Re: [Freesurfer] problem with skullstrip- shoulders and neck remaining

 Hi JuliaDoes the stuff left around mess anything up?  You are probably fine running it that wayBruceOn Nov 8, 2011, at 9:30 PM, Julia Hill wrote:Hi there,I am having difficulties with one of my images.  On first inspection, freesurfer had performed a bad skull strip, leav

Re: [Freesurfer] Loading Data Table

open the table in a text editor and add a line at the end of the file. n. On Tue, 2011-11-08 at 15:11 -0800, Dusan Hirjak wrote: > Dear Freesurfer experts, > > I created a data table with 25 subjects, 3 discrete and 6 continuous > factors. Then I tried to load my data table in qdec. However, an

[Freesurfer] Loading Data Table

Dear Freesurfer experts, I created a data table with 25 subjects, 3 discrete and 6 continuous factors. Then I tried to load my data table in qdec. However, an "error loading the data table" occured. I received an automatic notice generated at the end of the terminal as following, "This line (m

Re: [Freesurfer] Compilation warnings as errors

see ./configure --help for flags on how to point the build at your libs. also see: https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide note that typically we recommend building the 3rd party packages from scratch, as its hard to know whats really installed on your system already (see the R

Re: [Freesurfer] selxavg3 out of memory

Hi, I had the same problem with the matlab 32-bit version. Try to install the (recent) matlab 64-bit on your Mac. cheers, Erhan 2011/11/8 Douglas N Greve : > It is "only" trying to allocate 1.3GB, so it might be that matlab does > not have enough memory when it runs. Is there  a way to give mat

Re: [Freesurfer] Compilation warnings as errors

I forgot to attach the error log in the previous email. My sincere apologies. So here it is: In file included from ../../../src/freesurfer-src/dev/utils/cpputils.cpp:42: ../../../src/freesurfer-src/dev/include/MRISOBBTree

Re: [Freesurfer] Visualization of FreeSurfer-defined ROI

You can merge different labels into one big label with mri_mergelabels. If you want an annotation with those labels, you can use mris_label2annot to recombine your favorites back into a annotation. doug Simmons, Andy wrote: > Dear Doug, > > Thanks very much for this - that worked perfectly for o

Re: [Freesurfer] Compilation warnings as errors

I tried your suggestion for compiling the dev release and it worked. Now, I am getting compilation errors. It seems that the vnl include directory is not found (althought it exists in my system under /usr/include/vxl/core). I tried to symlink it under /usr/include but then I encounter other proble

Re: [Freesurfer] selxavg3 out of memory

It is "only" trying to allocate 1.3GB, so it might be that matlab does not have enough memory when it runs. Is there a way to give matlab more memory? If not, you can re-make your analysis with -acfbins 10. The default is 30, so this will reduce the needed memory by a factor of 3. I don't thin

Re: [Freesurfer] Visualization of FreeSurfer-defined ROI

Dear Doug, Thanks very much for this - that worked perfectly for one region. How would I display a series of labels simultaneously, for example superiorfrontal, superiorparietal and superiortemporal ? Best wishes, Andy -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.h

Re: [Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1

Sorry for incremental updates: c) you can pass the -flirt-motioncor flag to recon all to revert to the old way (using flirt) If your scans are decent quality I would recommend b) as it is unclear if averaging actually helps. -Martin On Tue, 2011-11-08 at 13:45 -0500, Martin Reuter wrote: > Hi J

Re: [Freesurfer] Visualization of FreeSurfer-defined ROI

You can run mri_annotation2label to break the annotation up into smaller labels, then display a single label in tksurfer (you can load it from the GUI or on the cmd line with -label). doug Simmons, Andy wrote: > > Dear Doug, > > > > What would the equivalent process for a surface rather than

Re: [Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1

I see you have only two inputs. 4GB should be enough. Are you running a lot of other stuff that takes up memory? -Martin On Tue, 2011-11-08 at 13:35 -0500, Jennifer Addicks wrote: > Hello, > > > I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 > with no issues. I recently in

Re: [Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1

Hi Jennifer for question 2. You run out of memory. How many within session inputs are you trying to motion correct? You can a) try downsample your hi-res images before processing b) try to only select a single input to recon-all instead of averaging inputs. Best, Martin On Tue, 2011-11-08 at

Re: [Freesurfer] Fwd: A question about recon-all

Or you can delete the IsRunning file in the scripts directory (make sure it's not actually running!). doug Bruce Fischl wrote: > Hi Nooshin, > > you can jsut add -no-isrunning to the command line if you are sure the > process has finished. This happens when it was killed in a strange way > (i.e

[Freesurfer] Upgraded Freesurfer: old version no longer working + recon-all error in 5.1

Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset and I am now having various issues with both FreeSurfer versions. 1. For Version 4.5, I path the free

Re: [Freesurfer] norm.mgz

Hi Yumi the mri_ca_normalize command creates the norm.mgz. You should be able to find it either in the scripts/recon-all.cmd or scripts/recon-all.log cheers Bruce On Tue, 8 Nov 2011, YUMI MAEDA wrote: > Hi, > > I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I > had to

Re: [Freesurfer] norm.mgz

Hi Yumi, just rerun recon-all with the -canorm flag on that subject Best, Martin On Tue, 2011-11-08 at 13:18 -0500, YUMI MAEDA wrote: > Hi, > > I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I > had to delete mri/norm.mgz. > > Is there any way that I can just creat no

Re: [Freesurfer] Fwd: A question about recon-all

Hi Nooshin, you can jsut add -no-isrunning to the command line if you are sure the process has finished. This happens when it was killed in a strange way (i.e. if you hit ctrl-c during processing) cheers Bruce On Tue, 8 Nov 2011, nooshin n.zade wrote: Dear Freesurfer Group I have found

[Freesurfer] norm.mgz

Hi, I had 2 bad blocks in freesurfer/subject/mri/norm.mgz on my disk drive. I had to delete mri/norm.mgz. Is there any way that I can just creat norm.mgz? or do I need to do recon-all? thank you. YUMI ___ Freesurfer mailing list Freesurfer@nmr.mgh.

[Freesurfer] Fwd: A question about recon-all

Dear Freesurfer Group I have found a problem in running my subjects. With "recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N?" I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject

Re: [Freesurfer] Recon-all step estimate

You can look at the touch files in the touch directory. I've attached a script that I use called rastat that does this. When I was the main recon-all programmer, each process would create a touch file when it completed, but I don't know if newer versions continue to do so. You can also look at

Re: [Freesurfer] Recon-all step estimate

Hi Pedro, Here's a script that (I think) will do what you're looking for: http://web.mit.edu/mwaskom/stuff/recon_status I hope it's useful Michael 2011/11/8 Bruce Fischl > the recon-all.cmd file I think gets written to the scripts dir with every > command that is run > > Bruce > > On Tue, 8

Re: [Freesurfer] Recon-all step estimate

the recon-all.cmd file I think gets written to the scripts dir with every command that is run Bruce On Tue, 8 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for reco

[Freesurfer] Recon-all step estimate

Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] Resize window using Tcl command

Hi Jeff sorry, I don't know of a way to do this. Bruce On Mon, 7 Nov 2011, Jeff Sadino wrote: Hello, I was wondering if there is a Tcl command to resize the window.  I saw this thread, but it would not work on my computer, and I don't see any documentation in the tkmedit tcl scripting guide

Re: [Freesurfer] surface cnr

Hi Mike, I think mris_ms_surface_CNR lets you use multiple input volumes and computes the Mahalanobis distance, while mri_cnr does the same thing but for each volume independently. I think they both have options for doing linear fitting across the boundary and looking at the slope. Sorry, they

[Freesurfer] Interpretation of the curvature analysis

Dear Freesurfer Users! Is it wise to interpret the increased curvature index in neurodegenerative disorders as a more expressed atrophy (which manifests as a flattening)... I am just doubting because I have never worked with curvature analysis previously and its interpretations in different art

Re: [Freesurfer] Freesurfer on CentOS 6.

It will work fine on centos 6. N. On Nov 8, 2011, at 7:07 AM, SHRIKANTH KULASHEKHAR wrote: > Hi, > > The recommed platform for Freesurfer is CentOS 4. Can anyone advice on how > stable the Freesurfer v5.1.0 will be on CentOS 6 ? > We need this information to setup a new server. > > Thanks

[Freesurfer] Freesurfer on CentOS 6.

Hi, The recommed platform for Freesurfer is CentOS 4. Can anyone advice on how stable the Freesurfer v5.1.0 will be on CentOS 6 ? We need this information to setup a new server. Thanks in advance. Shrikanth ___ Freesurfer mailing list Freesurfer@nmr.