Re: [Freesurfer] bvecs error from Tracula

Hi, The content is : freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Amirhossein, Can you please provide me with the contents of build-stamp.txt in the /Applications/freesurfer directory?

[Freesurfer] mri_convert errors

Hello, I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error messages: [pom@PomLinux /home/pom]% !mri mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

Running autorecon3 fixed the mri_label2label conversion problem. Thank you everyone! L yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote: Yes. The input label looks fine on fsaverage. But I just realized something. After

Re: [Freesurfer] how to threshold mgh surface and save the file

Hi Robert it would be pretty easy in matlab, or you can use mri_threshold. cheers Bruce On Wed, 24 Jul 2013, Robert Schulz wrote: Hi,   I'd like to theshold a surface mgh file at a certain value, set all values below the threshold 0 and save the file for further statistical analysis.

[Freesurfer] problem with nu_correct

Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can to read nu_correct: crashed while running nu_evaluate (termination status=9) Thank for your help ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

glad to hear it Bruce On Wed, 24 Jul 2013, Lingqiang Kong wrote: Running autorecon3 fixed the mri_label2label conversion problem. Thank you everyone! L yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote: Yes. The input label

[Freesurfer] asegstat values pre and post editing

Dear Freesurfers, we recently processed a sample of adult patients and then we reran autorecon-2 and autorecon-3 after editing contol points, white matter and pial surface. We exported the asegstat table both pre and post editing, and we got different volumes for most of the subjects. How is that

Re: [Freesurfer] asegstat values pre and post editing

Hi Claudia if you run autorecon2 you will rerun the aseg, which will use the control points to change the subcortical intensity normalization. If you don't want that to happen, you need to run -autorecon2-cp cheers Bruce On Wed, 24 Jul 2013, Claudia Dacquino wrote: Dear Freesurfers,we

[Freesurfer] Binary mask of the skull

Hi, I was wondering whether there was a command (or a flag in a command such as mri_binarize) that can give me the binary mask of my subject's skull. I was thinking of creating a binary ask of the subject's brain and then one of the brain and the skull and subtracting them, but I was wondering

Re: [Freesurfer] asegstat values pre and post editing

Thanks Bruce, but I'm sure I ran autorecon2-cp autorecon3: recon-all -autorecon2-cp -autorecon3 -subjid. However, is it ok to use aseg values post editing even if they look different from the pre editing ones? Thanks a lot. Claudia 2013/7/24 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi

[Freesurfer] how to use mri_surf2surf to smooth sulc ?

Dear Bruce, Would you mind help me. I have to smooth a sulc data with the command mri_surf2surf but it don't work. I have triyed with curv data it work very well i have put this command : mri_surf2surf --hemi lh --s s000_open_brain_sanlm_+TIR_normlalized --sval sulc --src_type sulc --fwhm-trg

Re: [Freesurfer] problem with nu_correct

Hello Andrea, Can you please attach the entire recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/scripts/recon-all.log -Zeke On 07/24/2013 09:35 AM, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can to read

Re: [Freesurfer] infant atlas segmentation

Thanks for the reply Doug. I recently ran the bbregister command and attempted to view the results using tkregister2. I received the following error: dhcp-165-124-23-232:Desktop IngvalsonLab$ tkregister2 --mov /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/mri/avgseg.mgz --reg

[Freesurfer] R: Re: problem with nu_correct

Hello zkaufman, thanks for your involvement Andrea Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 24-lug-2013 16.52 A: Andrea Tateoandrea.ta...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] problem with nu_correct Hello Andrea, Can you please attach

Re: [Freesurfer] mri_ca_train bug

no, it would be more like a talairach alignment On Wed, 24 Jul 2013, Mark Plantz wrote: Hi Bruce, Thanks for the reply. Would 'bbregister' work to register the files to eachother or would there be a more useful way to do that?  Also I noticed that across many of the subjects there is a

Re: [Freesurfer] mri_ca_train bug

Hi Bruce, Thanks for the reply. Would 'bbregister' work to register the files to eachother or would there be a more useful way to do that? Also I noticed that across many of the subjects there is a slight difference in the TR, TE, TI, and flip angle values. For instance, one of the subjects has

Re: [Freesurfer] asegstat values pre and post editing

Hi Bruce, I run FS 5.1. So for 5.1 version is it normal that post editing aseg values ar different from pre editing even using autorecon2-cp? Thanks again Claudia 2013/7/24 Bruce Fischl fis...@nmr.mgh.harvard.edu I think it is, but I would visually inspect them. What FS version are you

[Freesurfer] a second subjcts folder...

Hi: I has a subjects folder in one physical harddisk... How can I continue processing more images in another subjects folder in a new physical harddisk without erasing the first one ?... Sincerely Gonzalo Rojas Vosta -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing

Re: [Freesurfer] infant atlas segmentation

Nevermind, it turned out to be a permissions issue. Thanks! On Wed, Jul 24, 2013 at 10:12 AM, Mark Plantz markplantz2...@u.northwestern.edu wrote: Thanks for the reply Doug. I recently ran the bbregister command and attempted to view the results using tkregister2. I received the following

[Freesurfer] GCA atlas defined anatomical boundaries

Hello, I have attended short FSL/FreeSurfer course in New Zealand last year and have subscribed for mailing list, but in spite of all that I would I would appreciate very much to know. 1.) 1.)how GCA atlas that is used by FreeSurfer defines boundaries of subcortical volumes (especially

Re: [Freesurfer] how to use mri_surf2surf to smooth sulc ?

The output has to have a file format extension (eg, mgh, mgz). If you want to output curv, then spec --tfmt curv doug On 07/24/2013 10:49 AM, fatma zribi wrote: Dear Bruce, Would you mind help me. I have to smooth a sulc data with the command mri_surf2surf but it don't work. I have triyed

Re: [Freesurfer] infant atlas segmentation

I guess the problem is that those regions should not be out of bounds. Maybe I need to create a new Lookup Table for the infant mri's? Is that possible to do? On Wed, Jul 24, 2013 at 2:21 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Mark, please post to the list and not to me.

Re: [Freesurfer] error with fast_selxavg3

Hi Leila, yes, the problem is probably in that fsfast sets the TER=.05. I never expected the TR or the event duration to be less than this (silly me). The -refeventdur does not really effect much, it just controls some scaling. Setting it to 16ms is fine. doug On 07/23/2013 08:23 AM, Leila

Re: [Freesurfer] Fwd: qdec -- confused by glm output for custom ROIs

Hi Maria, how did you extract the thickness for each subject? mri_glmfit-sim will do this extraction for you. It will be stored in something.y.ocn.dat. Try it with that data. Also, how did you do your GLM analysis? Did you use the Xg.dat file created by QDEC? doug On 07/23/2013 11:48 AM,

Re: [Freesurfer] a second subjcts folder...

Hi Gonzalo just specify whichever one you want on the recon-all command line with -sd subjects_dir path. You can also use setenv SUBJECTS_DIR subects_dir path so that tkmedit/tksurfer operate properly cheers Bruce On Wed, 24 Jul 2013, Gonzalo Rojas Costa wrote: Hi: I has a subjects

Re: [Freesurfer] infant atlas segmentation

you need a new LUT. See my comment from a few emails ago. On 07/24/2013 03:29 PM, Mark Plantz wrote: I'm not actually quite sure what it means either. When I use the command line: tkmedit $Subject brain.mgz -segmentation seg.mgz, I can run the cursor over various regions and the name of the

Re: [Freesurfer] asegstat values pre and post editing

I don't think so, but perhaps Nick can comment. Are you positive you didn't run -autorecon2? Actually, maybe the placement of the ribbon will change the partial volume estimates for some subcortical structures? I can't remember the current sequence of events. Nick or Doug: do you know? On

Re: [Freesurfer] Average cortical diffusion

You can use mri_vol2surf and mri_segstats, something like mri_vol2surf --mov md.nii --reg register.dat --hemi lh --projfrac 0.5 --o lh.md.mgh mri_segstats --i lh.md.mgh --slabel yoursubject lh lh.cortex.label --id 1 --sum sum.lh.md.dat doug On 07/22/2013 07:02 AM, Afaf Elsarraj wrote:

Re: [Freesurfer] GCA atlas defined anatomical boundaries

Hi Zuzana 1. the subcortical segmentations are based on the protocol defined by the Center for Morphometric Analysis at MGH, so you will need to look at their papers for e.g. hippocampus/amygdala segmentations 2. You should check with the CMA, but I believe it refers to cases with a cavum

Re: [Freesurfer] Binary mask of the skull

Actually, never mind, I found a way through bet! Panos From: Fotiadis, Panagiotis Sent: Wednesday, July 24, 2013 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Binary mask of the skull Hi, I was wondering whether there was a command (or a flag in

[Freesurfer] MRI dimensions different from [256x256x256]

Hello, Is it possible to run recon-all without modifying the size of the input MRI volume? I have in input a volume [181x217x181], and all the steps of recon-all save it in a [256x256x256] volume. I tried skipping all the first steps to avoid this behavior (recon-all -all -nomotioncor

Re: [Freesurfer] MRI dimensions different from [256x256x256]

You can always convert the 256^3 back to the native space with mri_vol2vol or mri_label2vol doug On 7/24/13 8:34 PM, François Tadel wrote: Hello, Is it possible to run recon-all without modifying the size of the input MRI volume? I have in input a volume [181x217x181], and all the steps

[Freesurfer] different results between 5.1.0 and 5.2.0

Dear FreeSurfer Experts As in some other posts, I have also observed some differences between the two releases. The values from cuneus (thickness) are similar to the post from Ritobrato Datta, Ph.D. on 18 march. But I also observed some differences in volume of right / left thalami. Did

Re: [Freesurfer] different results between 5.1.0 and 5.2.0

I don't know, but I'm pretty sure the Freesurfer team will recommend you use v5.3.0. There are emails saying as much. Chris From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of clarissa yasuda