[Freesurfer] repeat: trouble loading nifti files

Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137

Re: [Freesurfer] repeat: trouble loading nifti files

Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May 2013, Akshay wrote: > Hi All, > > I am re-posting this question since there was no response to my previous > attempt. > > I have a problem conforming certain nifti files, the following is the > log when i try to co

[Freesurfer] Fwd: Re: repeat: trouble loading nifti files

mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 On 5/7/13 2:55 PM, Bruce Fischl wrote: > can you send me the full mri_convert command line that is run? > On Tue, 7 May 2013, Akshay wrote: > >> Hi Bruce >> >> Please find the file attached >> >> Best, >> >> Akshay >> >> >> O

Re: [Freesurfer] recon-all completes without all the info..

On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked be

[Freesurfer] TrackVis "either end" command

Dear Freesurfer/TrackVis experts, I am using the following command in a batchfile to identify tracks counts between dozens of preset ROIs. track_vis DATAPATHtob0.trk -roi DATAPATHTOROI1.nii -roi2 DATAPATHTOROI2.nii -o PATHTOOUTPUT.trk > OUTPUT.txt -nr', i, j, i, j, i, j Is there a line command

Re: [Freesurfer] TrackVis "either end" command

Hi Catherine, This question might not fit in freesurfer mailing list but I'll answer here anyway - Unfortunately, for the command-line track_vis, there is no such option. Ruopeng On May 7, 2013, at 9:53 AM, "Chu, Catherine,M.D." wrote: > Dear Freesurfer/TrackVis experts, > > I am using the

Re: [Freesurfer] Fwd: Re: repeat: trouble loading nifti files

Hi Akshay the -cs flag specifies the voxel size, not the field of view, so you are creating a volume with 256mm voxels! Try --cw256 instead. cheers Bruce On Tue, 7 May 2013, Akshay wrote: > > mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 > > On 5/7/13 2:55 PM, Bruce F

Re: [Freesurfer] recon-all completes without all the info..

Hi Sudhin, You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces and all the cortical/sub-cortical measures. -Louis On Tue, 7 May 2013, Sudhin A. Shah wrote: On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.

[Freesurfer] segfault during rfx with mri_glmfit

hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask $mask_

[Freesurfer] Qdec analysis for only particular regions of interest?

Hello, I'm new to Freesurfer and I was wondering whether anybody could tell me what steps I need to do in Freesurfer in order to conduct the following analysis? I would like to know which sex differences in cortical thickness (subjects 12-18 years old) are present in the 12 year olds already. I'v

[Freesurfer] NFS v4 on CentOS 5.4 or Red Hat 6.2

Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in Red Hat could not write or read. Is it a kn

[Freesurfer] Segmentation fault (core dumped) again in the BETA version

Hi Freesurfer experts, I've got Ubuntu version 13.04 installed on my computer, and after I saw the post : "http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html"; I d ecide to install the BETA version freesurfer-Linux-centos6_x86_64-stable-pub-v5. 3.0-BETA.tar.gz as adviced. I st

[Freesurfer] Neuroimaging Research Technician

* * * * ** *A Neuroimaging Research Technician position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center. * * The Neuroimaging Research Technician will provide technical support for image preprocessing and analysis (using programs such a

Re: [Freesurfer] recon-all completes without all the info..

Is there 1 command line? I used to just run the 1 line. On May 7, 2013, at 10:19 AM, "Louis Nicholas Vinke" wrote: > Hi Sudhin, > You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces > and all the cortical/sub-cortical measures. > -Louis > > On Tue, 7 May 2013, Sudhi

Re: [Freesurfer] recon-all completes without all the info..

Yes, the -all flag will run autorecon1, autorecon2, and autorecon3. recon-all -all -i -s For that uncompleted subject you have though if sounds like you just need to run autorecon2 and 3 recon-all -autorecon2 -autorecon3 -s On Tue, 7 May 2013, Sudhin A. Shah wrote: > Is there 1 command lin

[Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jone

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Nicola and Nick, Can you try the tkmedit.bin found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ copy it to the freesurfer/tktools directory (the wrapper script 'tkmedit' in the bin dir calls the binary in the tktools dir). I'm hoping the problem you ar

Re: [Freesurfer] Segmentation fault (core dumped) again in the BETA version

Martina, Can you send me the recon-all.log file? Nick On Tue, 2013-05-07 at 17:38 +0200, martina.andell...@fastwebnet.it wrote: > Hi Freesurfer experts, > I've got Ubuntu version 13.04 installed on my computer, and after I saw the > post > : "http://www.mail-archive.com/freesurfer@nmr.mgh.harv

Re: [Freesurfer] Issues with Cluster generation

Hi Joshua, there are several issues. First, you are using a threshold of p<.0001 which is pretty severe. It works for the tutorial, but you need to understand what this threshold is and pick one appropriate for your data. Second, you are only doing 5 iterations. You need to be doing something

Re: [Freesurfer] ROI analyses

On 05/07/2013 05:21 AM, Tudor Popescu wrote: > Hi Doug, > I was just wondering whether you received my last email, with > follow-ups on your answers. Sorry for the multitude of questions - as > ever, I really appreciate the help! > Best wishes, > Tudor > > On 4 May 2013 20:31, Tudor Popescu

Re: [Freesurfer] segfault during rfx with mri_glmfit

Hi Alex, is it actually running out of memory? Otherwise, nothing comes to mind. If you tar up all the inputs and drop them at our file drop I'll take a look. doug On 05/07/2013 10:24 AM, Alex Kell wrote: > hi freesurfers, > > i am running into a segfault whenever i try to use mri_glmfit to run

Re: [Freesurfer] Probably activation due to vessels

When you use -per-session, it uses the first image of the first run as the template. All runs are motion-corrected to this template, and the template is registered to the anatomical. In this way, all images get aligned to the anatomical. The -per-session command means that there is only one tem

Re: [Freesurfer] Using FSL matrix for Talairach transform

Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure what regdat2xfm is doing. doug On 05/07/2013 12:42 PM, Johannes Klein wrote: > Dear all, > I have some tricky subjects that I cannot get to register properly with the > standard Talairach process, or even the use-mritotal op

[Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scan

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der Ko

Re: [Freesurfer] segfault during rfx with mri_glmfit

hi doug, thanks for the quick response. i got it to work -- apparently the 5.1.x developmental version i was using had some problem in mri_glmfit. when i switched to the stable 5.1 version (build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0) it ran perfectly smoothly. unfortunately,

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Hi Nick, It complains about libtix8.1.8.4.so missing. I add $FREESURFER_HOME/lib/tcltktixblt/lib/ to the LD_LIBRARY_PATH variable, but it still complains about the license and does not open bert. Tried the dev build and 5.3 beta, which also fail at the license. Why not remove the requirement

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facility NIMH/NIH/DHHS souheil.in...@nih.gov On May 7, 20

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

no, of course not :) On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi Bruce, Out of curiosity and for reference for my users, do you have a paper on the T2 or FLAIR assisted segmentation? Cheers, Souheil - Souheil Inati, PhD Staff Scientist FMRI Facilit

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl wrote: > no, of course not :) > > On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] > wrote: > >> Hi Bruce, >> >> Out of curiosity and for reference for my users, do you have a paper on the >> T2 or FLAIR assisted segmentation? >> >> Chee

[Freesurfer] Qdec and GLM ROI analysis

I am interested ing doing a group surfaces analysis like that specified in: ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis, or http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28cortical%29%7C%28thickness%29 but I want to limit the analysis to a specific

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description in Andre's multi-echo mprage paper Bruce On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl wrote:

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Hi Nick, sorry - I should have been more specific. I get the same error with *any* FS command or script (recon-all, mri_glmfit), so in effect ever since the upgrade I am not able to use FS at all. The tkmedit patch you posted is only missing a library on my system though, which I can fix - so

[Freesurfer] Freesurfer segmntation for ICBM or Colin27

Hello FreeSurferusers, Has anyone processed ICBM or Colin27 template through Freesurfer V5.0.0 (or higher) or does anyone know if such data is available in public database? Thank you. Priyanka Bhatt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

Re: [Freesurfer] Freesurfer segmntation for ICBM or Colin27

Hi Priyanka, You can download it from the Surfrend web page and then recon-all it with the version you want (don`t use the -i, just the -s with the subject name you choose). Regards, Gari On May 7, 2013 10:56 PM, "Priyanka" wrote: > Hello FreeSurferusers, > > > Has anyone processed ICBM or Coli

[Freesurfer] error: can't allocate region / Cannot allocate memory

Dear FreeSurfer experts, I am trying to create a template for a longitudinal analysis. For each subject I have 7 time points. The resolution of the T1 images is 1.0x0.98x0.98 mm. The first step (i.e. the cross-sectional processing) finished without errors for all participants for all time poin

Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

Nick, Can you request another license file? The info in the .license file that is shown in your email below does not appear to be valid. There is no record of it in our license system (or more accurately, number 14743 has different data than that shown). Was it obtained recently? Our current l

[Freesurfer] ICV

Hi, I understand that ICV is an estimated measure based on a standard talairach transformation; however, I want to know how freesurfer is defining intracranial volume (i.e., is this a representation of everything within the cranium as the name implies or is it an estimate of total brain volume, whi

Re: [Freesurfer] ICV

It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV and/or Buckner et al. (2004) NeuroImage 23:724-738. "Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align

[Freesurfer] Google Talk 使用邀请

--- yufeng huang邀请您使用 Google Talk。 如果您已经拥有 Google 帐户，请登录 Gmail 并接受此聊天邀请： http://mail.google.com/mail/b-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7UCP0 要注册 Google 帐户并开始使用 Google Talk，您可以访问： http://mail.google.com/mail/a-60fdfa5

[Freesurfer] How to show the result with more color by using tksurfer?

In my study, I have to show more than 10 functional condition with different colour, I want to know how to define a certain colour in a certain functional condition, and show it using tksurfer. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

[Freesurfer] Issues in version 5.2

I apologize for the trivial question, but for me is urgent to understand if the issues that affect the version 5.2 are referred also to TRACULA and hippo-subfield.Do you advice me to cancel my analysis performed by 5.2. and re-run it by new version 5.3? Are the results obtained with version 5.2