Re: [Freesurfer] DTI - Tracula question

Hi Anastasia: Thank you so much. Yes that is very helpful. best, Alan On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Alan - Yes, you can give a single file for all data sets if they're all > acquired with the same gradient table and slice

Re: [Freesurfer] DTI - Tracula question

As an add-on to the add-on, starting in 6.0 we'll be able to figure it out from the dicom header, so hopefully people won't have to worry about any of this in the future. On Fri, 5 Feb 2016, Harms, Michael wrote: As an add-on to this, note that using a single table for all subjects is

Re: [Freesurfer] DTI - Tracula question

That was helpful. Thanks Michael. On Fri, Feb 5, 2016 at 5:19 PM, Harms, Michael wrote: > > As an add-on to this, note that using a single table for all subjects is > probably only appropriate if the DWI was acquired with a fixed orientation > relative to the scanner gradient

Re: [Freesurfer] Volume analysis in native space vs. mni305 space

Hi FreeSurfer experts, I'm writing to follow up on an email I sent on Monday. I'm working in 5.3 and switching over to running my 1st level analysis in fsaverage. I noticed that when visualizing the volume output from the mni305 analysis in tkmedit, there is only activation in subcortical

Re: [Freesurfer] DTI - Tracula question

Thanks Anastasia - that was very helpful. I have another question : I am working on a DTI dataset of around 70 subjects. This dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been acquired on the same scanner? thanks,

Re: [Freesurfer] hello freesurfer developer~

Hi A-reum we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb

Re: [Freesurfer] (no subject)

Hello Achcha: Detailed instructions on how to install FS on Windows via Virtual Box can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage best, Alan On Fri, Jan 22, 2016 at 3:28 PM, Ачча Чимагомедова wrote: > > Hello! > > My name

Re: [Freesurfer] freeview command line generic overlay colormap question

Dear all, I am currently trying to automatically generate Freesurfer screenshots and, to this purpose, I need to change the color scale of the surface overlay to "Color Wheel - Inverse" and with specific min and max threshold. Looking for a way to achieve this, I found this thread with

[Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

Dear All, I have a functional and a T1 registered, but they are not in anatomical coordinates. I put the anatomical in the desired position by using tkregister2. I was hoping to use the output reg file to re-position the functional as well. I got an unexpected output! The functional looks

Re: [Freesurfer] tracula preproc complains about missing bvec-file

Hi Peter - From your dicom header, it looks like the fields that it's looking for to guess which standard Siemens gradient table to use are not there. So you'll have to pass the gradient table and the b-value table as separate text files using bvecfile and bvalfile. Starting in 6.0 this'll

Re: [Freesurfer] Zero angle for retinotopy

Hi, I know Doug is away, so he may correct me later, but I believe it doesn't matter, as long as it is consistent across runs, and you know what it is. It will just determine where the angle 0 activity goes (in a color map etc.). The way FS-FAST does the mapping it just may mean your colors don't

Re: [Freesurfer] DTI - Tracula question

Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they are. If there are only very small

Re: [Freesurfer] DTI - Tracula question

As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects.  If the orientation was customized individually for each

Re: [Freesurfer] TRACULA Longitudinal can't find subject folder

Hi again Deniz - This may be confusing but with longitudinal TRACULA there are separate trac-all.log files in each time point's directory and in the within-subject template's directory. The former are for things that are run independently for each time point (mainly pre-processing) and the

[Freesurfer] use as seed a ROI.label as seed in FS-FAST

Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.How can I do it?Should I use mri_label2vol? Thanks. Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] seq.info

Or my guess is that this seq.info is not necessary for the further analysis.. so I can go ahead without it? Best, Ji Won 2016-02-05 15:06 GMT-05:00 Ji Won Bang : > If I use: > unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info > > I can get

Re: [Freesurfer] seq.info

If I use: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info I can get sequencename, nrows, ncols, nslcs, ntrs, but how can I check the exact value of slcpixelsize? Thanks, Ji Won 2016-02-05 14:54 GMT-05:00 Ji Won Bang : > Dear. Freesurfer team > >

[Freesurfer] seq.info

Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself Do you know how I can check the scan parameters: sequencename nrows ncols nslcs rowpixelsize colpixelsize slcpixelsize ntrs TR I know

Re: [Freesurfer] tracula preproc complains about missing bvec-file

Hi Anastasia, no, I did not define "bvecfile" and "bvalfile" in the configuration file, because the tutorial says, that these variables are not needed if the data is in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need this additional step to extract bvec and bval from

[Freesurfer] problem mri_convert

Dear FreeSurfers, On one of our Linux machines we encounter the following error message when calling mri_convert: /lib64/libz.so.1: no version information available (required by mri_convert) /usr/lib64/libstdc++.so6: version GLIBCXX_3.4.11 not found (required by mri_convert) Mri_convert has

Re: [Freesurfer] Brain stem segmentation-- FS6

Hi Mohamad, you might have run out of memory. Could you please try allocating more RAM for the job? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message

[Freesurfer] Combining lh. and rh. surfaces

Dear FreeSurfer Users, I have been using the recon-all FreeSurfer command to reconstruct surfaces from T1 weighted MRI scan. I need to import the surfaces I have into Homer2 Atlas Viewer and for this I need whole surface/volume files rather than the individual hemispheres. Does anybody have

[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

Re: [Freesurfer] TRACULA Longitudinal can't find subject folder

Dear Anastasia,Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one.In the inter-subject registration step,

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

I did that but it still does not work, it is almost the same error except the condno is now 15521.8 before it was 27492.1, though I am not sure if that tells something about the error. Could it be something else ? Thank you. Regards, Nabin On Thu, Feb 4, 2016 at 5:59 PM, Douglas Greve

Re: [Freesurfer] Combining lh. and rh. surfaces

Hi Maheen, I have been using SIMNIBS (www.simnibs.de) script for the exact same thing. This script gives a mesh output. Perhaps that helps,.. Kind regards, Jesu Jesu Kiran Spurgen Postgraduate Student in Advanced Medical Imaging KU Leuven, Belgium On Fri, Feb 5, 2016 at 1:29 PM, Maheen

Re: [Freesurfer] hello freesurfer developer~

hello experts i have some question to you What method do you use when measuring the cortical thickness? (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min : > Thank you for u r answer. > > I

Re: [Freesurfer] seq.info

you don't need an seq.info file anymore with fsfast On 2/5/16 2:54 PM, Ji Won Bang wrote: Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself Do you know how I can

[Freesurfer] spot checking results

Dear List, I have run recon-all -all on the same scan on two different machines likely running two different versions of Linux but in any case the runs were done with different numbers of cores. I haven't done anything fancy to compare that the results are identical except for some spot

Re: [Freesurfer] spot checking results

Don, Running FreeSurfer on two different versions of any operating system will not produce the same results. If you want the same results, you must use exactly the same version of an operating system for all of an analysis. hth d On 2/5/16 8:29 PM, Krieger, Donald N. wrote: > Dear List, > >