[Freesurfer] procedure to install QDEC

2013-08-21 Thread Muhammad Naveed Iqbal Qureshi
Dear List members, Please guide me about installing qdec on Ubuntu. Best Regards, Muhammad Naveed Iqbal Qureshi please don't print this e-mail unless you really need to ___ Freesurfer mailing list Free

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Z K
Getting 'make' on Mac systems requires installing XCode AND Command Line Tool. You can download these from Apple using the following link: https://developer.apple.com/downloads FYI: This will require opening a developer account (free) if you do not already have one. -Zeke On 08/21/2013 12:3

Re: [Freesurfer] Out of memory error in selxavg3....

2013-08-21 Thread Douglas N Greve
Hi Joe, right now I do not have another solution to this. Why can't you split it up? doug On 08/20/2013 04:36 PM, Joseph Andreano wrote: > I'm trying to run selxavg on a dataset with a rather large number (930) of > timepoints. Selxavg keeps erroring out with an 'out of memory. Type HELP > MEM

Re: [Freesurfer] Estimated Total Intra Cranial Vol

2013-08-21 Thread Douglas N Greve
Hi Stefano, the ICV is not computed by counting voxels. See this page: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV doug On 08/20/2013 02:34 PM, std...@virgilio.it wrote: > Hi list. > > I'm looking mailing list to find responce to this question. > > "Estimated Total Intra Cranial Vol" obtained

Re: [Freesurfer] fcseed-sess error

2013-08-21 Thread Douglas N Greve
OK, the problem is that this subject has very small ventricles and no ventricle voxel exceeds 95% partial volume fraction. To get around this you can configure the seed to allow a smaller PVF, say 75%, with the "-fillthresh .75". Specify -fillthresh AFTER -vcsf You will have to re-run it for al

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Douglas N Greve
try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.lion On 08/21/2013 01:43 PM, Pedro Rosa wrote: > Both are mountain lion. > > Pedro Rosa > > On 21 Aug 2013, at 01:11 PM, Douglas N Greve > wrote: > >> right the wmparc.mgz is not affected. Is your mac mo

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Pedro Rosa
Both are mountain lion. Pedro Rosa On 21 Aug 2013, at 01:11 PM, Douglas N Greve wrote: > > right the wmparc.mgz is not affected. Is your mac mountainlion or leopard or > snowleopard? > > > On 08/21/2013 01:05 PM, Pedro Rosa wrote: >> Hi, >> I use two Macs. One with OS X 10.8.4 and one with

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Douglas N Greve
right the wmparc.mgz is not affected. Is your mac mountainlion or leopard or snowleopard? On 08/21/2013 01:05 PM, Pedro Rosa wrote: > Hi, > I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. > I suppose that if the problem is with the mri_segstats the wmparc.mgz should > not have b

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Pedro Rosa
Hi, I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. I suppose that if the problem is with the mri_segstats the wmparc.mgz should not have been affected. I am correct? However, if I want to extract stats from volumetry/surface perhaps I will find myself in trouble. Pedro Rosa On 2

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Douglas N Greve
Yea, I don't think mac os comes with it by default. If you want to use this functionality, you'll have to install it. Zeke, can you point him in the right direction? to get back to your original problem, I think I gave you the wrong version of mri_segstats. What version of mac os do you have?

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Pedro Rosa
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks Pedro Rosa On 21 Aug 2013, at 10:51 AM, Douglas N Greve wrote: > > You will need to add the "make" program to your path. In Linux, it is > usually in /usr/bin > doug > > > On 08/20/2013 10:12 PM, Pedro Rosa wrote: >

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Pedro Rosa
Hi, I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Pedro Rosa On 20 Aug 2013, at 12:34 PM, Douglas N Greve wrote: > They should be fine. BTW, you can run > > recon-all -s subject -make all > > and i

Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

2013-08-21 Thread Douglas N Greve
You will need to add the "make" program to your path. In Linux, it is usually in /usr/bin doug On 08/20/2013 10:12 PM, Pedro Rosa wrote: > Hi, > Sorry for that! > I tried using several targets: all / autorecon1-2-3, and for all I get 'make: > command not found.' > I used recon-all -s subject -