinates from Group analysis

...@nmr.mgh.harvard.edu] Sent: Thu 5/20/2010 1:33 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Reporting coordinates from Group analysis If you click on a point, it should tell you in the control window what the talairach coordinates are doug

[Freesurfer] Reporting coordinates from Group analysis

Dear All, I checked the archives but couldn't get a complete answer. I performed group analysis of cortical thickness using mri_glmfit. I am wondering how to report the coordinates of regions where cortical thickness is significantly different, i used FDR for multiple comparisons in tksurfer.

[Freesurfer] correlation between thickness and volume

Dear All, I ran group comparison between control and patients independently on thickness, area and volume. I found significant difference between the two groups on volume and thickness, now i am wondering it is possible to run a correlation between the volume and thickness results to see how g

Re: [Freesurfer] fsgd file creation

. Thanks again, venkat From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Fri 5/7/2010 11:35 AM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsgd file creation How are you going to do the test? I'm not

[Freesurfer] Group comparison

Dear All, I am sorry to post this message again. Since i am not able to find from the tutorial and archives what i need i am posting it. I want to compare cortical thickness values in each region from aparc.stats file between control and patients. I am wondering whether it is possible to compa

[Freesurfer] fsgd file creation

Dear All, I am new to freesurfer, i am sorry i am confused so i am posting this message. I have two groups i want to compare cortical thickness values in all the areas reported in aparc.stats file between these two groups. So i started creating my fsgd file the problem i have is with the contr

[Freesurfer] fsgd file from qdec

Dear All, I am new to freesurfer. I am wondering is it possible to save the fsgd created automatically by qdec. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.

[Freesurfer] missing stats files -posting again

Dear All, I am new to freesurfer, in some of our patients stats files lh and rh.curv.stats are missing at the end of recon-all -all. recon-all finished without error in these patients so i am wondering what is the mistake i am doing and where will need these lh and rh.curv stats files. Thanks

[Freesurfer] Group comparison -qdec clarification

Dear All, I want to perform group comparison of cortical thickness between my patient and control group. I read qdec tutorial regarding how to do this. I was little bit puzzled and not able to understand the following. Before creating qdec table of patient data, fsaverage was suggested to run,

[Freesurfer] missing stats files

Hi All, In some of our subjects in stats folder i don't see lh and rh .curv.stats files (so only 6 stats files in total whereas in others i have 8 stats files in total) why is that. Recon-all finishes without any error what am i doing wrong. Thanks venkat ===

[Freesurfer] talairach registration-problem

Dear All, In two of my subjects talairach registeration is giving me wrong results in the sense instead of taking my input image to talairach space the talairach image is registered to my input image. This happens just only in two subjects out of 14 subjects. Can anyone please tell me how to

Re: [Freesurfer] Choroid plexus -filling

Thanks, no it is not causing problems i just wanted to know. Thanks again venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:15 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Choroid

Re: [Freesurfer] Choroid plexus -filling

So do i need to fill it in other regions (manual editing) Thanks venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:06 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Choroid plexus

[Freesurfer] Choroid plexus -filling

Hi All, In my "filled.mgz" volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e

Re: [Freesurfer] Pial surface- clarification

urfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Sat 3/13/2010 12:35 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pial surface- clarification Hi Venkat, the image looks ok, but it's hard to tell from a single slice or two and

Re: [Freesurfer] Inflated_surface

Thanks very much Doug. From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thu 2/18/2010 12:20 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated_surface Right, the dents and dimples in the

Re: [Freesurfer] Inflated_surface

-Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thu 2/18/2010 12:04 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Inflated_surface What is the problem? Just looking at those inflated surface, they look ok to me

[Freesurfer] Inflated_surface

Hello All, I am new to freesurfer and i am kind of sensing there is some problem in my inflated surface (i compared it to the one available in the documentation page).I have placed some marks on lh inflated to find out the coordinates these are x = (-28.5, -59.2, 21.1), n = (-0.5, -0.3, 0.8),x

[Freesurfer] Cortical thickness in controls

Hello All, I would like to clarify the following.I couldn't find the answers i was looking for in the archives so here are my questions; 1) In some of our subjects the WM/GM interface is identified correctly but the pial surface falls short of some voxels which i want to manually edit them i

Re: [Freesurfer] talairach registration-result

Okay thanks very much. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thu 11/19/2009 3:30 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] talairach registration-result tkregister2 applies the transform to

Re: [Freesurfer] talairach registration-result

aligned almost closely. So what is this image i looked at? Thanks venkateswaran -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thu 11/19/2009 12:43 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] talairach

[Freesurfer] talairach registration-result

Dear Freesurfer Users, Could anyone please tell me what is the name of the image file after talairach registration for instance like nu.mgz (after intensity correction). Thanks venkateswaran === P Please consider the environment before printing this e-mail

[Freesurfer] recon - local directory

Dear Freesurfer users, I don't have privileges to create directories in freesurfer installation folder as i am using freesurfer from server. So i am not able to run "recon-all -s Desktop/test/sub1/vol1.mgz -autorecon1" giving a path name to a folder in Desktop where my image volume is stored.

[Freesurfer] tkmedit

Hello, I am new to freesurfer, i having the following problem. I placed my subject's data in folder "Desktop/test/sub1/vol1.mgz". I used "tkmedit sub1 vol1 -f $bme/home..Desktop/test" the following command to open and view my image and i get the following error " bme undefined variable. What i

[Freesurfer] Books on Freesurfer

Hello, I am new to the field of cortical thickness analysis and freesurfer software. I looked at the tutorials (mainly Powerpoint slides and research articles)on freesurfer documentation pages. Being new to the field and with very little image processing background i find it difficult to grasp