[Freesurfer] Bus error when trying to launch tksurfer

Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a bus error. Please see the following script: DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial subject is bert hemiis rh surface is pial surfer: current subjects

Re: [Freesurfer] Bus error when trying to launch tksurfer

Daer Claire The bus error might be related to Xquartz. Installing Xquartz again solved the issue on most Intel-based Macs. Cheers Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University

Re: [Freesurfer] Bus error when trying to launch tksurfer

Hi Claire what version are you using? And what is your hardware and software environment? RAM, OS version, etc? Bruce On Mon, 20 Oct 2014, Claire Morley wrote: Good Morning, I have now been able to get the testing command: tksurfer bert rh pial to run, but it stops midway and issues a

[Freesurfer] Do not have 'recon edit' button! Please help!

Dear mailing list, I am really stuck here.. Please can someone tell me why I cannot find the recon edit button on freeview! I am not sure if the version of Freesurfer I have downloaded is old, or I have done something wrong, or I am just blind.. But I cannot find the 'recon edit' button in

Re: [Freesurfer] Do not have 'recon edit' button! Please help!

Hi Areti what version of freeview are you using? Bruce On Mon, 20 Oct 2014, Smaragdi A. wrote: Dear mailing list, I am really stuck here.. Please can someone tell me why I cannot find the recon edit button on freeview! I am not sure if the version of Freesurfer I have downloaded is old,

Re: [Freesurfer] Do not have 'recon edit' button! Please help!

Hi Bruce, Thank you for getting back to me! Its the 1.0 version, downloaded from the website. Thanks, Areti On 20/10/2014 14:24, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Areti what version of freeview are you using? Bruce On Mon, 20 Oct 2014, Smaragdi A. wrote: Dear mailing

[Freesurfer] unpacksdcmdir

Hi , The command unpacksdcmdir is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs? Thanks, Moahmad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] unpacksdcmdir

Hi Mohamad You could convert the Dicoms in other s/w to .nii and then read them. Maybe Bruce and Doug have more elegant solutions Hth Shantanu On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote: Hi , The command unpacksdcmdir is only used to unpack Siemens DICOM files, How can I

Re: [Freesurfer] GLM contrast vector for continuous variable interaction

I think this is the contrast you need 00000000 0.50.50.50.5 - 0.5 -0.5-0.5-0.5 On 10/19/2014 06:33 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three

Re: [Freesurfer] unpacksdcmdir

dcmunpack will unpack any dicoms On 10/20/2014 11:21 AM, Shantanu Ghosh wrote: Hi Mohamad You could convert the Dicoms in other s/w to .nii and then read them. Maybe Bruce and Doug have more elegant solutions Hth Shantanu On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:

Re: [Freesurfer] adding time points to longitudinal base template

Hi Koushik, no, I cc the list, maybe someone has done tests or seen papers. I read somewhere on atlas construction, that 10 images are fine, but that is cross subject. Here we only have small changes within subject, so from my experience less are fine , BUT - 2 of course are not enough: in 2

Re: [Freesurfer] adding time points to longitudinal base template

Thanks for your response Martin. From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 12:56 PM To: Govindarajan, Koushik Athreya Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template Hi Koushik, no, I cc

[Freesurfer] Longitudinal prediction

Dear FreeSurfer Experts, How could the longitudinal analysis be performed in order to show whether a parameter at time 1 is predictive of changes in cortical thickness over time ? and can thecorresponding regions be shown in FreeSurfer ? In a statistical analysis, as we see it, we must

Re: [Freesurfer] unpacksdcmdir

Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). when I used this command on a my data set it gives me an error for certain

Re: [Freesurfer] unpacksdcmdir

did you try dcmunpack? On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote: Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files).

Re: [Freesurfer] unpacksdcmdir

Sorry I did not notice that this is a different command. I will try it now. and I will let you now Thanks a lot From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve

[Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

Dear Freesurfer Experts, I have a label file of a number of ROI's I've made based on a mask. I'm trying to get an idea of what cluster are significant within a focused region of the label file. To make the correction a little less sever, I pre-computed some monte-carlo values using mri_mcsim

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

what do you mean it has trouble understanding? What is your command line and terminal output. Also, are you following these instructions? https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 10/20/2014 03:50 PM, Thomas DeRamus wrote: Dear Freesurfer Experts, I have a label

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag.

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

You should not spec --sim. If you do not, does it work? doug On 10/20/2014 04:10 PM, Thomas DeRamus wrote: I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

It does not I'm afraid. The error I get says the following: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces ERROR: must spec --sim Does the same if I remove the --sim-sign

[Freesurfer] (no subject)

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ?

[Freesurfer] Parenchyma/CSF

Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ?

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

you need to add --cache threshold sign (and don't use --sim-sign or --sim) On 10/20/2014 05:42 PM, Thomas DeRamus wrote: It does not I'm afraid. The error I get says the following: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir

Re: [Freesurfer] GLM contrast vector for continuous variable interaction

Thanks Douglas. That is exactly what I wanted. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

That one gives the following error: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cache 2 abs cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd

Re: [Freesurfer] skewed CT viewed in tkregister2

Hi Mia, sorry for the delay. I think the problem is that the geometry info in the CT header is incorrect. The directions are not orgthogonal, and, when made orthogonal, the pixel sizes look wrong. How did you create ct.mgz? doug On 10/12/2014 08:52 PM, Borzello, Mia wrote: Hi, Any insight

Re: [Freesurfer] unpacksdcmdir

Hi Doug, I ran the following command line dcmunpack -scr dicoms dir path in my script and it gives me a list of the run/series. How can I save this list as a log file. I tried to add the flag -targ and the flag -log but it gives me an error and asked me to specify the series run numbe? Any

Re: [Freesurfer] T1 white matter segmentation

In this case if I don't have T1 MPRAGE can I use any other available T1 like sag_T1 or Ax_T1 (the name of run/series after using unpacksdcmdir)? or it is imperative to use T1 MPRAGE for the segmentation. Bests, From: