Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

Hi Zeke, I tried the is new version. Now I am getting: mri_coreg: /lib64/libuuid.so.1: no version information available (required by mri_coreg) mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_coreg) mri_coreg: /usr/lib64/libstdc++.so.6: version

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

There were some recent changes in the build that eliminated the necessity for that library. Casper, can you try using this most recent version and let me know if it works? ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg Thanks, -Zeke > Zeke, is

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

Red Hat Enterprise Linux Server release 5.9 (Tikanga) freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Caspar 2015-11-23 14:37 GMT-05:00 : > What system are you running on? Also, what are the contents of your > build-stamp.txt file (in your FREESURFER_HOME

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an older RedHat system. Freesurfer v5.1 was released quite awhile ago and its entirely possible that the newest development version of the freesurfer binaries are not compatible with it. But here is a link to our centos4 build

Re: [Freesurfer] Fwd: creating ROIs for cortical thickness measurements

Hi Elissa I would create the ROI on the fsaverage surface using either freeview or tksurfer. You can then use mri_label2label to map it to any subject, and mris_anatomical_stats -l ... to compute thickness within the ROI cheers Bruce On Mon, 23 Nov 2015, Elissa Ash wrote: Dear list, I

Re: [Freesurfer] sheered CT in tkregister2

not that I know of (Ruopeng can chime in). You can use mri_convert to change the voxel size using the -ois, -ojs, or -oks flags. You'll have to experiment to see which done and what the value needs to be On 11/22/2015 04:59 PM, Borzello, Mia wrote: > Is there a way to change the scale in

Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

Hi Genevieve I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi Bruce, Please find the two files attached. Genevieve On Mon, Nov 23,

Re: [Freesurfer] fMRI maps without clusters on ventricle

You can mask it with the mri.2mm/aseg.mgz ventricle definitions. However, there is a flaw in your understanding. What you see as ventricle or WM may be GM in several/many subjects. The 12DOF registration is not so good that it get all these things lined up properly. On 11/23/2015 03:16 AM,

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

Hi Zeke, thanks for providing the link, and sorry for not clarifying which version I am using earlier. The centos4 version you provided now does not throw the previous errors. Thanks again, Caspar 2015-11-23 14:54 GMT-05:00 : > Oh, Sorry about that, I was unaware

[Freesurfer] fMRI maps without clusters on ventricle

Hi list,I'm performing fcMRI-seed based by FS-FAST.After group comparison and Monte Carlo correction I obtained cortical and subcortical clusters in pos and neg maps.On subcortiacal maps, significant clusters at grf.th1.3.pos.sig.cluster.nii.gz showed some voxels on ventricle or white matter.

Re: [Freesurfer] ERROR: Invalid FreeSurfer license key

Hi Neda how did you copy and past them? Make sure you didn't introduce any extra carriage return/line feeds and such. cheers Bruce On Sun, 22 Nov 2015, Neda Mohammadi wrote: > > Dear FreeSurfer experts, > > I have downloaded and installed FreeSurfer. I am trying to run the installat > ion

Re: [Freesurfer] Issue with Talaraich in recon-all

We are getting an error with recon-all at the stage of Talairach slignment. The error is the one described on the known issues: Can't locate shellwords.pl in @INC. We are running perl5.18, so I downloaded and installed perl5.12 and changed the first line of mritotal as indicated on the

[Freesurfer] Issue with Talaraich in recon-all

I was hoping someone could help with this issue... Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100

Re: [Freesurfer] Issue with Talaraich in recon-all

Hi Michael have you visualize the Talairach alignment to see if it indeed incorrect? Also, can you verify that the direction cosines from your data are properly read? That is, when you view the orig.mgz in freeview does what it thinks is inferior/superior etc... correspond to the true

Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

Hi Geneviève if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a look cheers Bruce On Mon, 23 Nov 2015, UQAM wrote: Hi, This a a "re-posting" of a question I've raised last week ; ) I would like to segment the corpus

Re: [Freesurfer] Which is the best volume to use to get intensity statistics?

On 11/23/15 10:18 PM, Guido Orlando Pascariello wrote: Hi FS Expert I have just looked for this subject a long the list but I haven't found anything about. I have been working with FreeSurfer and I could get some segmentation from my T1 data. I used 'mri_segstats' to quantify volume of

Re: [Freesurfer] How to create a 3g4v matrix

Hi Lee, Thank you for your reply. I had read the example tables, but I'm still not sure how to alter them into my study.May be you could help to check the matrix I designed and tell me my mistake? 3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca test score).

Re: [Freesurfer] QA tools

Hi Mike I agree! It's really hard to detect e.g. the tip of the nose wrapping into occipital cortex. I was thinking more of the tools that generate pages of snapshots so you can quickly scan through datasets to find dramatic failures cheers Bruce On Mon, 23 Nov 2015, Harms, Michael wrote: >

[Freesurfer] White matter and cp edits don't produce new results after reconall

Dear all, I have a faulty wm map (brainmask.mgz) where some regions are not labeled as white matter where they should. I tried to correct both the wm.mgz map and add control points (and saved these), afterwards running either -autorecon2-wm or autorecon2-cp, but neither of these work. I can see

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Hi Bruce, Thank you very much for your quick response. Yes I mean that wm.mgz underestimates true white matter. Values are between 95 and 108 where it should be 110 or above. I will upload my subj dir tomorrow. Is there specific place I can upload to or shall attach it in I reply to you? Thank

Re: [Freesurfer] subjects_dir

Hi Eric No, you can just symlink fsaverage and such Cheers Bruce > On Nov 23, 2015, at 9:40 PM, Eric Cunningham wrote: > > Greetings Freesurfer experts, > > The README file in the $SUBJECTS_DIR says that a different directory can be > specified by setting the env var

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

Hi Annelinde when you say a fault wm map, do you mean that the wm.mgz underestimates the true white matter (that is, there are many voxels that are 0 in the wm.mgz that are in the white matter)? What is the intensity of the brain.mgz at those voxels? If you tar, gzip and upload a subject dir

[Freesurfer] subjects_dir

Greetings Freesurfer experts, The README file in the $SUBJECTS_DIR says that a different directory can be specified by setting the env var SUBJECTS_DIR prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh' statement. Do the original contents of SUBJECTS_DIR (such as fsaverage) need to be

[Freesurfer] Which is the best volume to use to get intensity statistics?

Hi FS Expert I have just looked for this subject a long the list but I haven't found anything about. I have been working with FreeSurfer and I could get some segmentation from my T1 data. I used 'mri_segstats' to quantify volume of some subcortical region. Also I want to get intensity statistics

Re: [Freesurfer] subjects_dir

Other than fsaverage, are there any other files that need to be linked for recon-all to work? Thanks On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl wrote: > Hi Eric > No, you can just symlink fsaverage and such > Cheers > Bruce > > > On Nov 23, 2015, at 9:40 PM, Eric

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

P.s. You should use our filedrop which you can find on our website > On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke > wrote: > > Hi Bruce, > > Thank you very much for your quick response. > Yes I mean that wm.mgz underestimates true white matter. Values are

Re: [Freesurfer] White matter and cp edits don't produce new results after reconall

But is the wm.mgz 'off' (less than 5) there? If the wm.mgz is 95 or something it means we accurately segmented that voxel. If you upload we will take a look, but please include specific voxel coords Cheers Bruce > On Nov 23, 2015, at 9:43 PM, Annelinde Vandenbroucke >

Re: [Freesurfer] How to create a 3g4v matrix

Hi Li, You can find some example FSGD tables here, which you can alter to fit your analyses. https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Best, Lee On Sun, 22 Nov 2015, nellie wrote: Hi Freesurfer Experts, I’m a new user of Freesurfer, and I learn how to use this software

Re: [Freesurfer] fsl_rigid_register fails with wrong orientation

Zeke, is this a new library that we need for v6? doug On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote: > Hi Doug, > when I try to execute mri_coreg, I get the following error message: > > error while loading shared libraries: libnetcdf.so.6: cannot open > shared object file: no such file or

[Freesurfer] QA tools

Hi all, I am starting to use QAtools in Freesurfer. The scripts are working well, but I have two problems: 1. the interpretation of output is the first. Are there ranges of normality for SNR and intensity? Could you please give me some reference or link about how to interpret these data? Or do I

[Freesurfer] Fwd: creating ROIs for cortical thickness measurements

Dear list, I am resending a message that I sent on Friday. Any help would be most sincerely appreciated. Dear Freesurfers, I am new to freesurfer and I am trying to understand how to best perform a cortical thickness analysis for an ROI that is not pre-defined in freesurfer, such as the IFJ or

[Freesurfer] Get white and pial surfaces without using aseg.mgz

Hi FS Experts I'm using FreeSurfer to process my T1 data in order to get white and pial surfaces from it. I have a questions about usages of this file 'aseg.mgz'. In the 'recon-all' pipeline, there are some steps in which I can use it or don't use it depend on if I want or don't. I wonder What