[Freesurfer] Find point on pial surface closest in 3D space to known Talairach coordinates

Hi Freesurfers, I'm running a brain stimulation (TMS) study and wish to stimulate points on the pial surface that correspond most closely to known Talairach points (from fMRI studies). I'm wondering the best way to find these points using the beautiful Freesurfer cortical reconstructions. I've ext

Re: [Freesurfer] Dmri_trin error in trac-all

Hi Ana - I'll try to post the fix later this week. a.y > Hello freesurfer users. > > I'm trying to process a trac-all > and it works for a while, but i have always the same error when it going > to > process the error. > > this is the end of the message > > Loading cortex mask from > /Application

Re: [Freesurfer] mri_convert generates different mgz from nii and nii.gz

try running mri_diff on them. The image data should be the same. It's probably the difference between the command line gunzip and the libraries cheers Bruce On Mon, 15 Aug 2011, Forrest Sheng Bao wrote: > hi there, > > i noticed a strange problem tonight. I had a .nii.gz file. I used > mri_con

[Freesurfer] mri_convert generates different mgz from nii and nii.gz

hi there, i noticed a strange problem tonight. I had a .nii.gz file. I used mri_convert to convert it into a .mgz file. I also used gzip to unzip the .nii.gz file and then used mri_convert again to get another .mgz file. But the two .mgz files have different md5 sums. Does anyone know what caused

[Freesurfer] Dmri_trin error in trac-all

Hello freesurfer users. I'm trying to process a trac-all and it works for a while, but i have always the same error when it going to process the error. this is the end of the message Loading cortex mask from /Applications/freesurfer_v5.1//trctrain/trc032/dlabel/mni/cortex+2mm.nii.gz Processing p

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue

fyi, a change from 5.0 to 5.1 pertaining to this is that the talairach stage is now run before the nu_correct stage, so that creation of nu.mgz can benefit from talairach.xfm. this means talairach uses orig.mgz as input, which seems to be affecting your results. the next release of freesurfer wil

[Freesurfer] thickness-age correlation

Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age 2)what is the best iteration number for the simul

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue

Hi Myriam, did you check the aseg? Unless the talairach.xfm is *really* off I don't think it will have much impact, but you should visually inspect them. cheers Bruce On Mon, 15 Aug 2011, Myriam Siefert wrote: Hi Nick, I have this problem with quite a few of my subjects, usually the fuzzy

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue

Sorry I meant those same subjects' transforms look much better with *FS 5.0* . 2011/8/15 Myriam Siefert > Hi Nick, > I have this problem with quite a few of my subjects, usually the fuzzy > transform volume in tkregister looks smaller than the subject's brain. To > what extend should I manually

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue

Hi Nick, I have this problem with quite a few of my subjects, usually the fuzzy transform volume in tkregister looks smaller than the subject's brain. To what extend should I manually edit the xfm (what criterions are mandatory for that transform to be acceptable)? Actually what puzzles me is that

[Freesurfer] preproc-sess - cannot find AFNI command 3dvolreg

Hi Doug and Freesurfers, I encountered an error during preproc-sess (Stable 5) that I have never seen before: ERROR: cannot find AFNI command 3dvolreg The commands I entered were: setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env setenv SUBJECTS_DIR /cluster/roffman/use

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue

i'm able to replicate what you see in tkmedit when the transform is created using the -use-mritotal flag. i cant explain why this happens, and is a bit unsettling given that the -tal-check portion passed and the transform looks good in tkregister. the transform created by the default (not using t

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue

Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam 2011/8/11 Myriam Siefert > Hi Nick, > I just would like to make sure that you had received my data, otherwise I > can send it again possibly by another mean if better. >

Re: [Freesurfer] Hi Ubuntu- error on generate stats

this message indicates the problem: mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec': Permission denied you can make the subjects directory writable by typing: cd /usr/local/freesurfer chmod -R a+rwX subjects n. On Mon, 2011-08-15 at 15:36 +0100, rajeev krishnadas wrote:

Re: [Freesurfer] recon-all error with nu_correct

did you run recon-all from a directory that you don't have permission to write to? On Mon, 15 Aug 2011, Ahmed, F, Me wrote: I don?t understand why I would all of a sudden be getting permission denied errors, when I ran a  complete study prior to this with absolutely no problems at all.   Fr

Re: [Freesurfer] recon-all error with nu_correct

I don't understand why I would all of a sudden be getting permission denied errors, when I ran a complete study prior to this with absolutely no problems at all. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent:

Re: [Freesurfer] recon-all error with nu_correct

check this!!! /bin/mv: cannot move `./tmp.mri_nu_correct.mni.26621/1/nu2_residue.mnc' to `./ tmp.mri_nu_correct.mni.26621/1/nu2_est.mnc': Permission denied On Mon, Aug 15, 2011 at 6:03 PM, Ahmed, F, Me < fah...@sun.ac.za> wrote: > Hi Louis, > > The command line I am using at the beginning was

Re: [Freesurfer] recon-all error with nu_correct

Hi Louis, The command line I am using at the beginning was the following: recon-all-i NN_117_10/NN117_10.MR.RESEARCH_STELLENBOSCH.2.1.2010.02.09.13.10.21.390625.46080549.IMA -s NN_117_10 -force -autorecon-all -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:f

Re: [Freesurfer] recon-all error with nu_correct

Hi Fatima, What is the recon-all command line you are using to start the recon? -Louis On Mon, 15 Aug 2011, Ahmed, F, Me wrote: > Hello Freesurfer experts, > > I am having great difficulty in trying to run the recon-all process on some > scans of mine. I have tried running it a number of times,

[Freesurfer] recon-all error with nu_correct

Hello Freesurfer experts, I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope some

[Freesurfer] Hi Ubuntu- error on generate stats

Hi all, I am new to Freesurfer (and to linux) and appreciate if you could please help. Just managed to install FS onto Ubuntu 10.10 64 bit. I am going through buckner - tutorial for the group analysis with Qdec. I am at the step where I have to import the aseg and aparc data. I clicked on the "g

Re: [Freesurfer] Freesurfer Digest, Vol 90, Issue 54

Hi, Nick and all, I've checked my table and included an empty line after the last subject. I made my table first in excell and I have also to include an empty space after it cell content. And it worked. Thank you for your help, Best regards, Carolina  Em 12/08/2011 12:58, freesurfer-requ...@nmr

[Freesurfer] Contrast vector for gender difference and cortical/age regresion

Hi I wish to produce a contrast vector for two conditions in the tutorials. I wish to make a hypothesis for age verse cortical thickness and gender verse cortical thickness. The contrast vector for age verse cortical thickness is [1 0] where age is the first x and cortical thickness is y. The situ