[Freesurfer] mgz to dicom

Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for

[Freesurfer] defect 0

Hi All, I am running recon-all on a set of Diff images since last 2 days and it looks like FS stopped working.It says correcting defect 0 since yesterday afternoon. Any way to figure whats going on? Many Thanks Chikku #@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013 \n cp ../surf/l

[Freesurfer] Segstats

Dear FS team, Could any tell me what this numbers stands for in segstats. 3153 Right-Hippocampus 2953 2953 3254 Right-Amygdala 969 969 45 251 CC_Posterior 191 191 46 252 CC_Mid_Posterior 200 200 I am referring to this 31 53,32 54,45 251 etc is this the slice range? Many

[Freesurfer] volume called 001.mgz

Dear All, I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/fre

[Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'

Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to aseg_

[Freesurfer] Freesurfer-Error message

Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp

Re: [Freesurfer] Freesurfer-Error message

gt; > thanks > Bruce > > On Tue, 4 Sep 2012, Varghese Chikku wrote: > > Hi Bruce, >> Many thanks for you mail. >> Is this the command you referring to. >> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image1.**dcm >> -subjid test4 >

[Freesurfer] process exited abnormally

Dear all, I am trying to run recon all and FS will either exists with this * child process exited abnormally*...or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements

Re: [Freesurfer] process exited abnormally

Thanks Bruce,I am currently using 4GB ram and i5 intel processor. On 8 November 2012 15:08, Bruce Fischl wrote: > how much RAM does the VM have? > > On Thu, 8 Nov 2012, Varghese Chikku wrote: > > Dear all, >> I am trying to run recon all and FS will either exists w

[Freesurfer] Results Vary

Dear FS team, I processed two set of MRI data for a single patient,Thats BL scan and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine installed. Though I was expecting the same segstats,the results vary from Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but

[Freesurfer] Delay

Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,th

Re: [Freesurfer] Delay

Thanks Bruce,Its 64 bit. On 29 January 2013 15:12, Bruce Fischl wrote: > no, the longer time is probably because the mac version you are using is > 32 bit. > > cheers > Bruce > > > On Tue, 29 Jan 2013, Varghese Chikku wrote: > > Dear All,I ran a test subject

Re: [Freesurfer] Delay

Thanks Nick, Please find the attached. On 29 January 2013 19:33, Nick Schmansky wrote: > Chikku, > > Can you send us your recon-all.log and recon-all.cmd files? I'd like to > investigate why it ran so slowly. > > Nick > > > On Tue, 2013-01-29 at 06:53 +0100,

Re: [Freesurfer] Delay

#x27;d like to > investigate why it ran so slowly. > > Nick > > > On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: > > Dear All, > > I ran a test subject on VM and the process took 20 hrs to > > complete.But the same images on Mc pro took 58 hours.VM

[Freesurfer] cannot find eddy_correct

Dear Team, I tried to run dt_recon and the systems says *cannot find eddy_correct,Make sure FSL is installed*. So ,do I need to install the whole FSL package to run this. In Thanks Chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] CORRECTING DEFECT

Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processi

[Freesurfer] DEFECT 57

Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.l

[Freesurfer] libjpeg.so.62

Hi I am getting an error while using qdec. It says error while loading shared libraries ,libjpeg.so.62 cannot open shared object file No such file or directory I ran reconall with out any problem. Any idea, tx chikku ___ Freesurfer mailing list Fre

[Freesurfer] Qdec

Dear all, I am bit confused with the Qdec process. I finished recon all for 2 time points and want to create longitudinal data.From FS tutorial I learned to create within-subject templates for processing,which is running now with recon-all -base -tp -tp ... -all. Now,in an other link

[Freesurfer] --tablefile FILE error

Dear all, I am getting and error when trying this command, asegstats2table -s truetest1 truetest2 \ --segno 11 12 17 18 \ --tablefile FILE aseg.vol.table ERROR: output table name should be specified (use --tablefile FILE) child process exited abnormally command.I tried using Any Help Chikku

[Freesurfer] qdec.table

All, I have completed base and long runs for qdec longitudinal analysis.Now I am struggling to make qdec.table.dat.How can I do this. Tx chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Error

All, Any idea how can I sort this error, Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat... Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 1 ERROR: QdecDataTable::Load: problem parsing file /Users/chikkuvarghese/subject/qdec/qdec.table.da

[Freesurfer] Permission denied

Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied mkd

[Freesurfer] ELF class

Hi Fs Team, I am getting this errow while trying to use freeview. reesurfer@freesurfer-VirtualBox:~$ freeview freeview.bin: error while loading shared libraries: libjpeg.so.62: wrong ELF class: ELFCLASS32 Any Help Tx chikku ___ Freesurfer mailing list