[Freesurfer] orientation of the data

Hello experts, I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse

[Freesurfer] Rawavg wrong

Hello, I was wondering whether you could help me wit this. I had reported a talairach error during recon and was asked to check what the rawavg looked like. Sagital is shown instead of Coronal, and upside down at that! Clearly, there is some formatting error. Is there a way to fix this within Frees

Re: [Freesurfer] Error: Loading Segmentation

10 12:14, Bruce Fischl wrote: > does the file /home/s0964091/Desktop/jan/mri/aparc.a2005s+aseg.mgz exist? > Did recon-all complete properly? > > > On Tue, 16 Mar 2010, Janani Dhinakaran wrote: > > Hello, >> >> With reference to this mail- Re: [Freesurfer] Extracti

Re: [Freesurfer] Recon-all problem (with talairach)

t; > Martin > > On Tuesday 30 March 2010 12:30:35 Janani Dhinakaran wrote: > > Hello everyone, > > I wanted to know what I can do to fix this error- it occurs when I'm > > running recon-all -all -s Subjec

[Freesurfer] Recon-all problem (with talairach)

Hello everyone, I wanted to know what I can do to fix this error- it occurs when I'm running recon-all -all -s Subject Tue Mar 30 11:27:20 BST 2010 talairach_avi done # #...@# Talairach Failure Detection Tue Mar 30 11:27:20 BST 2010 /home/s0964091/Deskto

[Freesurfer] Recon runs longer than the previous time and exits this time with errors

I was unable to extract parts of the cortex with the commands you had told me to try last time. I realised then that it was because recon hadn't finished running and I was using partially processed data. So I tried running it again. Here below is what I got. Since I'm using a partitioned machine sp

[Freesurfer] q about disc space

Hello. How much space is required for running one recon-all? If I needed to work on several people's brains, say 4-5, how much memory am I likely to need? Thanks! -- I am the Sun, I know no darkness. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

[Freesurfer] Error: Loading Segmentation

Hello, With reference to this mail- Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgzI tried introducing segments to my image ERROR: Loading Segmentation aparc.a2005s+aseg.mgz Couldn't import the segmentation volume. Tkmedit wouldn't read the segmentation you specified. This could be bec

Re: [Freesurfer] Cortical thickness measurement

Looking to isolate and measure the thickness of certain brain cortex areas eg- broca's or sensory cortex On 8 March 2010 19:58, Allison Stevens wrote: > which labels are you looking for information on? > > -- > > On Mon, 8 Mar 2010, Janani Dhinakaran wrote: > >

Re: [Freesurfer] Cortical thickness measurement

written? On 8 March 2010 14:31, Douglas N Greve wrote: > Use mris_anatomical_stats > > Janani Dhinakaran wrote: > >> >> Hello all, >> >> Can anyone tell me the commands I'll need to use to extract and measure >> the cortical thickness and volum

Re: [Freesurfer] Error with Talairach Transform during recon-all

I also checked without the '--surf orig'. Still not found. On 8 March 2010 14:22, Janani Dhinakaran wrote: > Here is how I checked if it was done okay > Looks like it wasn't. > > s0964...@cric-0012:~$ export SUBJECTS_DIR=~/Desktop/Newdata > s0964...@cric

[Freesurfer] Cortical thickness measurement

Hello all, Can anyone tell me the commands I'll need to use to extract and measure the cortical thickness and volume of certain regions of the brain? thanks -- I am the Sun, I know no darkness. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Error with Talairach Transform during recon-all

du/fswiki/FsTutorial/Talairach for more > info. > > doug > > Janani Dhinakaran wrote: > >> Any idea what this means and what I can do about it? >> >> Mon Mar 8 12:46:58 GMT 2010 >> talairach_avi done >> # >>

[Freesurfer] Error with Talairach Transform during recon-all

Any idea what this means and what I can do about it? Mon Mar 8 12:46:58 GMT 2010 talairach_avi done # #...@# Talairach Failure Detection Mon Mar 8 12:46:58 GMT 2010 /home/s0964091/Desktop/Newdata/JS/mri talairach_afd -T 0.005 -xfm transforms/talairac

[Freesurfer] Error with Talairach Transform and tkregister?

Hello, I'm running recon-all on a second set of data. It ran smoothly until mpr2mni305 success and then it gave the following: tkregister2_cmdl --mov nu.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfmout transforms/talairach.auto.xfm

Re: [Freesurfer] Loading new data into Freesurfer

ing it the .img file as input and the .mgz as output? > > > On Tue, 2 Mar 2010, Janani Dhinakaran wrote: > > Hello to everyone! >> Hope the new month is bringing better weather to all of you. >> >> I am trying to load new data. I cd-d to the location of the files (.

[Freesurfer] Loading new data into Freesurfer

Hello to everyone! Hope the new month is bringing better weather to all of you. I am trying to load new data. I cd-d to the location of the files (.hdr and .img). Now I am trying to convert the data. It doesn't recognise the information. I've manually created the files JS, MRI, and Orig within to

Re: [Freesurfer] recon-all doesn't recon-all

-- recon-all finished without error at Tue Feb 23 12:33:27 GMT 2010 done I'm quite perplexed now as to why it is going wrong. Is it possible at all that my data is not suitable for Freesurfer? Thanks for your time, Jan On 23 February 2010 09:00, Xue, Feng wrote: > On Tue, Feb 2

Re: [Freesurfer] recon-all doesn't recon-all

On 22 February 2010 16:27, Janani Dhinakaran wrote: > When I set SUBJECTS_DIR to /Desktop/. I get this > > s0964...@cric-0012:~$ export > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > s0964...@cric-0012:~$ echo $SUBJECTS_DIR > /home/s0964091

Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 70

rt line should be: > > export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/ > > > SUBJECTS_DIR is the directory which contains ALL subjects _not_ the > current subject. > > > Justin Ales > > > From: Sita Kakunoori > To: Janani Dhinakaran > Date: Mon, 22 Feb 2010

Re: [Freesurfer] recon-all doesn't recon-all

esktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran > wrote: > > Hello, > > I ran recon-all on Friday. It ran for around a minute instead of 30-48 > > hours. Unfortunately, when I try tkmedit and other such commands,

[Freesurfer] recon-all doesn't recon-all

Hello, I ran recon-all on Friday. It ran for around a minute instead of 30-48 hours. Unfortunately, when I try tkmedit and other such commands, the pictures don't visualise. So today I first confirmed that the SUBJECTS_DIR was in Desktop path. (Because over the weekend it had gone back to usr/local

[Freesurfer] Recon successful- ran for half a minute instead of 30 hours. Visualisation problems

tkmedit subjectname rawavg.mgz is the way to visualise the volume. The first image. This is what happened. s0964...@cric-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ tkmedit subj001 rawavg.mgz ERROR: cannot find /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.ad

Re: [Freesurfer] A basic question about visualising data

e > space, then run recon-all something like > > recon-all -s yoursubject -i /Desktop/Allimages/MRIscan... and the full path > till DICOM/dicomfile > > the output will then be in $SUBJECTS_DIR/yoursubject > > doug > > Janani Dhinakaran wrote: > >> My data is on

[Freesurfer] A basic question about visualising data

My data is on the desktop. The subjects directory is under usr/local/freesurfer/subjects. I tried setting desktop as SUBJECTS_DIR by using 'export SUBJECTS_DIR="/Desktop/Allimages/MRIscan... and the full path till DICOM" ' but apparently it didn't work because when I tried to run recon, it says SU

[Freesurfer] Problem starting

Hello, I'm operating freesurfer through a virtual box. I checked the memory space it is around 4G. It's not starting. Any idea what I can do about it? -- I am the Sun, I know no darkness. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] Problem with Autorecon all

r/subjects/jan? Do you have > write permission? > > Bruce > > On Thu, 28 Jan 2010, Janani Dhinakaran wrote: > > Hello, >> >> I encountered a problem with the command >> recon-all -s jan -autorecon-all >> which is supposed to be for all the steps. A full

[Freesurfer] Problem with Autorecon all

Hello, I encountered a problem with the command recon-all -s jan -autorecon-all which is supposed to be for all the steps. A full reconstruction. INFO: set hdr.hist.orient to -1 ERROR: failure writing /usr/local/freesurfer/subjects/jan/mri/tmp-mri_motion_correct.fsl-5574/cor-2.img So I tried flip