Re: [Freesurfer] paradigm file - condition codes

The easiest way to solve this problem is to assign one or two events to be the missing conditions. This should not change any of the results. Make sure that you do not include these subjects if you want to do tests on the missing conditions. doug On 12/06/2013 04:24 PM, Eryilmaz, Huseyin Ha

Re: [Freesurfer] LGI　error

This is bizarre. The only other explanation is that the "you" who creates a file is not the same "you" who tries to delete it (it all sounds rather metaphysical:). Can you have that unix call run some unix commands to see who you are? Another thing is to make a unix command that creates a dele

Re: [Freesurfer] Segmentation misses sulci in posterior

ok, I'll take a look On Fri, 6 Dec 2013, Eve M. LoCastro wrote: > Thank you, Bruce. I have uploaded the 001.mgz here: > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=8xy0v6sj50o > > And the segmentation (aparc+aseg.mgz). > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7ibj59tsn6p > > > If there

Re: [Freesurfer] Segmentation misses sulci in posterior

Thank you, Bruce. I have uploaded the 001.mgz here: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=8xy0v6sj50o And the segmentation (aparc+aseg.mgz). http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7ibj59tsn6p If there are any other files of interest, please let me know. Much thanks, Eve LoCast

Re: [Freesurfer] Segmentation misses sulci in posterior

Hi Eve if you upload the subject we will take a look Bruce On Fri, 6 Dec 2013, Eve M. LoCastro wrote: We have a T1 image that has been problematic to process. This patient has thicker skull and extensive hypointensities in the white matter along with big vents. Skullstripping by modifying th

Re: [Freesurfer] LGI　error

Hi Doug, I already tried changing all the occurrence of "rm" to "rm -f" in load_mgh.m, but it did not change anything. The error message remains identical. The other strange thing is that, as the owner of the file, I have read and write permission on /tmp/tp9204736418620864.load_mgh.681685.mg

[Freesurfer] paradigm file - condition codes

Hi all, I'm trying to run a simple event-related analysis, in which the conditions are determined based on subject's performance. It is possible that some of the predicted conditions do not appear in the paradigm file (mostly because the subject performs well). In these cases, do I need to renu

[Freesurfer] Segmentation misses sulci in posterior

We have a T1 image that has been problematic to process. This patient has thicker skull and extensive hypointensities in the white matter along with big vents. Skullstripping by modifying the watershed parameter either leaves too much skull or removes entire chunks of the brain in this Siemens

Re: [Freesurfer] mri_convert Siemens .IMA error

Can you upload a single dicom file to me? One should be enough On 12/06/2013 04:02 PM, Paul Rasser wrote: >> >> We are using Freesurfer5.3 on os x 10.8. >> > > > On 6 Dec 2013, at 2:19 pm, Douglas Greve > wrote: > >> >> This may be a known problem. What

Re: [Freesurfer] trac-all version 5.3 crash

Jon, I tested this by completely removing XQuartz from my machine (which deletes /usr/X11/lib/libX11.6.dylib). I then ran freesurfer and got the same error as you. I then reinstalled XQuartz, which restored the /usr/X11/lib/libX11.6.dylib file, reran freesurfer, and everything worked fine. S

Re: [Freesurfer] LGI　error

OK, if yours had load_mgh in the file name, then it is definitely from load_mgh.m. Strange that the one below does not have that. I think know what is going on. The rm command will sometimes ask if you want to remove a file, esp if you don't have write permissions. In general, if you create a

Re: [Freesurfer] mri_convert Siemens .IMA error

> We are using Freesurfer5.3 on os x 10.8. > > On 6 Dec 2013, at 2:19 pm, Douglas Greve wrote: > > > This may be a known problem. What version of FS are you using and what is > your platform? > doug > > > > >> On 12/5/13 3:26 PM, prasser wrote: >> Thanks, but the orientation shift appear

Re: [Freesurfer] bad skull strip but pial and white matter borders ok

nope, you should be all set cheers Bruce On Fri, 6 Dec 2013, krista kelly wrote: > Hi, > I have one subject with a poor skull strip - much of the skull and neck are > left over. I have used one of the automated processes to remove the problems > areas and I now the skull strip is fine. If the tal

[Freesurfer] bad skull strip but pial and white matter borders ok

Hi, I have one subject with a poor skull strip - much of the skull and neck are left over. I have used one of the automated processes to remove the problems areas and I now the skull strip is fine. If the talarairching, pial and white matter borders, and labels were fine, do I need to rerun any of

Re: [Freesurfer] LGI　error

Many thanks Doug for your reply! For me it happened every time the lGI was launched, but none of the other freesurfer commands that I used on this system ever resulted in a similar error, everything else is perfectly fine. The process can hang for days without going further, it will never come

Re: [Freesurfer] Freeview question

Thanks Bruce. On Fri, Dec 6, 2013 at 2:51 PM, Bruce Fischl wrote: > Hi Alan > > yes, this one: > > https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf > > although it is based on the CMA manual definitions > > cheers > Bruce > > On Fri, 6 Dec 2013, Alan Francis wrote: > > Than

Re: [Freesurfer] LGI　error

How often does it happen? Does the process just hang or does it produce the correct results (eventually)? I don't think it is related to load_mgh.m because the temporary filename would be different. However, it is consistent with the temp files used with nifti reading and writing. Does that ha

Re: [Freesurfer] Freeview question

Hi Alan yes, this one: https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf although it is based on the CMA manual definitions cheers Bruce On Fri, 6 Dec 2013, Alan Francis wrote: Thanks Louis and Bruce. One more question: Is there any paper that outlines the boundaries of

Re: [Freesurfer] Freeview question

Thanks Louis and Bruce. One more question: Is there any paper that outlines the boundaries of the FreeSurfer version of the Hippocampus. thanks so much, Alan On Thu, Dec 5, 2013 at 3:49 PM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Alan, > You can use mri_binarize to pull i

Re: [Freesurfer] empty norm.mgz file {Disarmed}

if you upload the subject I'll take a look On Fri, 6 Dec 2013, Adam Mezher wrote: Hi Bruce, I'm not too sure why it is blank, the talairach.lta and .xfm look fine to me (but I could be mistaken, see below). The brainmask.mgz is actually quite grainy but I'm not sure if that alone would contri

Re: [Freesurfer] empty norm.mgz file {Disarmed}

Hi Bruce, I'm not too sure why it is blank, the talairach.lta and .xfm look fine to me (but I could be mistaken, see below). The brainmask.mgz is actually quite grainy but I'm not sure if that alone would contribute to this issue. # transform file transforms/talairach.lta # created by vhasfcngp o

Re: [Freesurfer] empty norm.mgz file {Disarmed}

Hi Adam yes, this is mri_cc in an infinite loop. This bug is fixed in 5.3, but it won't generate anything reasonable with an empty input volume. Do you know why it is blank? Is the brainmask.mgz ok? The talariach.lta and .xfm? cheers Bruce On Fri, 6 Dec 2013, Adam Mezher wrote: > Hi all, >

[Freesurfer] empty norm.mgz file {Disarmed}

Hi all, I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that

Re: [Freesurfer] LGI　error

Hi Kangchen, I also had the same error recently on a unix machine, but I unfortunately did not find the solution and some help would be greatly appreciated. I think that the bug is due to the fact that make_outer_surface.m calls MRIread.m, which calls load_mgh.m and that something gets wrong a

Re: [Freesurfer] Significance of value in sig.nii file under 'polar' directory

you can try doing the same thing using the -per-session flag. The problem is that it tries to use the motion correction to correct across sessions, which may or may not work doug On 12/06/2013 12:37 PM, Cesar Echavarria wrote: > I want to do the analysis in native space. I saw in a past thread

[Freesurfer] trac-all version 5.3 crash

Hi freesurfer experts, I've recnetly upgraded to freesurfer 5.3 (lion) 64bit version on our Mac Pro when I run trac-all -prep, I get the following error: writing to /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 > /Stud

Re: [Freesurfer] Significance of value in sig.nii file under 'polar' directory

I want to do the analysis in native space. I saw in a past thread that the native space analysis cannot make use of the -per-run flag. Does this still hold? If so, is there another way to get fsig.nii file after analyzing each session separately in native space? Thanks for your help! Cesar On T

Re: [Freesurfer] label to curv .mgh

Not sure. What do you mean by "not getting there"? You can also use mri_label2label with the --outmask option doug On 12/05/2013 02:47 PM, Gregory Kirk wrote: > > hello, trying to convert a medial wall label to a curv format .mgh file > > running > > mris_convert --label lh.Medial_wall.label lh.

Re: [Freesurfer] refeventdur in mkanalysis-sess

It has no influence on the design matrix. It controls a scaling factor so that the beta value (regression coef) will equal to the height of the hemodynamic response when viewed in the raw data. This sounds like it should be simple but it is actually quite tricky. The bottom line is that it is

Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after recon-all

it comes up upside down in tksurfer without pressing any buttons or anything? Never seen that before - if you upload the subject I'll take a look cheers Bruce On Fri, 6 Dec 2013, Xiaojun.Huang wrote: hi all, I am processing the 3D PD patients brain now . After recon-all running, the segment

[Freesurfer] infant template

Dear Freesurfer experts, I'm involved in the neonatal research (infants less than 1 year of age). I tried running the recon-all command, however it fails and I get error messages at the Talriach registration step. Is there any way in which I can incorporate our own custom infant atlas or template

[Freesurfer] CUDA problem with FreeSurfer 5.3.0 on CentOS6

Hi, We have encountered a serious problem running recon-all FREESURFER_HOME: /opt/freesurfer-530 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.el6.x86_64 x86_64 The entire command-line executed: /opt/free

[Freesurfer] LGI　error

Dear all， When I run "recon-all -s ${subject} -localGI", it appear "rm: remove regular file `/tmp/tmp4653077.mgh'? ". Then, I write yes, however, it didn't response anyway. How shold I do next? Thank you! The echo for the process is followed -- running subject Emotion_xun

[Freesurfer] v5.3.0 nu.mgz, -1): could not open file

Hi I am trying to Install Freesurfer V 5.3.0 on a cluster in Southampton University but when I run a job on the cluster it always fails. I have checked all configurations files, I have looked to your manual many times but still can not figure out the problem. Could you please help me out with